USSES Spring Fall RxFire Soils
Spiess
2025-01-22
Intro
Models for the Spring Fall RxFire Soils Project looking at how burn season does or does not affect different soil nutrient pools over time.
#Burn and Depth ## NH4 Ammonium
Pretreatment - 2008 Depth 0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NH4 + 1) ~ Burn + (1 | Site)
## Data: N_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 34.3 44.2 -12.1 24.3 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.68457 -0.76482 0.07353 0.73824 2.34517
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.09414 0.3068
## Residual 0.06251 0.2500
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.80351 0.18669 9.00000 9.661 4.77e-06 ***
## BurnSB -0.08691 0.26401 9.00000 -0.329 0.75
## BurnUB 0.23863 0.26401 9.00000 0.904 0.39
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NH4 + 1)
## Chisq Df Pr(>Chisq)
## Burn 1.6305 2 0.4425## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 1.80 0.229 13.5 1.31 2.30
## SB 1.72 0.229 13.5 1.22 2.21
## UB 2.04 0.229 13.5 1.55 2.53
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0869 0.323 13.5 0.269 0.9611
## FB - UB -0.2386 0.323 13.5 -0.738 0.7457
## SB - UB -0.3255 0.323 13.5 -1.007 0.5852
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 1.80 0.229 13.5 1.31 2.30
## SB 1.72 0.229 13.5 1.22 2.21
## UB 2.04 0.229 13.5 1.55 2.53
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0869 0.323 13.5 -0.763 0.937
## FB - UB -0.2386 0.323 13.5 -1.089 0.611
## SB - UB -0.3255 0.323 13.5 -1.175 0.524
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesPretreatment - 2008 Depth 5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NH4 + 1) ~ Burn + (1 | Site)
## Data: N_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 16.5 26.4 -3.2 6.5 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8764 -0.5411 0.1128 0.7253 2.0113
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.1124 0.3353
## Residual 0.0410 0.2025
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.54388 0.19937 9.00000 7.744 2.87e-05 ***
## BurnSB -0.16592 0.28196 9.00000 -0.588 0.571
## BurnUB 0.05751 0.28196 9.00000 0.204 0.843
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NH4 + 1)
## Chisq Df Pr(>Chisq)
## Burn 0.6772 2 0.7128## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 1.54 0.244 13.5 1.018 2.07
## SB 1.38 0.244 13.5 0.852 1.90
## UB 1.60 0.244 13.5 1.076 2.13
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1659 0.345 13.5 0.480 0.8816
## FB - UB -0.0575 0.345 13.5 -0.167 0.9848
## SB - UB -0.2234 0.345 13.5 -0.647 0.7972
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 1.54 0.244 13.5 1.018 2.07
## SB 1.38 0.244 13.5 0.852 1.90
## UB 1.60 0.244 13.5 1.076 2.13
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1659 0.345 13.5 -0.742 1.074
## FB - UB -0.0575 0.345 13.5 -0.965 0.850
## SB - UB -0.2234 0.345 13.5 -1.131 0.684
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NH4 + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(N_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 310.8 358.0 -141.4 282.8 201
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.82888 -0.62297 0.04314 0.68022 2.83916
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.007716 0.08784
## Residual 0.212498 0.46097
## Number of obs: 215, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.08507 0.11991 54.80827 34.069 <2e-16 ***
## BurnSB 0.01601 0.16957 54.80827 0.094 0.9251
## BurnUB -0.17661 0.16957 54.80827 -1.042 0.3022
## Year2010 -2.51497 0.15366 206.04482 -16.367 <2e-16 ***
## Year2011 -2.59642 0.15366 206.04482 -16.897 <2e-16 ***
## Year2012 -1.48471 0.15366 206.04482 -9.662 <2e-16 ***
## BurnSB:Year2010 0.03991 0.21731 206.04482 0.184 0.8545
## BurnUB:Year2010 0.43023 0.21731 206.04482 1.980 0.0491 *
## BurnSB:Year2011 0.22087 0.21731 206.04482 1.016 0.3106
## BurnUB:Year2011 0.12580 0.21731 206.04482 0.579 0.5633
## BurnSB:Year2012 -0.39219 0.21731 206.04482 -1.805 0.0726 .
## BurnUB:Year2012 -0.37602 0.21892 206.14082 -1.718 0.0874 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 Yr2011 Yr2012 BSB:Y2010 BUB:Y2010
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.641 0.453 0.453
## Year2011 -0.641 0.453 0.453 0.500
## Year2012 -0.641 0.453 0.453 0.500 0.500
## BrnSB:Y2010 0.453 -0.641 -0.320 -0.707 -0.354 -0.354
## BrnUB:Y2010 0.453 -0.320 -0.641 -0.707 -0.354 -0.354 0.500
## BrnSB:Y2011 0.453 -0.641 -0.320 -0.354 -0.707 -0.354 0.500 0.250
## BrnUB:Y2011 0.453 -0.320 -0.641 -0.354 -0.707 -0.354 0.250 0.500
## BrnSB:Y2012 0.453 -0.641 -0.320 -0.354 -0.354 -0.707 0.500 0.250
## BrnUB:Y2012 0.450 -0.318 -0.636 -0.351 -0.351 -0.702 0.248 0.496
## BSB:Y2011 BUB:Y2011 BSB:Y2012
## BurnSB
## BurnUB
## Year2010
## Year2011
## Year2012
## BrnSB:Y2010
## BrnUB:Y2010
## BrnSB:Y2011
## BrnUB:Y2011 0.500
## BrnSB:Y2012 0.500 0.250
## BrnUB:Y2012 0.248 0.496 0.496## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NH4 + 1)
## Chisq Df Pr(>Chisq)
## Burn 1.7798 2 0.410703
## Year 996.6207 3 < 2.2e-16 ***
## Burn:Year 18.8331 6 0.004455 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.44 0.0910 13.4 2.24 2.63
## SB 2.42 0.0910 13.4 2.22 2.62
## UB 2.30 0.0912 13.5 2.11 2.50
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0168 0.129 13.4 0.131 0.9906
## FB - UB 0.1316 0.129 13.5 1.021 0.5766
## SB - UB 0.1148 0.129 13.5 0.891 0.6551
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.44 0.0910 13.4 2.24 2.63
## SB 2.42 0.0910 13.4 2.22 2.62
## UB 2.30 0.0912 13.5 2.11 2.50
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0168 0.129 13.4 -0.322 0.355
## FB - UB 0.1316 0.129 13.5 -0.207 0.470
## SB - UB 0.1148 0.129 13.5 -0.224 0.454
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.03 0.0765 78.3 3.88 4.18
## 2010 1.67 0.0765 78.3 1.52 1.83
## 2011 1.55 0.0765 78.3 1.40 1.70
## 2012 2.29 0.0770 80.2 2.14 2.44
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 2.358 0.0907 215 25.995 <.0001
## Year2009 - Year2011 2.481 0.0907 215 27.346 <.0001
## Year2009 - Year2012 1.741 0.0912 216 19.093 <.0001
## Year2010 - Year2011 0.123 0.0907 215 1.351 0.5313
## Year2010 - Year2012 -0.617 0.0912 216 -6.772 <.0001
## Year2011 - Year2012 -0.740 0.0912 216 -8.117 <.0001
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.03 0.0765 78.3 3.88 4.18
## 2010 1.67 0.0765 78.3 1.52 1.83
## 2011 1.55 0.0765 78.3 1.40 1.70
## 2012 2.29 0.0770 80.2 2.14 2.44
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 2.358 0.0907 215 2.123 2.593
## Year2009 - Year2011 2.481 0.0907 215 2.246 2.716
## Year2009 - Year2012 1.741 0.0912 216 1.505 1.977
## Year2010 - Year2011 0.123 0.0907 215 -0.112 0.357
## Year2010 - Year2012 -0.617 0.0912 216 -0.854 -0.381
## Year2011 - Year2012 -0.740 0.0912 216 -0.976 -0.504
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 4.09 0.132 78.5 3.82 4.35
## SB 4.10 0.132 78.5 3.84 4.36
## UB 3.91 0.132 77.9 3.64 4.17
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 1.57 0.132 78.5 1.31 1.83
## SB 1.63 0.132 78.5 1.36 1.89
## UB 1.82 0.132 77.9 1.56 2.09
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 1.49 0.132 78.5 1.23 1.75
## SB 1.73 0.132 78.5 1.46 1.99
## UB 1.44 0.132 77.9 1.17 1.70
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 2.60 0.132 78.5 2.34 2.86
## SB 2.22 0.132 78.5 1.96 2.49
## UB 2.05 0.135 83.6 1.78 2.32
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB -0.0160 0.187 78.5 -0.086 0.9960
## FB - UB 0.1766 0.187 78.2 0.943 0.6149
## SB - UB 0.1926 0.187 78.2 1.029 0.5612
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB -0.0559 0.187 78.5 -0.299 0.9521
## FB - UB -0.2536 0.187 78.2 -1.354 0.3699
## SB - UB -0.1977 0.187 78.2 -1.056 0.5444
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## FB - SB -0.2369 0.187 78.5 -1.265 0.4192
## FB - UB 0.0508 0.187 78.2 0.271 0.9603
## SB - UB 0.2877 0.187 78.2 1.536 0.2798
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.3762 0.187 78.5 2.009 0.1169
## FB - UB 0.5526 0.189 81.1 2.920 0.0125
## SB - UB 0.1765 0.189 81.1 0.932 0.6215
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 4.09 0.132 78.5 3.82 4.35
## SB 4.10 0.132 78.5 3.84 4.36
## UB 3.91 0.132 77.9 3.64 4.17
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 1.57 0.132 78.5 1.31 1.83
## SB 1.63 0.132 78.5 1.36 1.89
## UB 1.82 0.132 77.9 1.56 2.09
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 1.49 0.132 78.5 1.23 1.75
## SB 1.73 0.132 78.5 1.46 1.99
## UB 1.44 0.132 77.9 1.17 1.70
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 2.60 0.132 78.5 2.34 2.86
## SB 2.22 0.132 78.5 1.96 2.49
## UB 2.05 0.135 83.6 1.78 2.32
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.0160 0.187 78.5 -0.4634 0.431
## FB - UB 0.1766 0.187 78.2 -0.2708 0.624
## SB - UB 0.1926 0.187 78.2 -0.2548 0.640
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.0559 0.187 78.5 -0.5034 0.392
## FB - UB -0.2536 0.187 78.2 -0.7011 0.194
## SB - UB -0.1977 0.187 78.2 -0.6452 0.250
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.2369 0.187 78.5 -0.6843 0.211
## FB - UB 0.0508 0.187 78.2 -0.3967 0.498
## SB - UB 0.2877 0.187 78.2 -0.1598 0.735
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.3762 0.187 78.5 -0.0713 0.824
## FB - UB 0.5526 0.189 81.1 0.1008 1.005
## SB - UB 0.1765 0.189 81.1 -0.2754 0.628
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NH4 + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(N_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 229.7 276.9 -100.9 201.7 201
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.5855 -0.5696 0.0721 0.7003 3.6022
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.01464 0.1210
## Residual 0.14206 0.3769
## Number of obs: 215, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 3.412952 0.113013 30.002674 30.200 <2e-16 ***
## BurnSB -0.168259 0.159825 30.002675 -1.053 0.3009
## BurnUB -0.083313 0.159825 30.002675 -0.521 0.6060
## Year2010 -1.813886 0.125636 205.934905 -14.438 <2e-16 ***
## Year2011 -1.943814 0.125636 205.934905 -15.472 <2e-16 ***
## Year2012 -1.292505 0.125636 205.934905 -10.288 <2e-16 ***
## BurnSB:Year2010 0.347983 0.177676 205.934905 1.959 0.0515 .
## BurnUB:Year2010 0.254158 0.177676 205.934905 1.430 0.1541
## BurnSB:Year2011 0.119625 0.177676 205.934905 0.673 0.5015
## BurnUB:Year2011 0.086982 0.179005 205.988008 0.486 0.6275
## BurnSB:Year2012 -0.003866 0.177676 205.934905 -0.022 0.9827
## BurnUB:Year2012 0.033934 0.177676 205.934905 0.191 0.8487
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 Yr2011 Yr2012 BSB:Y2010 BUB:Y2010
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.556 0.393 0.393
## Year2011 -0.556 0.393 0.393 0.500
## Year2012 -0.556 0.393 0.393 0.500 0.500
## BrnSB:Y2010 0.393 -0.556 -0.278 -0.707 -0.354 -0.354
## BrnUB:Y2010 0.393 -0.278 -0.556 -0.707 -0.354 -0.354 0.500
## BrnSB:Y2011 0.393 -0.556 -0.278 -0.354 -0.707 -0.354 0.500 0.250
## BrnUB:Y2011 0.390 -0.276 -0.552 -0.351 -0.702 -0.351 0.248 0.496
## BrnSB:Y2012 0.393 -0.556 -0.278 -0.354 -0.354 -0.707 0.500 0.250
## BrnUB:Y2012 0.393 -0.278 -0.556 -0.354 -0.354 -0.707 0.250 0.500
## BSB:Y2011 BUB:Y2011 BSB:Y2012
## BurnSB
## BurnUB
## Year2010
## Year2011
## Year2012
## BrnSB:Y2010
## BrnUB:Y2010
## BrnSB:Y2011
## BrnUB:Y2011 0.496
## BrnSB:Y2012 0.500 0.248
## BrnUB:Y2012 0.250 0.496 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NH4 + 1)
## Chisq Df Pr(>Chisq)
## Burn 0.3304 2 0.8477
## Year 784.4927 3 <2e-16 ***
## Burn:Year 5.4536 6 0.4871
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.15 0.102 13.5 1.93 2.37
## SB 2.10 0.102 13.5 1.88 2.32
## UB 2.16 0.102 13.6 1.94 2.38
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0523 0.144 13.5 0.364 0.9298
## FB - UB -0.0105 0.144 13.6 -0.073 0.9971
## SB - UB -0.0628 0.144 13.6 -0.437 0.9009
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.15 0.102 13.5 1.93 2.37
## SB 2.10 0.102 13.5 1.88 2.32
## UB 2.16 0.102 13.6 1.94 2.38
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0523 0.144 13.5 -0.325 0.430
## FB - UB -0.0105 0.144 13.6 -0.388 0.367
## SB - UB -0.0628 0.144 13.6 -0.440 0.315
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 3.33 0.0742 44.9 3.18 3.48
## 2010 1.72 0.0742 44.9 1.57 1.87
## 2011 1.45 0.0745 45.9 1.30 1.60
## 2012 2.05 0.0742 44.9 1.90 2.20
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 1.613 0.0742 215 21.749 <.0001
## Year2009 - Year2011 1.875 0.0745 215 25.152 <.0001
## Year2009 - Year2012 1.282 0.0742 215 17.291 <.0001
## Year2010 - Year2011 0.262 0.0745 215 3.512 0.0030
## Year2010 - Year2012 -0.331 0.0742 215 -4.458 0.0001
## Year2011 - Year2012 -0.592 0.0745 215 -7.948 <.0001
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 3.33 0.0742 44.9 3.18 3.48
## 2010 1.72 0.0742 44.9 1.57 1.87
## 2011 1.45 0.0745 45.9 1.30 1.60
## 2012 2.05 0.0742 44.9 1.90 2.20
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 1.613 0.0742 215 1.4211 1.805
## Year2009 - Year2011 1.875 0.0745 215 1.6819 2.068
## Year2009 - Year2012 1.282 0.0742 215 1.0904 1.475
## Year2010 - Year2011 0.262 0.0745 215 0.0688 0.455
## Year2010 - Year2012 -0.331 0.0742 215 -0.5227 -0.139
## Year2011 - Year2012 -0.592 0.0745 215 -0.7855 -0.399
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 3.41 0.128 44.9 3.15 3.67
## SB 3.24 0.128 44.9 2.99 3.50
## UB 3.33 0.128 44.7 3.07 3.59
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 1.60 0.128 44.9 1.34 1.86
## SB 1.78 0.128 44.9 1.52 2.04
## UB 1.77 0.128 44.7 1.51 2.03
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 1.47 0.128 44.9 1.21 1.73
## SB 1.42 0.128 44.9 1.16 1.68
## UB 1.47 0.130 47.7 1.21 1.73
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 2.12 0.128 44.9 1.86 2.38
## SB 1.95 0.128 44.9 1.69 2.21
## UB 2.07 0.128 44.7 1.81 2.33
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.16826 0.182 44.9 0.926 0.6267
## FB - UB 0.08331 0.182 44.8 0.459 0.8908
## SB - UB -0.08495 0.182 44.8 -0.468 0.8867
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB -0.17972 0.182 44.9 -0.989 0.5872
## FB - UB -0.17085 0.182 44.8 -0.941 0.6178
## SB - UB 0.00888 0.182 44.8 0.049 0.9987
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.04863 0.182 44.9 0.268 0.9613
## FB - UB -0.00367 0.183 46.3 -0.020 0.9998
## SB - UB -0.05230 0.183 46.3 -0.286 0.9560
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.17212 0.182 44.9 0.948 0.6134
## FB - UB 0.04938 0.182 44.8 0.272 0.9601
## SB - UB -0.12275 0.182 44.8 -0.676 0.7787
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 3.41 0.128 44.9 3.15 3.67
## SB 3.24 0.128 44.9 2.99 3.50
## UB 3.33 0.128 44.7 3.07 3.59
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 1.60 0.128 44.9 1.34 1.86
## SB 1.78 0.128 44.9 1.52 2.04
## UB 1.77 0.128 44.7 1.51 2.03
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 1.47 0.128 44.9 1.21 1.73
## SB 1.42 0.128 44.9 1.16 1.68
## UB 1.47 0.130 47.7 1.21 1.73
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 2.12 0.128 44.9 1.86 2.38
## SB 1.95 0.128 44.9 1.69 2.21
## UB 2.07 0.128 44.7 1.81 2.33
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.16826 0.182 44.9 -0.272 0.608
## FB - UB 0.08331 0.182 44.8 -0.357 0.524
## SB - UB -0.08495 0.182 44.8 -0.525 0.355
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.17972 0.182 44.9 -0.620 0.261
## FB - UB -0.17085 0.182 44.8 -0.611 0.269
## SB - UB 0.00888 0.182 44.8 -0.431 0.449
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.04863 0.182 44.9 -0.392 0.489
## FB - UB -0.00367 0.183 46.3 -0.447 0.439
## SB - UB -0.05230 0.183 46.3 -0.495 0.391
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.17212 0.182 44.9 -0.268 0.612
## FB - UB 0.04938 0.182 44.8 -0.391 0.490
## SB - UB -0.12275 0.182 44.8 -0.563 0.318
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesN03 Nitrate
Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NO3 + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(N_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 202.4 249.6 -87.2 174.4 201
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.2827 -0.4539 0.0484 0.5830 3.2992
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.006758 0.0822
## Residual 0.127331 0.3568
## Number of obs: 215, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.94108 0.09657 44.46040 20.100 < 2e-16 ***
## BurnSB -0.41929 0.13658 44.46040 -3.070 0.00364 **
## BurnUB -1.14435 0.13658 44.46040 -8.379 1.07e-10 ***
## Year2010 0.52842 0.11894 205.90910 4.443 1.45e-05 ***
## Year2011 -1.00252 0.11894 205.90910 -8.428 6.05e-15 ***
## Year2012 -0.90451 0.11894 205.90910 -7.604 9.99e-13 ***
## BurnSB:Year2010 0.21467 0.16821 205.90910 1.276 0.20333
## BurnUB:Year2010 0.97195 0.16821 205.90910 5.778 2.76e-08 ***
## BurnSB:Year2011 0.33999 0.16821 205.90910 2.021 0.04456 *
## BurnUB:Year2011 1.09482 0.16821 205.90910 6.509 5.67e-10 ***
## BurnSB:Year2012 0.54312 0.16821 205.90910 3.229 0.00145 **
## BurnUB:Year2012 1.21409 0.16947 205.98971 7.164 1.37e-11 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 Yr2011 Yr2012 BSB:Y2010 BUB:Y2010
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.616 0.435 0.435
## Year2011 -0.616 0.435 0.435 0.500
## Year2012 -0.616 0.435 0.435 0.500 0.500
## BrnSB:Y2010 0.435 -0.616 -0.308 -0.707 -0.354 -0.354
## BrnUB:Y2010 0.435 -0.308 -0.616 -0.707 -0.354 -0.354 0.500
## BrnSB:Y2011 0.435 -0.616 -0.308 -0.354 -0.707 -0.354 0.500 0.250
## BrnUB:Y2011 0.435 -0.308 -0.616 -0.354 -0.707 -0.354 0.250 0.500
## BrnSB:Y2012 0.435 -0.616 -0.308 -0.354 -0.354 -0.707 0.500 0.250
## BrnUB:Y2012 0.432 -0.306 -0.611 -0.351 -0.351 -0.702 0.248 0.496
## BSB:Y2011 BUB:Y2011 BSB:Y2012
## BurnSB
## BurnUB
## Year2010
## Year2011
## Year2012
## BrnSB:Y2010
## BrnUB:Y2010
## BrnSB:Y2011
## BrnUB:Y2011 0.500
## BrnSB:Y2012 0.500 0.250
## BrnUB:Y2012 0.248 0.496 0.496## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NO3 + 1)
## Chisq Df Pr(>Chisq)
## Burn 13.279 2 0.001308 **
## Year 521.031 3 < 2.2e-16 ***
## Burn:Year 69.668 6 4.784e-13 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 1.60 0.0778 13.6 1.43 1.76
## SB 1.45 0.0778 13.6 1.28 1.62
## UB 1.27 0.0780 13.6 1.10 1.44
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.145 0.11 13.6 1.316 0.4104
## FB - UB 0.324 0.11 13.6 2.942 0.0278
## SB - UB 0.179 0.11 13.6 1.627 0.2680
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 1.60 0.0778 13.6 1.43 1.76
## SB 1.45 0.0778 13.6 1.28 1.62
## UB 1.27 0.0780 13.6 1.10 1.44
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.145 0.11 13.6 -0.1442 0.434
## FB - UB 0.324 0.11 13.6 0.0348 0.613
## SB - UB 0.179 0.11 13.6 -0.1100 0.469
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 1.420 0.0622 65.6 1.296 1.54
## 2010 2.344 0.0622 65.6 2.220 2.47
## 2011 0.896 0.0622 65.6 0.771 1.02
## 2012 1.101 0.0626 67.2 0.976 1.23
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.924 0.0702 215 -13.158 <.0001
## Year2009 - Year2011 0.524 0.0702 215 7.466 <.0001
## Year2009 - Year2012 0.319 0.0706 215 4.517 0.0001
## Year2010 - Year2011 1.448 0.0702 215 20.624 <.0001
## Year2010 - Year2012 1.243 0.0706 215 17.609 <.0001
## Year2011 - Year2012 -0.205 0.0706 215 -2.912 0.0206
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 1.420 0.0622 65.6 1.296 1.54
## 2010 2.344 0.0622 65.6 2.220 2.47
## 2011 0.896 0.0622 65.6 0.771 1.02
## 2012 1.101 0.0626 67.2 0.976 1.23
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.924 0.0702 215 -1.106 -0.7421
## Year2009 - Year2011 0.524 0.0702 215 0.342 0.7061
## Year2009 - Year2012 0.319 0.0706 215 0.136 0.5015
## Year2010 - Year2011 1.448 0.0702 215 1.266 1.6300
## Year2010 - Year2012 1.243 0.0706 215 1.060 1.4255
## Year2011 - Year2012 -0.205 0.0706 215 -0.388 -0.0228
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 1.941 0.108 65.8 1.726 2.16
## SB 1.522 0.108 65.8 1.307 1.74
## UB 0.797 0.108 65.3 0.582 1.01
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 2.469 0.108 65.8 2.254 2.68
## SB 2.265 0.108 65.8 2.050 2.48
## UB 2.297 0.108 65.3 2.082 2.51
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 0.939 0.108 65.8 0.723 1.15
## SB 0.859 0.108 65.8 0.644 1.07
## UB 0.889 0.108 65.3 0.674 1.10
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 1.037 0.108 65.8 0.822 1.25
## SB 1.160 0.108 65.8 0.945 1.38
## UB 1.106 0.110 70.2 0.887 1.33
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.4193 0.152 65.8 2.753 0.0206
## FB - UB 1.1443 0.152 65.5 7.513 <.0001
## SB - UB 0.7251 0.152 65.5 4.760 <.0001
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.2046 0.152 65.8 1.343 0.3766
## FB - UB 0.1724 0.152 65.5 1.132 0.4982
## SB - UB -0.0322 0.152 65.5 -0.212 0.9756
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0793 0.152 65.8 0.521 0.8616
## FB - UB 0.0495 0.152 65.5 0.325 0.9434
## SB - UB -0.0298 0.152 65.5 -0.196 0.9792
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## FB - SB -0.1238 0.152 65.8 -0.813 0.6964
## FB - UB -0.0697 0.154 68.0 -0.453 0.8930
## SB - UB 0.0541 0.154 68.0 0.352 0.9341
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 1.941 0.108 65.8 1.726 2.16
## SB 1.522 0.108 65.8 1.307 1.74
## UB 0.797 0.108 65.3 0.582 1.01
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 2.469 0.108 65.8 2.254 2.68
## SB 2.265 0.108 65.8 2.050 2.48
## UB 2.297 0.108 65.3 2.082 2.51
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 0.939 0.108 65.8 0.723 1.15
## SB 0.859 0.108 65.8 0.644 1.07
## UB 0.889 0.108 65.3 0.674 1.10
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 1.037 0.108 65.8 0.822 1.25
## SB 1.160 0.108 65.8 0.945 1.38
## UB 1.106 0.110 70.2 0.887 1.33
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.4193 0.152 65.8 0.054 0.785
## FB - UB 1.1443 0.152 65.5 0.779 1.510
## SB - UB 0.7251 0.152 65.5 0.360 1.090
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.2046 0.152 65.8 -0.161 0.570
## FB - UB 0.1724 0.152 65.5 -0.193 0.538
## SB - UB -0.0322 0.152 65.5 -0.398 0.333
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0793 0.152 65.8 -0.286 0.445
## FB - UB 0.0495 0.152 65.5 -0.316 0.415
## SB - UB -0.0298 0.152 65.5 -0.395 0.336
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.1238 0.152 65.8 -0.489 0.241
## FB - UB -0.0697 0.154 68.0 -0.438 0.299
## SB - UB 0.0541 0.154 68.0 -0.314 0.423
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NO3 + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(N_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 162.8 210.0 -67.4 134.8 201
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.1299 -0.4449 0.0479 0.4903 3.2382
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.01509 0.1228
## Residual 0.10292 0.3208
## Number of obs: 215, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.2135 0.1037 24.4442 11.706 1.64e-11 ***
## BurnSB -0.3821 0.1466 24.4442 -2.607 0.015346 *
## BurnUB -0.5604 0.1466 24.4442 -3.823 0.000804 ***
## Year2010 0.8051 0.1069 206.0177 7.529 1.58e-12 ***
## Year2011 -0.2313 0.1069 206.0177 -2.163 0.031727 *
## Year2012 -0.2782 0.1069 206.0177 -2.602 0.009947 **
## BurnSB:Year2010 -0.0391 0.1512 206.0177 -0.259 0.796224
## BurnUB:Year2010 -0.2497 0.1512 206.0177 -1.651 0.100175
## BurnSB:Year2011 0.2704 0.1512 206.0177 1.788 0.075240 .
## BurnUB:Year2011 0.3405 0.1524 206.0584 2.235 0.026502 *
## BurnSB:Year2012 0.5445 0.1512 206.0177 3.600 0.000398 ***
## BurnUB:Year2012 0.7167 0.1512 206.0177 4.739 4.00e-06 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 Yr2011 Yr2012 BSB:Y2010 BUB:Y2010
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.516 0.365 0.365
## Year2011 -0.516 0.365 0.365 0.500
## Year2012 -0.516 0.365 0.365 0.500 0.500
## BrnSB:Y2010 0.365 -0.516 -0.258 -0.707 -0.354 -0.354
## BrnUB:Y2010 0.365 -0.258 -0.516 -0.707 -0.354 -0.354 0.500
## BrnSB:Y2011 0.365 -0.516 -0.258 -0.354 -0.707 -0.354 0.500 0.250
## BrnUB:Y2011 0.362 -0.256 -0.512 -0.351 -0.702 -0.351 0.248 0.496
## BrnSB:Y2012 0.365 -0.516 -0.258 -0.354 -0.354 -0.707 0.500 0.250
## BrnUB:Y2012 0.365 -0.258 -0.516 -0.354 -0.354 -0.707 0.250 0.500
## BSB:Y2011 BUB:Y2011 BSB:Y2012
## BurnSB
## BurnUB
## Year2010
## Year2011
## Year2012
## BrnSB:Y2010
## BrnUB:Y2010
## BrnSB:Y2011
## BrnUB:Y2011 0.496
## BrnSB:Y2012 0.500 0.248
## BrnUB:Y2012 0.250 0.496 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NO3 + 1)
## Chisq Df Pr(>Chisq)
## Burn 10.000 2 0.006737 **
## Year 185.447 3 < 2.2e-16 ***
## Burn:Year 48.246 6 1.055e-08 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 1.287 0.0984 13.5 1.076 1.50
## SB 1.099 0.0984 13.5 0.887 1.31
## UB 0.929 0.0985 13.5 0.717 1.14
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.188 0.139 13.5 1.352 0.3922
## FB - UB 0.359 0.139 13.5 2.575 0.0551
## SB - UB 0.170 0.139 13.5 1.223 0.4601
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 1.287 0.0984 13.5 1.076 1.50
## SB 1.099 0.0984 13.5 0.887 1.31
## UB 0.929 0.0985 13.5 0.717 1.14
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.188 0.139 13.5 -0.17771 0.554
## FB - UB 0.359 0.139 13.5 -0.00748 0.725
## SB - UB 0.170 0.139 13.5 -0.19567 0.536
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.899 0.0687 36.3 0.760 1.04
## 2010 1.608 0.0687 36.3 1.469 1.75
## 2011 0.872 0.0690 37.0 0.732 1.01
## 2012 1.041 0.0687 36.3 0.902 1.18
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.7088 0.0631 215 -11.227 <.0001
## Year2009 - Year2011 0.0276 0.0635 215 0.435 0.9723
## Year2009 - Year2012 -0.1422 0.0631 215 -2.252 0.1128
## Year2010 - Year2011 0.7364 0.0635 215 11.606 <.0001
## Year2010 - Year2012 0.5666 0.0631 215 8.975 <.0001
## Year2011 - Year2012 -0.1698 0.0635 215 -2.676 0.0398
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.899 0.0687 36.3 0.760 1.04
## 2010 1.608 0.0687 36.3 1.469 1.75
## 2011 0.872 0.0690 37.0 0.732 1.01
## 2012 1.041 0.0687 36.3 0.902 1.18
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.7088 0.0631 215 -0.872 -0.5453
## Year2009 - Year2011 0.0276 0.0635 215 -0.137 0.1919
## Year2009 - Year2012 -0.1422 0.0631 215 -0.306 0.0213
## Year2010 - Year2011 0.7364 0.0635 215 0.572 0.9007
## Year2010 - Year2012 0.5666 0.0631 215 0.403 0.7301
## Year2011 - Year2012 -0.1698 0.0635 215 -0.334 -0.0055
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 1.214 0.119 36.3 0.972 1.455
## SB 0.831 0.119 36.3 0.590 1.073
## UB 0.653 0.119 36.2 0.412 0.894
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 2.019 0.119 36.3 1.777 2.260
## SB 1.597 0.119 36.3 1.356 1.839
## UB 1.208 0.119 36.2 0.967 1.450
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 0.982 0.119 36.3 0.741 1.224
## SB 0.871 0.119 36.3 0.629 1.112
## UB 0.762 0.121 38.3 0.518 1.006
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 0.935 0.119 36.3 0.694 1.177
## SB 1.098 0.119 36.3 0.856 1.339
## UB 1.092 0.119 36.2 0.850 1.333
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.38214 0.168 36.3 2.270 0.0731
## FB - UB 0.56044 0.168 36.2 3.329 0.0056
## SB - UB 0.17830 0.168 36.2 1.059 0.5451
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.42124 0.168 36.3 2.502 0.0438
## FB - UB 0.81018 0.168 36.2 4.813 0.0001
## SB - UB 0.38894 0.168 36.2 2.310 0.0670
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.11173 0.168 36.3 0.664 0.7858
## FB - UB 0.21993 0.169 37.3 1.298 0.4051
## SB - UB 0.10820 0.169 37.3 0.639 0.7998
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## FB - SB -0.16235 0.168 36.3 -0.964 0.6037
## FB - UB -0.15628 0.168 36.2 -0.928 0.6261
## SB - UB 0.00607 0.168 36.2 0.036 0.9993
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 1.214 0.119 36.3 0.972 1.455
## SB 0.831 0.119 36.3 0.590 1.073
## UB 0.653 0.119 36.2 0.412 0.894
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 2.019 0.119 36.3 1.777 2.260
## SB 1.597 0.119 36.3 1.356 1.839
## UB 1.208 0.119 36.2 0.967 1.450
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 0.982 0.119 36.3 0.741 1.224
## SB 0.871 0.119 36.3 0.629 1.112
## UB 0.762 0.121 38.3 0.518 1.006
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 0.935 0.119 36.3 0.694 1.177
## SB 1.098 0.119 36.3 0.856 1.339
## UB 1.092 0.119 36.2 0.850 1.333
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.38214 0.168 36.3 -0.02919 0.793
## FB - UB 0.56044 0.168 36.2 0.14908 0.972
## SB - UB 0.17830 0.168 36.2 -0.23306 0.590
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.42124 0.168 36.3 0.00991 0.833
## FB - UB 0.81018 0.168 36.2 0.39883 1.222
## SB - UB 0.38894 0.168 36.2 -0.02241 0.800
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.11173 0.168 36.3 -0.29959 0.523
## FB - UB 0.21993 0.169 37.3 -0.19354 0.633
## SB - UB 0.10820 0.169 37.3 -0.30527 0.522
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.16235 0.168 36.3 -0.57367 0.249
## FB - UB -0.15628 0.168 36.2 -0.56764 0.255
## SB - UB 0.00607 0.168 36.2 -0.40529 0.417
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NO3 + 1) ~ Burn + (1 | Site)
## Data: N_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 17.5 27.4 -3.8 7.5 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7345 -0.7224 -0.1097 0.5876 1.9543
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.005488 0.07408
## Residual 0.062706 0.25041
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.88198 0.07289 9.00000 12.100 7.17e-07 ***
## BurnSB -0.01418 0.10308 9.00000 -0.138 0.894
## BurnUB -0.01197 0.10308 9.00000 -0.116 0.910
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NO3 + 1)
## Chisq Df Pr(>Chisq)
## Burn 0.0219 2 0.9891## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.882 0.0893 13.5 0.690 1.07
## SB 0.868 0.0893 13.5 0.676 1.06
## UB 0.870 0.0893 13.5 0.678 1.06
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.01418 0.126 13.5 0.112 0.9931
## FB - UB 0.01197 0.126 13.5 0.095 0.9951
## SB - UB -0.00222 0.126 13.5 -0.018 0.9998
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.882 0.0893 13.5 0.690 1.07
## SB 0.868 0.0893 13.5 0.676 1.06
## UB 0.870 0.0893 13.5 0.678 1.06
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.01418 0.126 13.5 -0.318 0.346
## FB - UB 0.01197 0.126 13.5 -0.320 0.344
## SB - UB -0.00222 0.126 13.5 -0.334 0.330
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesPretreatment - 2008 Depth 5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NO3 + 1) ~ Burn + (1 | Site)
## Data: N_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -74.5 -64.6 42.3 -84.5 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.48865 -0.59265 -0.09298 0.47247 3.05554
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.007841 0.08855
## Residual 0.009028 0.09501
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.66653 0.05581 9.00000 11.942 8.02e-07 ***
## BurnSB -0.14123 0.07893 9.00000 -1.789 0.1072
## BurnUB -0.21467 0.07893 9.00000 -2.720 0.0236 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NO3 + 1)
## Chisq Df Pr(>Chisq)
## Burn 7.6425 2 0.0219 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.667 0.0684 13.5 0.519 0.814
## SB 0.525 0.0684 13.5 0.378 0.672
## UB 0.452 0.0684 13.5 0.305 0.599
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1412 0.0967 13.5 1.461 0.3394
## FB - UB 0.2147 0.0967 13.5 2.221 0.1034
## SB - UB 0.0734 0.0967 13.5 0.760 0.7331
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.667 0.0684 13.5 0.519 0.814
## SB 0.525 0.0684 13.5 0.378 0.672
## UB 0.452 0.0684 13.5 0.305 0.599
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1412 0.0967 13.5 -0.1129 0.395
## FB - UB 0.2147 0.0967 13.5 -0.0394 0.469
## SB - UB 0.0734 0.0967 13.5 -0.1807 0.328
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesTN Total Nitrogen
2008 pretreatment TN D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TN ~ Burn + (1 | Site)
## Data: WNC_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -187.9 -178.0 99.0 -197.9 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.9362 -0.5608 -0.1188 0.6531 2.3628
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0001393 0.01180
## Residual 0.0013852 0.03722
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.21111 0.01111 9.00000 19.005 1.42e-08 ***
## BurnSB 0.01833 0.01571 9.00000 1.167 0.273
## BurnUB 0.02722 0.01571 9.00000 1.733 0.117
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TN
## Chisq Df Pr(>Chisq)
## Burn 3.1234 2 0.2098## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.211 0.0136 13.5 0.182 0.240
## SB 0.229 0.0136 13.5 0.200 0.259
## UB 0.238 0.0136 13.5 0.209 0.268
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB -0.01833 0.0192 13.5 -0.953 0.6176
## FB - UB -0.02722 0.0192 13.5 -1.415 0.3612
## SB - UB -0.00889 0.0192 13.5 -0.462 0.8899
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.211 0.0136 13.5 0.182 0.240
## SB 0.229 0.0136 13.5 0.200 0.259
## UB 0.238 0.0136 13.5 0.209 0.268
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.01833 0.0192 13.5 -0.0689 0.0322
## FB - UB -0.02722 0.0192 13.5 -0.0778 0.0233
## SB - UB -0.00889 0.0192 13.5 -0.0595 0.0417
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesTN D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TN ~ Burn + (1 | Site)
## Data: WNC_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -221.8 -211.8 115.9 -231.8 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0200 -0.5788 -0.1197 0.6557 3.0060
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 2.685e-05 0.005182
## Residual 7.759e-04 0.027855
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.179444 0.007215 9.000000 24.871 1.32e-09 ***
## BurnSB 0.001111 0.010204 9.000000 0.109 0.916
## BurnUB 0.007778 0.010204 9.000000 0.762 0.465
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TN
## Chisq Df Pr(>Chisq)
## Burn 0.6798 2 0.7118## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.179 0.00884 13.5 0.160 0.198
## SB 0.181 0.00884 13.5 0.162 0.200
## UB 0.187 0.00884 13.5 0.168 0.206
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB -0.00111 0.0125 13.5 -0.089 0.9957
## FB - UB -0.00778 0.0125 13.5 -0.622 0.8105
## SB - UB -0.00667 0.0125 13.5 -0.533 0.8564
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.179 0.00884 13.5 0.160 0.198
## SB 0.181 0.00884 13.5 0.162 0.200
## UB 0.187 0.00884 13.5 0.168 0.206
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.00111 0.0125 13.5 -0.0340 0.0317
## FB - UB -0.00778 0.0125 13.5 -0.0406 0.0251
## SB - UB -0.00667 0.0125 13.5 -0.0395 0.0262
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TN ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(WNC_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -579.3 -532.1 303.7 -607.3 202
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.1389 -0.7146 -0.1081 0.6086 4.3174
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0005796 0.02407
## Residual 0.0032842 0.05731
## Number of obs: 216, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.320556 0.019381 21.956806 16.539 7.03e-14 ***
## BurnSB -0.017778 0.027410 21.956806 -0.649 0.52332
## BurnUB -0.056111 0.027410 21.956806 -2.047 0.05280 .
## Year2010 -0.046667 0.019103 207.000000 -2.443 0.01541 *
## Year2011 -0.051667 0.019103 207.000000 -2.705 0.00741 **
## Year2012 -0.047222 0.019103 207.000000 -2.472 0.01424 *
## BurnSB:Year2010 0.016111 0.027015 207.000000 0.596 0.55158
## BurnUB:Year2010 0.055556 0.027015 207.000000 2.056 0.04099 *
## BurnSB:Year2011 0.007778 0.027015 207.000000 0.288 0.77371
## BurnUB:Year2011 0.041667 0.027015 207.000000 1.542 0.12452
## BurnSB:Year2012 -0.006111 0.027015 207.000000 -0.226 0.82126
## BurnUB:Year2012 0.017222 0.027015 207.000000 0.637 0.52451
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 Yr2011 Yr2012 BSB:Y2010 BUB:Y2010
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.493 0.348 0.348
## Year2011 -0.493 0.348 0.348 0.500
## Year2012 -0.493 0.348 0.348 0.500 0.500
## BrnSB:Y2010 0.348 -0.493 -0.246 -0.707 -0.354 -0.354
## BrnUB:Y2010 0.348 -0.246 -0.493 -0.707 -0.354 -0.354 0.500
## BrnSB:Y2011 0.348 -0.493 -0.246 -0.354 -0.707 -0.354 0.500 0.250
## BrnUB:Y2011 0.348 -0.246 -0.493 -0.354 -0.707 -0.354 0.250 0.500
## BrnSB:Y2012 0.348 -0.493 -0.246 -0.354 -0.354 -0.707 0.500 0.250
## BrnUB:Y2012 0.348 -0.246 -0.493 -0.354 -0.354 -0.707 0.250 0.500
## BSB:Y2011 BUB:Y2011 BSB:Y2012
## BurnSB
## BurnUB
## Year2010
## Year2011
## Year2012
## BrnSB:Y2010
## BrnUB:Y2010
## BrnSB:Y2011
## BrnUB:Y2011 0.500
## BrnSB:Y2012 0.500 0.250
## BrnUB:Y2012 0.250 0.500 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TN
## Chisq Df Pr(>Chisq)
## Burn 1.5839 2 0.4529538
## Year 17.6928 3 0.0005089 ***
## Burn:Year 5.5461 6 0.4758976
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.284 0.0189 13.5 0.243 0.325
## SB 0.271 0.0189 13.5 0.230 0.312
## UB 0.257 0.0189 13.5 0.216 0.297
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0133 0.0268 13.5 0.498 0.8734
## FB - UB 0.0275 0.0268 13.5 1.027 0.5729
## SB - UB 0.0142 0.0268 13.5 0.529 0.8585
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.284 0.0189 13.5 0.243 0.325
## SB 0.271 0.0189 13.5 0.230 0.312
## UB 0.257 0.0189 13.5 0.216 0.297
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0133 0.0268 13.5 -0.0570 0.0837
## FB - UB 0.0275 0.0268 13.5 -0.0429 0.0979
## SB - UB 0.0142 0.0268 13.5 -0.0562 0.0845
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.296 0.0129 32.7 0.270 0.322
## 2010 0.273 0.0129 32.7 0.247 0.299
## 2011 0.261 0.0129 32.7 0.234 0.287
## 2012 0.252 0.0129 32.7 0.226 0.279
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.02278 0.0113 216 2.020 0.1838
## Year2009 - Year2011 0.03519 0.0113 216 3.120 0.0110
## Year2009 - Year2012 0.04352 0.0113 216 3.859 0.0009
## Year2010 - Year2011 0.01241 0.0113 216 1.100 0.6898
## Year2010 - Year2012 0.02074 0.0113 216 1.839 0.2579
## Year2011 - Year2012 0.00833 0.0113 216 0.739 0.8812
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.296 0.0129 32.7 0.270 0.322
## 2010 0.273 0.0129 32.7 0.247 0.299
## 2011 0.261 0.0129 32.7 0.234 0.287
## 2012 0.252 0.0129 32.7 0.226 0.279
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.02278 0.0113 216 -0.00642 0.0520
## Year2009 - Year2011 0.03519 0.0113 216 0.00599 0.0644
## Year2009 - Year2012 0.04352 0.0113 216 0.01432 0.0727
## Year2010 - Year2011 0.01241 0.0113 216 -0.01679 0.0416
## Year2010 - Year2012 0.02074 0.0113 216 -0.00846 0.0499
## Year2011 - Year2012 0.00833 0.0113 216 -0.02086 0.0375
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 0.321 0.0224 32.7 0.275 0.366
## SB 0.303 0.0224 32.7 0.257 0.348
## UB 0.264 0.0224 32.7 0.219 0.310
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 0.274 0.0224 32.7 0.228 0.319
## SB 0.272 0.0224 32.7 0.227 0.318
## UB 0.273 0.0224 32.7 0.228 0.319
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 0.269 0.0224 32.7 0.223 0.314
## SB 0.259 0.0224 32.7 0.213 0.304
## UB 0.254 0.0224 32.7 0.209 0.300
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 0.273 0.0224 32.7 0.228 0.319
## SB 0.249 0.0224 32.7 0.204 0.295
## UB 0.234 0.0224 32.7 0.189 0.280
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.017778 0.0317 32.7 0.561 0.8413
## FB - UB 0.056111 0.0317 32.7 1.772 0.1947
## SB - UB 0.038333 0.0317 32.7 1.211 0.4555
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.001667 0.0317 32.7 0.053 0.9985
## FB - UB 0.000556 0.0317 32.7 0.018 0.9998
## SB - UB -0.001111 0.0317 32.7 -0.035 0.9993
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.010000 0.0317 32.7 0.316 0.9466
## FB - UB 0.014444 0.0317 32.7 0.456 0.8920
## SB - UB 0.004444 0.0317 32.7 0.140 0.9892
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.023889 0.0317 32.7 0.754 0.7331
## FB - UB 0.038889 0.0317 32.7 1.228 0.4454
## SB - UB 0.015000 0.0317 32.7 0.474 0.8841
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 0.321 0.0224 32.7 0.275 0.366
## SB 0.303 0.0224 32.7 0.257 0.348
## UB 0.264 0.0224 32.7 0.219 0.310
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 0.274 0.0224 32.7 0.228 0.319
## SB 0.272 0.0224 32.7 0.227 0.318
## UB 0.273 0.0224 32.7 0.228 0.319
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 0.269 0.0224 32.7 0.223 0.314
## SB 0.259 0.0224 32.7 0.213 0.304
## UB 0.254 0.0224 32.7 0.209 0.300
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 0.273 0.0224 32.7 0.228 0.319
## SB 0.249 0.0224 32.7 0.204 0.295
## UB 0.234 0.0224 32.7 0.189 0.280
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.017778 0.0317 32.7 -0.0599 0.0955
## FB - UB 0.056111 0.0317 32.7 -0.0216 0.1338
## SB - UB 0.038333 0.0317 32.7 -0.0394 0.1161
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.001667 0.0317 32.7 -0.0761 0.0794
## FB - UB 0.000556 0.0317 32.7 -0.0772 0.0783
## SB - UB -0.001111 0.0317 32.7 -0.0788 0.0766
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.010000 0.0317 32.7 -0.0677 0.0877
## FB - UB 0.014444 0.0317 32.7 -0.0633 0.0922
## SB - UB 0.004444 0.0317 32.7 -0.0733 0.0822
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.023889 0.0317 32.7 -0.0538 0.1016
## FB - UB 0.038889 0.0317 32.7 -0.0388 0.1166
## SB - UB 0.015000 0.0317 32.7 -0.0627 0.0927
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TN ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(WNC_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -923.6 -876.3 475.8 -951.6 202
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0699 -0.5383 -0.0641 0.5397 6.6896
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0001230 0.01109
## Residual 0.0006663 0.02581
## Number of obs: 216, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.889e-01 8.833e-03 2.141e+01 21.385 6.26e-16 ***
## BurnSB -3.889e-03 1.249e-02 2.141e+01 -0.311 0.759
## BurnUB 5.556e-04 1.249e-02 2.141e+01 0.044 0.965
## Year2010 6.111e-03 8.604e-03 2.070e+02 0.710 0.478
## Year2011 1.333e-02 8.604e-03 2.070e+02 1.550 0.123
## Year2012 4.444e-03 8.604e-03 2.070e+02 0.517 0.606
## BurnSB:Year2010 1.111e-03 1.217e-02 2.070e+02 0.091 0.927
## BurnUB:Year2010 -1.222e-02 1.217e-02 2.070e+02 -1.004 0.316
## BurnSB:Year2011 -1.111e-03 1.217e-02 2.070e+02 -0.091 0.927
## BurnUB:Year2011 -7.222e-03 1.217e-02 2.070e+02 -0.594 0.553
## BurnSB:Year2012 2.222e-03 1.217e-02 2.070e+02 0.183 0.855
## BurnUB:Year2012 -1.944e-02 1.217e-02 2.070e+02 -1.598 0.112
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 Yr2011 Yr2012 BSB:Y2010 BUB:Y2010
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.487 0.344 0.344
## Year2011 -0.487 0.344 0.344 0.500
## Year2012 -0.487 0.344 0.344 0.500 0.500
## BrnSB:Y2010 0.344 -0.487 -0.244 -0.707 -0.354 -0.354
## BrnUB:Y2010 0.344 -0.244 -0.487 -0.707 -0.354 -0.354 0.500
## BrnSB:Y2011 0.344 -0.487 -0.244 -0.354 -0.707 -0.354 0.500 0.250
## BrnUB:Y2011 0.344 -0.244 -0.487 -0.354 -0.707 -0.354 0.250 0.500
## BrnSB:Y2012 0.344 -0.487 -0.244 -0.354 -0.354 -0.707 0.500 0.250
## BrnUB:Y2012 0.344 -0.244 -0.487 -0.354 -0.354 -0.707 0.250 0.500
## BSB:Y2011 BUB:Y2011 BSB:Y2012
## BurnSB
## BurnUB
## Year2010
## Year2011
## Year2012
## BrnSB:Y2010
## BrnUB:Y2010
## BrnSB:Y2011
## BrnUB:Y2011 0.500
## BrnSB:Y2012 0.500 0.250
## BrnUB:Y2012 0.250 0.500 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TN
## Chisq Df Pr(>Chisq)
## Burn 0.8567 2 0.65158
## Year 6.8779 3 0.07589 .
## Burn:Year 4.2300 6 0.64558
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.195 0.00868 13.5 0.176 0.214
## SB 0.192 0.00868 13.5 0.173 0.210
## UB 0.186 0.00868 13.5 0.167 0.204
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.00333 0.0123 13.5 0.271 0.9603
## FB - UB 0.00917 0.0123 13.5 0.747 0.7407
## SB - UB 0.00583 0.0123 13.5 0.475 0.8841
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 0.195 0.00868 13.5 0.176 0.214
## SB 0.192 0.00868 13.5 0.173 0.210
## UB 0.186 0.00868 13.5 0.167 0.204
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.00333 0.0123 13.5 -0.0289 0.0356
## FB - UB 0.00917 0.0123 13.5 -0.0231 0.0414
## SB - UB 0.00583 0.0123 13.5 -0.0264 0.0381
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.188 0.0059 31.9 0.176 0.200
## 2010 0.190 0.0059 31.9 0.178 0.202
## 2011 0.198 0.0059 31.9 0.186 0.210
## 2012 0.186 0.0059 31.9 0.174 0.198
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.00241 0.00508 216 -0.474 0.9647
## Year2009 - Year2011 -0.01056 0.00508 216 -2.078 0.1636
## Year2009 - Year2012 0.00130 0.00508 216 0.255 0.9942
## Year2010 - Year2011 -0.00815 0.00508 216 -1.604 0.3784
## Year2010 - Year2012 0.00370 0.00508 216 0.729 0.8853
## Year2011 - Year2012 0.01185 0.00508 216 2.333 0.0937
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.188 0.0059 31.9 0.176 0.200
## 2010 0.190 0.0059 31.9 0.178 0.202
## 2011 0.198 0.0059 31.9 0.186 0.210
## 2012 0.186 0.0059 31.9 0.174 0.198
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.00241 0.00508 216 -0.01556 0.0107
## Year2009 - Year2011 -0.01056 0.00508 216 -0.02371 0.0026
## Year2009 - Year2012 0.00130 0.00508 216 -0.01185 0.0144
## Year2010 - Year2011 -0.00815 0.00508 216 -0.02130 0.0050
## Year2010 - Year2012 0.00370 0.00508 216 -0.00945 0.0169
## Year2011 - Year2012 0.01185 0.00508 216 -0.00130 0.0250
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 0.189 0.0102 31.9 0.168 0.210
## SB 0.185 0.0102 31.9 0.164 0.206
## UB 0.189 0.0102 31.9 0.169 0.210
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 0.195 0.0102 31.9 0.174 0.216
## SB 0.192 0.0102 31.9 0.171 0.213
## UB 0.183 0.0102 31.9 0.163 0.204
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 0.202 0.0102 31.9 0.181 0.223
## SB 0.197 0.0102 31.9 0.176 0.218
## UB 0.196 0.0102 31.9 0.175 0.216
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 0.193 0.0102 31.9 0.173 0.214
## SB 0.192 0.0102 31.9 0.171 0.212
## UB 0.174 0.0102 31.9 0.154 0.195
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.003889 0.0145 31.9 0.269 0.9609
## FB - UB -0.000556 0.0145 31.9 -0.038 0.9992
## SB - UB -0.004444 0.0145 31.9 -0.308 0.9493
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.002778 0.0145 31.9 0.192 0.9798
## FB - UB 0.011667 0.0145 31.9 0.807 0.7013
## SB - UB 0.008889 0.0145 31.9 0.615 0.8130
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.005000 0.0145 31.9 0.346 0.9363
## FB - UB 0.006667 0.0145 31.9 0.461 0.8897
## SB - UB 0.001667 0.0145 31.9 0.115 0.9927
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.001667 0.0145 31.9 0.115 0.9927
## FB - UB 0.018889 0.0145 31.9 1.307 0.4017
## SB - UB 0.017222 0.0145 31.9 1.192 0.4666
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 0.189 0.0102 31.9 0.168 0.210
## SB 0.185 0.0102 31.9 0.164 0.206
## UB 0.189 0.0102 31.9 0.169 0.210
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 0.195 0.0102 31.9 0.174 0.216
## SB 0.192 0.0102 31.9 0.171 0.213
## UB 0.183 0.0102 31.9 0.163 0.204
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 0.202 0.0102 31.9 0.181 0.223
## SB 0.197 0.0102 31.9 0.176 0.218
## UB 0.196 0.0102 31.9 0.175 0.216
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 0.193 0.0102 31.9 0.173 0.214
## SB 0.192 0.0102 31.9 0.171 0.212
## UB 0.174 0.0102 31.9 0.154 0.195
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.003889 0.0145 31.9 -0.0316 0.0394
## FB - UB -0.000556 0.0145 31.9 -0.0361 0.0350
## SB - UB -0.004444 0.0145 31.9 -0.0400 0.0311
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.002778 0.0145 31.9 -0.0327 0.0383
## FB - UB 0.011667 0.0145 31.9 -0.0238 0.0472
## SB - UB 0.008889 0.0145 31.9 -0.0266 0.0444
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.005000 0.0145 31.9 -0.0305 0.0405
## FB - UB 0.006667 0.0145 31.9 -0.0288 0.0422
## SB - UB 0.001667 0.0145 31.9 -0.0338 0.0372
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.001667 0.0145 31.9 -0.0338 0.0372
## FB - UB 0.018889 0.0145 31.9 -0.0166 0.0544
## SB - UB 0.017222 0.0145 31.9 -0.0183 0.0527
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesTC Total Carbon
2008 pretreatment TC D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TC ~ Burn + (1 | Site)
## Data: WNC_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 97.6 107.5 -43.8 87.6 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.9121 -0.7561 -0.1407 0.6956 2.5804
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.001531 0.03913
## Residual 0.294996 0.54313
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 2.6461 0.1300 9.0000 20.355 7.77e-09 ***
## BurnSB 0.1883 0.1838 9.0000 1.024 0.3324
## BurnUB 0.3567 0.1838 9.0000 1.940 0.0843 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TC
## Chisq Df Pr(>Chisq)
## Burn 3.7678 2 0.152## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.65 0.159 13.5 2.30 2.99
## SB 2.83 0.159 13.5 2.49 3.18
## UB 3.00 0.159 13.5 2.66 3.35
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB -0.188 0.225 13.5 -0.836 0.6876
## FB - UB -0.357 0.225 13.5 -1.584 0.2857
## SB - UB -0.168 0.225 13.5 -0.748 0.7401
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.65 0.159 13.5 2.30 2.99
## SB 2.83 0.159 13.5 2.49 3.18
## UB 3.00 0.159 13.5 2.66 3.35
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.188 0.225 13.5 -0.780 0.403
## FB - UB -0.357 0.225 13.5 -0.948 0.235
## SB - UB -0.168 0.225 13.5 -0.760 0.423
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesTC D5 2008
## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TC ~ Burn + (1 | Site)
## Data: WNC_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 64.4 74.4 -27.2 54.4 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7991 -0.6703 -0.2421 0.4484 3.2694
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0000 0.0000
## Residual 0.1604 0.4005
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 2.16389 0.09440 54.00000 22.922 <2e-16 ***
## BurnSB 0.02611 0.13350 54.00000 0.196 0.846
## BurnUB 0.11667 0.13350 54.00000 0.874 0.386
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TC
## Chisq Df Pr(>Chisq)
## Burn 0.8413 2 0.6566## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.16 0.106 9.38 1.93 2.40
## SB 2.19 0.106 9.38 1.95 2.43
## UB 2.28 0.106 9.38 2.04 2.52
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB -0.0261 0.149 9.38 -0.175 0.9833
## FB - UB -0.1167 0.149 9.38 -0.781 0.7227
## SB - UB -0.0906 0.149 9.38 -0.607 0.8200
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.16 0.106 9.38 1.93 2.40
## SB 2.19 0.106 9.38 1.95 2.43
## UB 2.28 0.106 9.38 2.04 2.52
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB -0.0261 0.149 9.38 -0.440 0.388
## FB - UB -0.1167 0.149 9.38 -0.530 0.297
## SB - UB -0.0906 0.149 9.38 -0.504 0.323
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TC ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(WNC_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 580.0 627.3 -276.0 552.0 202
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0218 -0.7710 -0.0321 0.6443 3.8933
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.05256 0.2293
## Residual 0.72310 0.8504
## Number of obs: 216, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.29889 0.24019 37.48428 17.898 < 2e-16 ***
## BurnSB -0.40944 0.33968 37.48428 -1.205 0.23561
## BurnUB -0.96667 0.33968 37.48428 -2.846 0.00714 **
## Year2010 -0.74889 0.28345 207.00000 -2.642 0.00887 **
## Year2011 -0.79889 0.28345 207.00000 -2.818 0.00529 **
## Year2012 -0.66444 0.28345 207.00000 -2.344 0.02002 *
## BurnSB:Year2010 0.30944 0.40086 207.00000 0.772 0.44103
## BurnUB:Year2010 0.97778 0.40086 207.00000 2.439 0.01556 *
## BurnSB:Year2011 0.09722 0.40086 207.00000 0.243 0.80861
## BurnUB:Year2011 0.64944 0.40086 207.00000 1.620 0.10673
## BurnSB:Year2012 -0.06833 0.40086 207.00000 -0.170 0.86481
## BurnUB:Year2012 0.34389 0.40086 207.00000 0.858 0.39195
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 Yr2011 Yr2012 BSB:Y2010 BUB:Y2010
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.590 0.417 0.417
## Year2011 -0.590 0.417 0.417 0.500
## Year2012 -0.590 0.417 0.417 0.500 0.500
## BrnSB:Y2010 0.417 -0.590 -0.295 -0.707 -0.354 -0.354
## BrnUB:Y2010 0.417 -0.295 -0.590 -0.707 -0.354 -0.354 0.500
## BrnSB:Y2011 0.417 -0.590 -0.295 -0.354 -0.707 -0.354 0.500 0.250
## BrnUB:Y2011 0.417 -0.295 -0.590 -0.354 -0.707 -0.354 0.250 0.500
## BrnSB:Y2012 0.417 -0.590 -0.295 -0.354 -0.354 -0.707 0.500 0.250
## BrnUB:Y2012 0.417 -0.295 -0.590 -0.354 -0.354 -0.707 0.250 0.500
## BSB:Y2011 BUB:Y2011 BSB:Y2012
## BurnSB
## BurnUB
## Year2010
## Year2011
## Year2012
## BrnSB:Y2010
## BrnUB:Y2010
## BrnSB:Y2011
## BrnUB:Y2011 0.500
## BrnSB:Y2012 0.500 0.250
## BrnUB:Y2012 0.250 0.500 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TC
## Chisq Df Pr(>Chisq)
## Burn 4.2609 2 0.118783
## Year 15.8697 3 0.001206 **
## Burn:Year 7.1449 6 0.307657
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 3.75 0.203 13.5 3.31 4.18
## SB 3.42 0.203 13.5 2.98 3.86
## UB 3.27 0.203 13.5 2.83 3.71
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.325 0.288 13.5 1.130 0.5129
## FB - UB 0.474 0.288 13.5 1.648 0.2603
## SB - UB 0.149 0.288 13.5 0.518 0.8638
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 3.75 0.203 13.5 3.31 4.18
## SB 3.42 0.203 13.5 2.98 3.86
## UB 3.27 0.203 13.5 2.83 3.71
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.325 0.288 13.5 -0.431 1.081
## FB - UB 0.474 0.288 13.5 -0.282 1.230
## SB - UB 0.149 0.288 13.5 -0.607 0.905
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 3.84 0.156 55 3.53 4.15
## 2010 3.52 0.156 55 3.21 3.83
## 2011 3.29 0.156 55 2.98 3.60
## 2012 3.27 0.156 55 2.96 3.58
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.3198 0.167 216 1.911 0.2263
## Year2009 - Year2011 0.5500 0.167 216 3.287 0.0064
## Year2009 - Year2012 0.5726 0.167 216 3.422 0.0041
## Year2010 - Year2011 0.2302 0.167 216 1.376 0.5160
## Year2010 - Year2012 0.2528 0.167 216 1.511 0.4329
## Year2011 - Year2012 0.0226 0.167 216 0.135 0.9991
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 3.84 0.156 55 3.53 4.15
## 2010 3.52 0.156 55 3.21 3.83
## 2011 3.29 0.156 55 2.98 3.60
## 2012 3.27 0.156 55 2.96 3.58
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.3198 0.167 216 -0.113 0.753
## Year2009 - Year2011 0.5500 0.167 216 0.117 0.983
## Year2009 - Year2012 0.5726 0.167 216 0.139 1.006
## Year2010 - Year2011 0.2302 0.167 216 -0.203 0.663
## Year2010 - Year2012 0.2528 0.167 216 -0.180 0.686
## Year2011 - Year2012 0.0226 0.167 216 -0.411 0.456
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 4.30 0.27 55 3.76 4.84
## SB 3.89 0.27 55 3.35 4.43
## UB 3.33 0.27 55 2.79 3.87
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 3.55 0.27 55 3.01 4.09
## SB 3.45 0.27 55 2.91 3.99
## UB 3.56 0.27 55 3.02 4.10
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 3.50 0.27 55 2.96 4.04
## SB 3.19 0.27 55 2.65 3.73
## UB 3.18 0.27 55 2.64 3.72
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 3.63 0.27 55 3.09 4.18
## SB 3.16 0.27 55 2.62 3.70
## UB 3.01 0.27 55 2.47 3.55
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.4094 0.382 55 1.073 0.5349
## FB - UB 0.9667 0.382 55 2.533 0.0372
## SB - UB 0.5572 0.382 55 1.460 0.3180
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1000 0.382 55 0.262 0.9629
## FB - UB -0.0111 0.382 55 -0.029 0.9995
## SB - UB -0.1111 0.382 55 -0.291 0.9544
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.3122 0.382 55 0.818 0.6935
## FB - UB 0.3172 0.382 55 0.831 0.6855
## SB - UB 0.0050 0.382 55 0.013 0.9999
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.4778 0.382 55 1.252 0.4283
## FB - UB 0.6228 0.382 55 1.632 0.2411
## SB - UB 0.1450 0.382 55 0.380 0.9236
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 4.30 0.27 55 3.76 4.84
## SB 3.89 0.27 55 3.35 4.43
## UB 3.33 0.27 55 2.79 3.87
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 3.55 0.27 55 3.01 4.09
## SB 3.45 0.27 55 2.91 3.99
## UB 3.56 0.27 55 3.02 4.10
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 3.50 0.27 55 2.96 4.04
## SB 3.19 0.27 55 2.65 3.73
## UB 3.18 0.27 55 2.64 3.72
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 3.63 0.27 55 3.09 4.18
## SB 3.16 0.27 55 2.62 3.70
## UB 3.01 0.27 55 2.47 3.55
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.4094 0.382 55 -0.5099 1.329
## FB - UB 0.9667 0.382 55 0.0473 1.886
## SB - UB 0.5572 0.382 55 -0.3621 1.477
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1000 0.382 55 -0.8194 1.019
## FB - UB -0.0111 0.382 55 -0.9305 0.908
## SB - UB -0.1111 0.382 55 -1.0305 0.808
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.3122 0.382 55 -0.6071 1.232
## FB - UB 0.3172 0.382 55 -0.6021 1.237
## SB - UB 0.0050 0.382 55 -0.9144 0.924
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.4778 0.382 55 -0.4416 1.397
## FB - UB 0.6228 0.382 55 -0.2966 1.542
## SB - UB 0.1450 0.382 55 -0.7744 1.064
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TC ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(WNC_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 250.3 297.6 -111.2 222.3 202
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0090 -0.5965 -0.0941 0.4638 6.9193
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.009717 0.09857
## Residual 0.157797 0.39724
## Number of obs: 216, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 2.29500 0.10957 41.35018 20.946 <2e-16 ***
## BurnSB -0.10000 0.15495 41.35018 -0.645 0.522
## BurnUB -0.03444 0.15495 41.35018 -0.222 0.825
## Year2010 0.09944 0.13241 207.00000 0.751 0.453
## Year2011 0.19500 0.13241 207.00000 1.473 0.142
## Year2012 0.14444 0.13241 207.00000 1.091 0.277
## BurnSB:Year2010 -0.01667 0.18726 207.00000 -0.089 0.929
## BurnUB:Year2010 -0.11556 0.18726 207.00000 -0.617 0.538
## BurnSB:Year2011 -0.05667 0.18726 207.00000 -0.303 0.762
## BurnUB:Year2011 -0.16833 0.18726 207.00000 -0.899 0.370
## BurnSB:Year2012 0.01667 0.18726 207.00000 0.089 0.929
## BurnUB:Year2012 -0.26389 0.18726 207.00000 -1.409 0.160
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 Yr2011 Yr2012 BSB:Y2010 BUB:Y2010
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.604 0.427 0.427
## Year2011 -0.604 0.427 0.427 0.500
## Year2012 -0.604 0.427 0.427 0.500 0.500
## BrnSB:Y2010 0.427 -0.604 -0.302 -0.707 -0.354 -0.354
## BrnUB:Y2010 0.427 -0.302 -0.604 -0.707 -0.354 -0.354 0.500
## BrnSB:Y2011 0.427 -0.604 -0.302 -0.354 -0.707 -0.354 0.500 0.250
## BrnUB:Y2011 0.427 -0.302 -0.604 -0.354 -0.707 -0.354 0.250 0.500
## BrnSB:Y2012 0.427 -0.604 -0.302 -0.354 -0.354 -0.707 0.500 0.250
## BrnUB:Y2012 0.427 -0.302 -0.604 -0.354 -0.354 -0.707 0.250 0.500
## BSB:Y2011 BUB:Y2011 BSB:Y2012
## BurnSB
## BurnUB
## Year2010
## Year2011
## Year2012
## BrnSB:Y2010
## BrnUB:Y2010
## BrnSB:Y2011
## BrnUB:Y2011 0.500
## BrnSB:Y2012 0.500 0.250
## BrnUB:Y2012 0.250 0.500 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TC
## Chisq Df Pr(>Chisq)
## Burn 2.8040 2 0.2461
## Year 2.4721 3 0.4804
## Burn:Year 3.0395 6 0.8039## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.40 0.0903 13.5 2.21 2.60
## SB 2.29 0.0903 13.5 2.10 2.48
## UB 2.23 0.0903 13.5 2.04 2.43
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1142 0.128 13.5 0.894 0.6528
## FB - UB 0.1714 0.128 13.5 1.343 0.3969
## SB - UB 0.0572 0.128 13.5 0.448 0.8960
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 2.40 0.0903 13.5 2.21 2.60
## SB 2.29 0.0903 13.5 2.10 2.48
## UB 2.23 0.0903 13.5 2.04 2.43
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1142 0.128 13.5 -0.221 0.450
## FB - UB 0.1714 0.128 13.5 -0.164 0.507
## SB - UB 0.0572 0.128 13.5 -0.278 0.393
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 2.25 0.0708 60.5 2.11 2.39
## 2010 2.31 0.0708 60.5 2.16 2.45
## 2011 2.37 0.0708 60.5 2.23 2.51
## 2012 2.31 0.0708 60.5 2.17 2.45
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.05537 0.0782 216 -0.708 0.8937
## Year2009 - Year2011 -0.12000 0.0782 216 -1.535 0.4183
## Year2009 - Year2012 -0.06204 0.0782 216 -0.794 0.8573
## Year2010 - Year2011 -0.06463 0.0782 216 -0.827 0.8417
## Year2010 - Year2012 -0.00667 0.0782 216 -0.085 0.9998
## Year2011 - Year2012 0.05796 0.0782 216 0.742 0.8802
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 2.25 0.0708 60.5 2.11 2.39
## 2010 2.31 0.0708 60.5 2.16 2.45
## 2011 2.37 0.0708 60.5 2.23 2.51
## 2012 2.31 0.0708 60.5 2.17 2.45
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.05537 0.0782 216 -0.258 0.1470
## Year2009 - Year2011 -0.12000 0.0782 216 -0.322 0.0824
## Year2009 - Year2012 -0.06204 0.0782 216 -0.264 0.1403
## Year2010 - Year2011 -0.06463 0.0782 216 -0.267 0.1378
## Year2010 - Year2012 -0.00667 0.0782 216 -0.209 0.1957
## Year2011 - Year2012 0.05796 0.0782 216 -0.144 0.2603
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 2.29 0.123 60.5 2.05 2.54
## SB 2.19 0.123 60.5 1.95 2.44
## UB 2.26 0.123 60.5 2.02 2.51
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 2.39 0.123 60.5 2.15 2.64
## SB 2.28 0.123 60.5 2.03 2.52
## UB 2.24 0.123 60.5 2.00 2.49
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 2.49 0.123 60.5 2.24 2.74
## SB 2.33 0.123 60.5 2.09 2.58
## UB 2.29 0.123 60.5 2.04 2.53
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 2.44 0.123 60.5 2.19 2.68
## SB 2.36 0.123 60.5 2.11 2.60
## UB 2.14 0.123 60.5 1.90 2.39
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1000 0.173 60.5 0.577 0.8329
## FB - UB 0.0344 0.173 60.5 0.199 0.9785
## SB - UB -0.0656 0.173 60.5 -0.378 0.9243
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1167 0.173 60.5 0.673 0.7799
## FB - UB 0.1500 0.173 60.5 0.865 0.6640
## SB - UB 0.0333 0.173 60.5 0.192 0.9798
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1567 0.173 60.5 0.904 0.6399
## FB - UB 0.2028 0.173 60.5 1.170 0.4755
## SB - UB 0.0461 0.173 60.5 0.266 0.9618
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0833 0.173 60.5 0.481 0.8806
## FB - UB 0.2983 0.173 60.5 1.721 0.2056
## SB - UB 0.2150 0.173 60.5 1.240 0.4343
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 2.29 0.123 60.5 2.05 2.54
## SB 2.19 0.123 60.5 1.95 2.44
## UB 2.26 0.123 60.5 2.02 2.51
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 2.39 0.123 60.5 2.15 2.64
## SB 2.28 0.123 60.5 2.03 2.52
## UB 2.24 0.123 60.5 2.00 2.49
##
## Year = 2011:
## Burn emmean SE df lower.CL upper.CL
## FB 2.49 0.123 60.5 2.24 2.74
## SB 2.33 0.123 60.5 2.09 2.58
## UB 2.29 0.123 60.5 2.04 2.53
##
## Year = 2012:
## Burn emmean SE df lower.CL upper.CL
## FB 2.44 0.123 60.5 2.19 2.68
## SB 2.36 0.123 60.5 2.11 2.60
## UB 2.14 0.123 60.5 1.90 2.39
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1000 0.173 60.5 -0.316 0.516
## FB - UB 0.0344 0.173 60.5 -0.382 0.451
## SB - UB -0.0656 0.173 60.5 -0.482 0.351
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1167 0.173 60.5 -0.300 0.533
## FB - UB 0.1500 0.173 60.5 -0.266 0.566
## SB - UB 0.0333 0.173 60.5 -0.383 0.450
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1567 0.173 60.5 -0.260 0.573
## FB - UB 0.2028 0.173 60.5 -0.214 0.619
## SB - UB 0.0461 0.173 60.5 -0.370 0.463
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0833 0.173 60.5 -0.333 0.500
## FB - UB 0.2983 0.173 60.5 -0.118 0.715
## SB - UB 0.2150 0.173 60.5 -0.201 0.631
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesAl -Aluminum
Al D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Al ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 941.3 951.2 -465.6 931.3 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.95587 -0.53197 -0.04864 0.53833 2.28153
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 219833 468.9
## Residual 1638993 1280.2
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 22269.5 405.4 9.0 54.935 1.1e-12 ***
## BurnSB -2162.6 573.3 9.0 -3.772 0.0044 **
## BurnUB -407.8 573.3 9.0 -0.711 0.4949
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Al
## Chisq Df Pr(>Chisq)
## Burn 16.07 2 0.0003239 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 22270 496 13.5 21201 23338
## SB 20107 496 13.5 19038 21175
## UB 21862 496 13.5 20793 22930
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 2163 702 13.5 3.080 0.0215
## FB - UB 408 702 13.5 0.581 0.8325
## SB - UB -1755 702 13.5 -2.499 0.0632
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 22270 496 13.5 21201 23338
## SB 20107 496 13.5 19038 21175
## UB 21862 496 13.5 20793 22930
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 2163 702 13.5 317 4008.1
## FB - UB 408 702 13.5 -1438 2253.3
## SB - UB -1755 702 13.5 -3600 90.7
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesAl D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Al ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 940.4 950.3 -465.2 930.4 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.6691 -0.6981 0.1178 0.6074 1.7138
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 348147 590
## Residual 1542217 1242
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 23249.7 449.1 9.0 51.765 1.88e-12 ***
## BurnSB -2373.6 635.2 9.0 -3.737 0.00465 **
## BurnUB 172.2 635.2 9.0 0.271 0.79247
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Al
## Chisq Df Pr(>Chisq)
## Burn 20.068 2 4.389e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 23250 550 13.5 22066 24434
## SB 20876 550 13.5 19692 22060
## UB 23422 550 13.5 22238 24606
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 2374 778 13.5 3.051 0.0228
## FB - UB -172 778 13.5 -0.221 0.9734
## SB - UB -2546 778 13.5 -3.272 0.0150
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 23250 550 13.5 22066 24434
## SB 20876 550 13.5 19692 22060
## UB 23422 550 13.5 22238 24606
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 2374 778 13.5 329 4418
## FB - UB -172 778 13.5 -2217 1873
## SB - UB -2546 778 13.5 -4590 -501
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Al ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 1911.4 1932.9 -947.7 1895.4 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4848 -0.7832 0.0619 0.7610 2.0856
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 914341 956.2
## Residual 2105533 1451.0
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 20100.1 649.4 12.1 30.951 6.80e-13 ***
## BurnSB -490.9 918.4 12.1 -0.534 0.6027
## BurnUB 1487.8 918.4 12.1 1.620 0.1310
## Year2010 2000.5 483.7 99.0 4.136 7.42e-05 ***
## BurnSB:Year2010 -1028.9 684.0 99.0 -1.504 0.1357
## BurnUB:Year2010 -1253.4 684.0 99.0 -1.832 0.0699 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.372 0.263 0.263
## BrnSB:Y2010 0.263 -0.372 -0.186 -0.707
## BrnUB:Y2010 0.263 -0.186 -0.372 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Al
## Chisq Df Pr(>Chisq)
## Burn 4.8047 2 0.09051 .
## Year 19.7084 1 9.021e-06 ***
## Burn:Year 3.8186 2 0.14818
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 21100 738 13.5 19512 22689
## SB 20095 738 13.5 18506 21684
## UB 21962 738 13.5 20373 23550
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 1005 1040 13.5 0.963 0.6115
## FB - UB -861 1040 13.5 -0.825 0.6945
## SB - UB -1866 1040 13.5 -1.788 0.2106
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 21100 738 13.5 19512 22689
## SB 20095 738 13.5 18506 21684
## UB 21962 738 13.5 20373 23550
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 1005 1040 13.5 -1739 3749
## FB - UB -861 1040 13.5 -3605 1883
## SB - UB -1866 1040 13.5 -4610 877
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 20432 449 18.1 19489 21376
## 2010 21672 449 18.1 20729 22615
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -1240 284 102 -4.372 <.0001
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 20432 449 18.1 19489 21376
## 2010 21672 449 18.1 20729 22615
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -1240 284 102 -1802 -677
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 20100 778 18.1 18467 21734
## SB 19609 778 18.1 17976 21243
## UB 21588 778 18.1 19954 23221
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 22101 778 18.1 20467 23734
## SB 20581 778 18.1 18947 22214
## UB 22335 778 18.1 20702 23969
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 491 1100 18.1 0.446 0.8967
## FB - UB -1488 1100 18.1 -1.352 0.3857
## SB - UB -1979 1100 18.1 -1.799 0.1981
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 1520 1100 18.1 1.381 0.3709
## FB - UB -234 1100 18.1 -0.213 0.9753
## SB - UB -1754 1100 18.1 -1.595 0.2733
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 20100 778 18.1 18467 21734
## SB 19609 778 18.1 17976 21243
## UB 21588 778 18.1 19954 23221
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 22101 778 18.1 20467 23734
## SB 20581 778 18.1 18947 22214
## UB 22335 778 18.1 20702 23969
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 491 1100 18.1 -2315 3297
## FB - UB -1488 1100 18.1 -4294 1318
## SB - UB -1979 1100 18.1 -4785 827
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 1520 1100 18.1 -1286 4326
## FB - UB -234 1100 18.1 -3040 2572
## SB - UB -1754 1100 18.1 -4560 1052
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Al ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 1998.7 2020.2 -991.4 1982.7 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.8124 -0.3743 0.0452 0.3792 6.1934
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 635370 797.1
## Residual 5097987 2257.9
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 22662.72 703.57 17.40 32.211 <2e-16 ***
## BurnSB -2099.33 995.00 17.40 -2.110 0.0496 *
## BurnUB 31.56 995.00 17.40 0.032 0.9751
## Year2010 81.78 752.62 99.00 0.109 0.9137
## BurnSB:Year2010 1179.61 1064.37 99.00 1.108 0.2704
## BurnUB:Year2010 796.56 1064.37 99.00 0.748 0.4560
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.535 0.378 0.378
## BrnSB:Y2010 0.378 -0.535 -0.267 -0.707
## BrnUB:Y2010 0.378 -0.267 -0.535 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Al
## Chisq Df Pr(>Chisq)
## Burn 5.8711 2 0.05310 .
## Year 2.9041 1 0.08835 .
## Burn:Year 1.2786 2 0.52767
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 22704 728 13.5 21137 24271
## SB 21194 728 13.5 19627 22761
## UB 23133 728 13.5 21566 24700
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 1510 1030 13.5 1.466 0.3371
## FB - UB -430 1030 13.5 -0.417 0.9090
## SB - UB -1939 1030 13.5 -1.883 0.1812
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 22704 728 13.5 21137 24271
## SB 21194 728 13.5 19627 22761
## UB 23133 728 13.5 21566 24700
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 1510 1030 13.5 -1197 4216
## FB - UB -430 1030 13.5 -3136 2277
## SB - UB -1939 1030 13.5 -4646 767
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 21973 475 25.9 20998 22949
## 2010 22714 475 25.9 21738 23690
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -740 441 102 -1.678 0.0964
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 21973 475 25.9 20998 22949
## 2010 22714 475 25.9 21738 23690
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -740 441 102 -1616 135
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 22663 822 25.9 20972 24353
## SB 20563 822 25.9 18873 22254
## UB 22694 822 25.9 21004 24385
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 22745 822 25.9 21054 24435
## SB 21825 822 25.9 20134 23515
## UB 23573 822 25.9 21882 25263
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 2099.3 1160 25.9 1.805 0.1877
## FB - UB -31.6 1160 25.9 -0.027 0.9996
## SB - UB -2130.9 1160 25.9 -1.832 0.1790
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 919.7 1160 25.9 0.791 0.7118
## FB - UB -828.1 1160 25.9 -0.712 0.7586
## SB - UB -1747.8 1160 25.9 -1.503 0.3060
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 22663 822 25.9 20972 24353
## SB 20563 822 25.9 18873 22254
## UB 22694 822 25.9 21004 24385
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 22745 822 25.9 21054 24435
## SB 21825 822 25.9 20134 23515
## UB 23573 822 25.9 21882 25263
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 2099.3 1160 25.9 -791 4989
## FB - UB -31.6 1160 25.9 -2922 2858
## SB - UB -2130.9 1160 25.9 -5021 759
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 919.7 1160 25.9 -1970 3810
## FB - UB -828.1 1160 25.9 -3718 2062
## SB - UB -1747.8 1160 25.9 -4638 1142
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesCa -Calcium
Ca D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Ca + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 71.0 80.9 -30.5 61.0 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.6036 -0.6513 -0.1911 0.4948 2.9917
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.02923 0.1710
## Residual 0.16008 0.4001
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.7675 0.1365 9.0000 64.222 2.72e-13 ***
## BurnSB -0.1526 0.1931 9.0000 -0.791 0.449
## BurnUB -0.2620 0.1931 9.0000 -1.357 0.208
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Ca + 1)
## Chisq Df Pr(>Chisq)
## Burn 1.8581 2 0.3949## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.77 0.167 13.5 8.41 9.13
## SB 8.61 0.167 13.5 8.25 8.97
## UB 8.51 0.167 13.5 8.15 8.87
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.153 0.236 13.5 0.646 0.7979
## FB - UB 0.262 0.236 13.5 1.108 0.5255
## SB - UB 0.109 0.236 13.5 0.462 0.8898
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.77 0.167 13.5 8.41 9.13
## SB 8.61 0.167 13.5 8.25 8.97
## UB 8.51 0.167 13.5 8.15 8.87
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.153 0.236 13.5 -0.469 0.774
## FB - UB 0.262 0.236 13.5 -0.360 0.883
## SB - UB 0.109 0.236 13.5 -0.512 0.731
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesCa D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Ca + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 79.7 89.6 -34.8 69.7 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.3788 -0.6388 -0.2238 0.3857 2.9907
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.05615 0.2370
## Residual 0.17829 0.4222
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.85407 0.16918 9.00000 52.334 1.71e-12 ***
## BurnSB -0.03093 0.23926 9.00000 -0.129 0.900
## BurnUB -0.09075 0.23926 9.00000 -0.379 0.713
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Ca + 1)
## Chisq Df Pr(>Chisq)
## Burn 0.1487 2 0.9283## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.85 0.207 13.5 8.41 9.30
## SB 8.82 0.207 13.5 8.38 9.27
## UB 8.76 0.207 13.5 8.32 9.21
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0309 0.293 13.5 0.106 0.9939
## FB - UB 0.0907 0.293 13.5 0.310 0.9487
## SB - UB 0.0598 0.293 13.5 0.204 0.9773
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.85 0.207 13.5 8.41 9.30
## SB 8.82 0.207 13.5 8.38 9.27
## UB 8.76 0.207 13.5 8.32 9.21
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0309 0.293 13.5 -0.739 0.801
## FB - UB 0.0907 0.293 13.5 -0.679 0.861
## SB - UB 0.0598 0.293 13.5 -0.710 0.830
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Ca + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 105.2 126.6 -44.6 89.2 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3856 -0.5814 -0.1079 0.4361 3.3126
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.04482 0.2117
## Residual 0.11574 0.3402
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.96414 0.14618 12.43441 61.322 <2e-16 ***
## BurnSB -0.18603 0.20673 12.43441 -0.900 0.3853
## BurnUB -0.37368 0.20673 12.43441 -1.808 0.0949 .
## Year2010 -0.14685 0.11340 99.00000 -1.295 0.1984
## BurnSB:Year2010 -0.02791 0.16037 99.00000 -0.174 0.8622
## BurnUB:Year2010 0.17170 0.16037 99.00000 1.071 0.2869
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.388 0.274 0.274
## BrnSB:Y2010 0.274 -0.388 -0.194 -0.707
## BrnUB:Y2010 0.274 -0.194 -0.388 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Ca + 1)
## Chisq Df Pr(>Chisq)
## Burn 2.3972 2 0.3016
## Year 2.2826 1 0.1308
## Burn:Year 1.8173 2 0.4031## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.89 0.165 13.5 8.54 9.25
## SB 8.69 0.165 13.5 8.34 9.05
## UB 8.60 0.165 13.5 8.25 8.96
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.2000 0.233 13.5 0.857 0.6753
## FB - UB 0.2878 0.233 13.5 1.233 0.4547
## SB - UB 0.0878 0.233 13.5 0.376 0.9253
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.89 0.165 13.5 8.54 9.25
## SB 8.69 0.165 13.5 8.34 9.05
## UB 8.60 0.165 13.5 8.25 8.96
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.2000 0.233 13.5 -0.413 0.813
## FB - UB 0.2878 0.233 13.5 -0.326 0.901
## SB - UB 0.0878 0.233 13.5 -0.526 0.701
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.78 0.101 18.6 8.57 8.99
## 2010 8.68 0.101 18.6 8.47 8.89
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0989 0.0665 102 1.488 0.1399
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.78 0.101 18.6 8.57 8.99
## 2010 8.68 0.101 18.6 8.47 8.89
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0989 0.0665 102 -0.033 0.231
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 8.96 0.175 18.6 8.60 9.33
## SB 8.78 0.175 18.6 8.41 9.14
## UB 8.59 0.175 18.6 8.22 8.96
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 8.82 0.175 18.6 8.45 9.18
## SB 8.60 0.175 18.6 8.24 8.97
## UB 8.62 0.175 18.6 8.25 8.98
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.186 0.247 18.6 0.753 0.7358
## FB - UB 0.374 0.247 18.6 1.512 0.3083
## SB - UB 0.188 0.247 18.6 0.759 0.7319
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.214 0.247 18.6 0.866 0.6680
## FB - UB 0.202 0.247 18.6 0.817 0.6973
## SB - UB -0.012 0.247 18.6 -0.048 0.9987
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 8.96 0.175 18.6 8.60 9.33
## SB 8.78 0.175 18.6 8.41 9.14
## UB 8.59 0.175 18.6 8.22 8.96
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 8.82 0.175 18.6 8.45 9.18
## SB 8.60 0.175 18.6 8.24 8.97
## UB 8.62 0.175 18.6 8.25 8.98
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.186 0.247 18.6 -0.443 0.815
## FB - UB 0.374 0.247 18.6 -0.255 1.003
## SB - UB 0.188 0.247 18.6 -0.441 0.817
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.214 0.247 18.6 -0.415 0.843
## FB - UB 0.202 0.247 18.6 -0.427 0.831
## SB - UB -0.012 0.247 18.6 -0.641 0.617
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Ca + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 168.3 189.7 -76.1 152.3 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.2224 -0.5386 -0.1973 0.4467 3.7634
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.07305 0.2703
## Residual 0.20908 0.4573
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.94426 0.18965 12.75699 47.162 1.07e-15 ***
## BurnSB -0.08984 0.26821 12.75699 -0.335 0.743
## BurnUB -0.24480 0.26821 12.75699 -0.913 0.378
## Year2010 -0.15559 0.15242 99.00000 -1.021 0.310
## BurnSB:Year2010 0.03972 0.21555 99.00000 0.184 0.854
## BurnUB:Year2010 0.20802 0.21555 99.00000 0.965 0.337
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.402 0.284 0.284
## BrnSB:Y2010 0.284 -0.402 -0.201 -0.707
## BrnUB:Y2010 0.284 -0.201 -0.402 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Ca + 1)
## Chisq Df Pr(>Chisq)
## Burn 0.3286 2 0.8485
## Year 0.6884 1 0.4067
## Burn:Year 1.0500 2 0.5916## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.87 0.213 13.5 8.41 9.32
## SB 8.80 0.213 13.5 8.34 9.25
## UB 8.73 0.213 13.5 8.27 9.18
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0700 0.301 13.5 0.233 0.9707
## FB - UB 0.1408 0.301 13.5 0.468 0.8872
## SB - UB 0.0708 0.301 13.5 0.235 0.9700
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.87 0.213 13.5 8.41 9.32
## SB 8.80 0.213 13.5 8.34 9.25
## UB 8.73 0.213 13.5 8.27 9.18
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0700 0.301 13.5 -0.721 0.861
## FB - UB 0.1408 0.301 13.5 -0.650 0.931
## SB - UB 0.0708 0.301 13.5 -0.720 0.861
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.83 0.131 19.1 8.56 9.11
## 2010 8.76 0.131 19.1 8.49 9.03
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.073 0.0894 102 0.817 0.4158
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.83 0.131 19.1 8.56 9.11
## 2010 8.76 0.131 19.1 8.49 9.03
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.073 0.0894 102 -0.104 0.25
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 8.94 0.226 19.1 8.47 9.42
## SB 8.85 0.226 19.1 8.38 9.33
## UB 8.70 0.226 19.1 8.23 9.17
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 8.79 0.226 19.1 8.32 9.26
## SB 8.74 0.226 19.1 8.26 9.21
## UB 8.75 0.226 19.1 8.28 9.23
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0898 0.32 19.1 0.281 0.9576
## FB - UB 0.2448 0.32 19.1 0.765 0.7285
## SB - UB 0.1550 0.32 19.1 0.484 0.8796
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0501 0.32 19.1 0.157 0.9866
## FB - UB 0.0368 0.32 19.1 0.115 0.9927
## SB - UB -0.0133 0.32 19.1 -0.042 0.9990
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 8.94 0.226 19.1 8.47 9.42
## SB 8.85 0.226 19.1 8.38 9.33
## UB 8.70 0.226 19.1 8.23 9.17
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 8.79 0.226 19.1 8.32 9.26
## SB 8.74 0.226 19.1 8.26 9.21
## UB 8.75 0.226 19.1 8.28 9.23
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0898 0.32 19.1 -0.723 0.903
## FB - UB 0.2448 0.32 19.1 -0.568 1.058
## SB - UB 0.1550 0.32 19.1 -0.658 0.968
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0501 0.32 19.1 -0.763 0.863
## FB - UB 0.0368 0.32 19.1 -0.776 0.850
## SB - UB -0.0133 0.32 19.1 -0.826 0.799
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesFe - Iron
Fe D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Fe ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 1011.6 1021.5 -500.8 1001.6 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3160 -0.3850 -0.0481 0.3167 3.8861
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 4152401 2038
## Residual 4923698 2219
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 25215 1288 9 19.584 1.09e-08 ***
## BurnSB -2379 1821 9 -1.307 0.224
## BurnUB -2652 1821 9 -1.456 0.179
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Fe
## Chisq Df Pr(>Chisq)
## Burn 2.5671 2 0.277## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 25215 1580 13.5 21821 28609
## SB 22836 1580 13.5 19442 26230
## UB 22563 1580 13.5 19169 25957
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 2379 2230 13.5 1.067 0.5496
## FB - UB 2652 2230 13.5 1.189 0.4792
## SB - UB 273 2230 13.5 0.122 0.9918
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 25215 1580 13.5 21821 28609
## SB 22836 1580 13.5 19442 26230
## UB 22563 1580 13.5 19169 25957
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 2379 2230 13.5 -3482 8240
## FB - UB 2652 2230 13.5 -3209 8513
## SB - UB 273 2230 13.5 -5588 6134
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesFe D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Fe ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 1023.7 1033.7 -506.9 1013.7 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0181 -0.4181 -0.0350 0.3184 4.3053
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 3162826 1778
## Residual 6648650 2578
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 26251 1193 9 22.001 3.91e-09 ***
## BurnSB -3008 1687 9 -1.783 0.1083
## BurnUB -3095 1687 9 -1.834 0.0999 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Fe
## Chisq Df Pr(>Chisq)
## Burn 4.3625 2 0.1129## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 26251 1460 13.5 23106 29396
## SB 23243 1460 13.5 20098 26389
## UB 23157 1460 13.5 20011 26302
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 3007.8 2070 13.5 1.455 0.3420
## FB - UB 3094.7 2070 13.5 1.497 0.3228
## SB - UB 86.9 2070 13.5 0.042 0.9990
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 26251 1460 13.5 23106 29396
## SB 23243 1460 13.5 20098 26389
## UB 23157 1460 13.5 20011 26302
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 3007.8 2070 13.5 -2424 8440
## FB - UB 3094.7 2070 13.5 -2337 8527
## SB - UB 86.9 2070 13.5 -5345 5519
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Fe ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 1931.6 1953.1 -957.8 1915.6 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.55604 -0.58956 0.03681 0.58753 2.08050
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 446034 667.9
## Residual 2698576 1642.7
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 22831.83 546.44 15.88 41.783 < 2e-16 ***
## BurnSB -496.83 772.79 15.88 -0.643 0.52945
## BurnUB -367.33 772.79 15.88 -0.475 0.64102
## Year2010 1612.00 547.58 99.00 2.944 0.00404 **
## BurnSB:Year2010 42.67 774.39 99.00 0.055 0.95617
## BurnUB:Year2010 21.39 774.39 99.00 0.028 0.97802
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.501 0.354 0.354
## BrnSB:Y2010 0.354 -0.501 -0.251 -0.707
## BrnUB:Y2010 0.354 -0.251 -0.501 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Fe
## Chisq Df Pr(>Chisq)
## Burn 0.5476 2 0.7605
## Year 26.6925 1 2.386e-07 ***
## Burn:Year 0.0030 2 0.9985
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 23638 579 13.5 22391 24884
## SB 23162 579 13.5 21916 24409
## UB 23281 579 13.5 22035 24528
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 476 819 13.5 0.581 0.8326
## FB - UB 357 819 13.5 0.435 0.9015
## SB - UB -119 819 13.5 -0.145 0.9885
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 23638 579 13.5 22391 24884
## SB 23162 579 13.5 21916 24409
## UB 23281 579 13.5 22035 24528
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 476 819 13.5 -1677 2628
## FB - UB 357 819 13.5 -1796 2510
## SB - UB -119 819 13.5 -2272 2034
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 22544 371 23.7 21778 23310
## 2010 24177 371 23.7 23411 24943
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -1633 321 102 -5.088 <.0001
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 22544 371 23.7 21778 23310
## 2010 24177 371 23.7 23411 24943
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -1633 321 102 -2270 -997
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 22832 642 23.7 21505 24159
## SB 22335 642 23.7 21008 23662
## UB 22465 642 23.7 21138 23791
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 24444 642 23.7 23117 25771
## SB 23990 642 23.7 22663 25316
## UB 24098 642 23.7 22771 25425
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 497 909 23.7 0.547 0.8491
## FB - UB 367 909 23.7 0.404 0.9142
## SB - UB -130 909 23.7 -0.143 0.9889
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 454 909 23.7 0.500 0.8721
## FB - UB 346 909 23.7 0.381 0.9235
## SB - UB -108 909 23.7 -0.119 0.9922
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 22832 642 23.7 21505 24159
## SB 22335 642 23.7 21008 23662
## UB 22465 642 23.7 21138 23791
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 24444 642 23.7 23117 25771
## SB 23990 642 23.7 22663 25316
## UB 24098 642 23.7 22771 25425
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 497 909 23.7 -1774 2768
## FB - UB 367 909 23.7 -1903 2638
## SB - UB -130 909 23.7 -2400 2141
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 454 909 23.7 -1817 2725
## FB - UB 346 909 23.7 -1925 2617
## SB - UB -108 909 23.7 -2379 2163
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Fe ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 2000.9 2022.4 -992.4 1984.9 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.0094 -0.5671 0.0507 0.5653 3.5991
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 316132 562.3
## Residual 5369556 2317.2
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 24974.39 635.36 21.95 39.307 <2e-16 ***
## BurnSB -1790.61 898.54 21.95 -1.993 0.0589 .
## BurnUB -1443.06 898.54 21.95 -1.606 0.1226
## Year2010 -12.94 772.41 99.00 -0.017 0.9867
## BurnSB:Year2010 1358.67 1092.35 99.00 1.244 0.2165
## BurnUB:Year2010 1747.56 1092.35 99.00 1.600 0.1128
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.608 0.430 0.430
## BrnSB:Y2010 0.430 -0.608 -0.304 -0.707
## BrnUB:Y2010 0.430 -0.304 -0.608 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Fe
## Chisq Df Pr(>Chisq)
## Burn 2.4264 2 0.29725
## Year 5.2568 1 0.02186 *
## Burn:Year 2.8221 2 0.24389
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 24968 618 13.5 23638 26298
## SB 23857 618 13.5 22527 25187
## UB 24399 618 13.5 23069 25729
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 1111 874 13.5 1.272 0.4340
## FB - UB 569 874 13.5 0.651 0.7947
## SB - UB -542 874 13.5 -0.620 0.8117
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 24968 618 13.5 23638 26298
## SB 23857 618 13.5 22527 25187
## UB 24399 618 13.5 23069 25729
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 1111 874 13.5 -1186 3408
## FB - UB 569 874 13.5 -1728 2866
## SB - UB -542 874 13.5 -2839 1755
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 23897 423 32.5 23036 24757
## 2010 24919 423 32.5 24059 25779
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -1022 453 102 -2.258 0.0261
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 23897 423 32.5 23036 24757
## 2010 24919 423 32.5 24059 25779
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -1022 453 102 -1921 -124
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 24974 732 32.5 23485 26464
## SB 23184 732 32.5 21694 24674
## UB 23531 732 32.5 22041 25021
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 24961 732 32.5 23472 26451
## SB 24530 732 32.5 23040 26019
## UB 25266 732 32.5 23776 26756
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 1791 1040 32.5 1.730 0.2095
## FB - UB 1443 1040 32.5 1.394 0.3556
## SB - UB -348 1040 32.5 -0.336 0.9398
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 432 1040 32.5 0.417 0.9087
## FB - UB -304 1040 32.5 -0.294 0.9535
## SB - UB -736 1040 32.5 -0.712 0.7585
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 24974 732 32.5 23485 26464
## SB 23184 732 32.5 21694 24674
## UB 23531 732 32.5 22041 25021
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 24961 732 32.5 23472 26451
## SB 24530 732 32.5 23040 26019
## UB 25266 732 32.5 23776 26756
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 1791 1040 32.5 -751 4332
## FB - UB 1443 1040 32.5 -1099 3985
## SB - UB -348 1040 32.5 -2889 2194
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 432 1040 32.5 -2110 2974
## FB - UB -304 1040 32.5 -2846 2237
## SB - UB -736 1040 32.5 -3278 1805
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesK - Potassium normal dist
K D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: K ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 818.5 828.5 -404.3 808.5 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.9601 -0.7115 -0.0402 0.5165 2.0629
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 96062 309.9
## Residual 142201 377.1
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 5083.4 199.8 9.0 25.442 1.08e-09 ***
## BurnSB -350.2 282.6 9.0 -1.239 0.247
## BurnUB -232.3 282.6 9.0 -0.822 0.432
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: K
## Chisq Df Pr(>Chisq)
## Burn 1.5904 2 0.4515## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 5083 245 13.5 4557 5610
## SB 4733 245 13.5 4207 5260
## UB 4851 245 13.5 4324 5378
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 350 346 13.5 1.012 0.5822
## FB - UB 232 346 13.5 0.671 0.7838
## SB - UB -118 346 13.5 -0.341 0.9383
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 5083 245 13.5 4557 5610
## SB 4733 245 13.5 4207 5260
## UB 4851 245 13.5 4324 5378
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 350 346 13.5 -559 1260
## FB - UB 232 346 13.5 -677 1142
## SB - UB -118 346 13.5 -1027 792
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesK D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: K ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 831.5 841.5 -410.8 821.5 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.5603 -0.7670 -0.1202 0.7276 2.3269
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 51856 227.7
## Residual 202893 450.4
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 5114.4 169.0 9.0 30.265 2.3e-10 ***
## BurnSB -535.6 239.0 9.0 -2.241 0.0518 .
## BurnUB -194.7 239.0 9.0 -0.815 0.4362
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: K
## Chisq Df Pr(>Chisq)
## Burn 5.1464 2 0.07629 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 5114 207 13.5 4669 5560
## SB 4579 207 13.5 4133 5024
## UB 4920 207 13.5 4474 5365
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 536 293 13.5 1.830 0.1973
## FB - UB 195 293 13.5 0.665 0.7871
## SB - UB -341 293 13.5 -1.164 0.4931
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 5114 207 13.5 4669 5560
## SB 4579 207 13.5 4133 5024
## UB 4920 207 13.5 4474 5365
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 536 293 13.5 -234 1305
## FB - UB 195 293 13.5 -575 964
## SB - UB -341 293 13.5 -1110 428
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: K ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 1657.3 1678.7 -820.6 1641.3 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.22725 -0.69630 -0.05128 0.55123 2.45300
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 27715 166.5
## Residual 215633 464.4
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 5267.22 145.66 17.23 36.160 < 2e-16 ***
## BurnSB -79.22 206.00 17.23 -0.385 0.70526
## BurnUB 394.39 206.00 17.23 1.915 0.07231 .
## Year2010 679.67 154.79 99.00 4.391 2.83e-05 ***
## BurnSB:Year2010 -366.17 218.90 99.00 -1.673 0.09754 .
## BurnUB:Year2010 -735.56 218.90 99.00 -3.360 0.00111 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.531 0.376 0.376
## BrnSB:Y2010 0.376 -0.531 -0.266 -0.707
## BrnUB:Y2010 0.376 -0.266 -0.531 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: K
## Chisq Df Pr(>Chisq)
## Burn 3.3487 2 0.1874290
## Year 12.2220 1 0.0004723 ***
## Burn:Year 11.2910 2 0.0035334 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 5607 151 13.5 5282 5932
## SB 5345 151 13.5 5019 5670
## UB 5634 151 13.5 5308 5959
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 262.3 214 13.5 1.227 0.4581
## FB - UB -26.6 214 13.5 -0.125 0.9915
## SB - UB -288.9 214 13.5 -1.352 0.3923
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 5607 151 13.5 5282 5932
## SB 5345 151 13.5 5019 5670
## UB 5634 151 13.5 5308 5959
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 262.3 214 13.5 -299 824
## FB - UB -26.6 214 13.5 -588 535
## SB - UB -288.9 214 13.5 -851 273
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 5372 98.4 25.7 5170 5575
## 2010 5685 98.4 25.7 5482 5887
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -312 90.8 102 -3.443 0.0008
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 5372 98.4 25.7 5170 5575
## 2010 5685 98.4 25.7 5482 5887
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -312 90.8 102 -492 -132
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 5267 170 25.7 4917 5618
## SB 5188 170 25.7 4838 5538
## UB 5662 170 25.7 5311 6012
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 5947 170 25.7 5597 6297
## SB 5502 170 25.7 5151 5852
## UB 5606 170 25.7 5255 5956
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 79.2 241 25.7 0.329 0.9423
## FB - UB -394.4 241 25.7 -1.637 0.2487
## SB - UB -473.6 241 25.7 -1.966 0.1411
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 445.4 241 25.7 1.849 0.1742
## FB - UB 341.2 241 25.7 1.416 0.3477
## SB - UB -104.2 241 25.7 -0.433 0.9024
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 5267 170 25.7 4917 5618
## SB 5188 170 25.7 4838 5538
## UB 5662 170 25.7 5311 6012
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 5947 170 25.7 5597 6297
## SB 5502 170 25.7 5151 5852
## UB 5606 170 25.7 5255 5956
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 79.2 241 25.7 -520 678
## FB - UB -394.4 241 25.7 -993 205
## SB - UB -473.6 241 25.7 -1073 125
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 445.4 241 25.7 -154 1044
## FB - UB 341.2 241 25.7 -258 940
## SB - UB -104.2 241 25.7 -703 495
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: K ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 1740.3 1761.8 -862.2 1724.3 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.9079 -0.5678 0.0263 0.4556 5.8627
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0 0.0
## Residual 502902 709.2
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 5587.44 167.15 108.00 33.428 < 2e-16 ***
## BurnSB -755.44 236.39 108.00 -3.196 0.00183 **
## BurnUB 61.83 236.39 108.00 0.262 0.79414
## Year2010 280.00 236.39 108.00 1.185 0.23881
## BurnSB:Year2010 332.89 334.30 108.00 0.996 0.32158
## BurnUB:Year2010 -287.06 334.30 108.00 -0.859 0.39242
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.707 0.500 0.500
## BrnSB:Y2010 0.500 -0.707 -0.354 -0.707
## BrnUB:Y2010 0.500 -0.354 -0.707 -0.707 0.500
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: K
## Chisq Df Pr(>Chisq)
## Burn 14.5783 2 0.0006829 ***
## Year 4.6810 1 0.0304974 *
## Burn:Year 3.4453 2 0.1785936
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 5727 130 8.91 5432 6023
## SB 5138 130 8.91 4843 5434
## UB 5646 130 8.91 5350 5941
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 589.0 185 8.91 3.192 0.0271
## FB - UB 81.7 185 8.91 0.443 0.8988
## SB - UB -507.3 185 8.91 -2.749 0.0539
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 5727 130 8.91 5432 6023
## SB 5138 130 8.91 4843 5434
## UB 5646 130 8.91 5350 5941
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 589.0 185 8.91 72.9 1105.14
## FB - UB 81.7 185 8.91 -434.4 597.83
## SB - UB -507.3 185 8.91 -1023.4 8.83
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 5356 103 32.9 5147 5565
## 2010 5652 103 32.9 5442 5861
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -295 140 106 -2.113 0.0370
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 5356 103 32.9 5147 5565
## 2010 5652 103 32.9 5442 5861
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -295 140 106 -572 -18.2
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 5587 178 32.9 5225 5950
## SB 4832 178 32.9 4470 5194
## UB 5649 178 32.9 5287 6011
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 5867 178 32.9 5505 6230
## SB 5445 178 32.9 5083 5807
## UB 5642 178 32.9 5280 6004
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 755.4 252 32.9 3.001 0.0138
## FB - UB -61.8 252 32.9 -0.246 0.9673
## SB - UB -817.3 252 32.9 -3.247 0.0074
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 422.6 252 32.9 1.679 0.2284
## FB - UB 225.2 252 32.9 0.895 0.6474
## SB - UB -197.3 252 32.9 -0.784 0.7153
##
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 5587 178 32.9 5225 5950
## SB 4832 178 32.9 4470 5194
## UB 5649 178 32.9 5287 6011
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 5867 178 32.9 5505 6230
## SB 5445 178 32.9 5083 5807
## UB 5642 178 32.9 5280 6004
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 755.4 252 32.9 138 1373
## FB - UB -61.8 252 32.9 -680 556
## SB - UB -817.3 252 32.9 -1435 -200
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 422.6 252 32.9 -195 1040
## FB - UB 225.2 252 32.9 -393 843
## SB - UB -197.3 252 32.9 -815 420
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesMg - Magnesium
Mg D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mg + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -58.6 -48.7 34.3 -68.6 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.89469 -0.58823 0.06566 0.54387 2.16430
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.01037 0.1018
## Residual 0.01215 0.1102
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.63197 0.06427 8.99999 134.312 3.57e-16 ***
## BurnSB -0.21950 0.09089 8.99999 -2.415 0.0389 *
## BurnUB -0.13914 0.09089 8.99999 -1.531 0.1602
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mg + 1)
## Chisq Df Pr(>Chisq)
## Burn 5.9719 2 0.05049 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.63 0.0787 13.5 8.46 8.80
## SB 8.41 0.0787 13.5 8.24 8.58
## UB 8.49 0.0787 13.5 8.32 8.66
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.2195 0.111 13.5 1.972 0.1571
## FB - UB 0.1391 0.111 13.5 1.250 0.4457
## SB - UB -0.0804 0.111 13.5 -0.722 0.7550
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.63 0.0787 13.5 8.46 8.80
## SB 8.41 0.0787 13.5 8.24 8.58
## UB 8.49 0.0787 13.5 8.32 8.66
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.2195 0.111 13.5 -0.0731 0.512
## FB - UB 0.1391 0.111 13.5 -0.1534 0.432
## SB - UB -0.0804 0.111 13.5 -0.3729 0.212
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesMg D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mg + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -87.2 -77.3 48.6 -97.2 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.85093 -0.79628 0.00975 0.66461 1.97618
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.009065 0.09521
## Residual 0.006690 0.08179
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.68369 0.05825 9.00000 149.070 <2e-16 ***
## BurnSB -0.21770 0.08238 9.00000 -2.643 0.0268 *
## BurnUB -0.10569 0.08238 9.00000 -1.283 0.2316
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mg + 1)
## Chisq Df Pr(>Chisq)
## Burn 6.9853 2 0.03042 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.68 0.0713 13.5 8.53 8.84
## SB 8.47 0.0713 13.5 8.31 8.62
## UB 8.58 0.0713 13.5 8.42 8.73
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.218 0.101 13.5 2.158 0.1152
## FB - UB 0.106 0.101 13.5 1.047 0.5610
## SB - UB -0.112 0.101 13.5 -1.110 0.5242
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.68 0.0713 13.5 8.53 8.84
## SB 8.47 0.0713 13.5 8.31 8.62
## UB 8.58 0.0713 13.5 8.42 8.73
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.218 0.101 13.5 -0.0475 0.483
## FB - UB 0.106 0.101 13.5 -0.1595 0.371
## SB - UB -0.112 0.101 13.5 -0.3772 0.153
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mg + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -104.6 -83.1 60.3 -120.6 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.2126 -0.6965 -0.2467 0.6491 2.6108
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.001437 0.03791
## Residual 0.018128 0.13464
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.78485 0.03855 20.10715 227.870 < 2e-16 ***
## BurnSB -0.10211 0.05452 20.10715 -1.873 0.075704 .
## BurnUB -0.14147 0.05452 20.10715 -2.595 0.017272 *
## Year2010 -0.16901 0.04488 99.00000 -3.766 0.000282 ***
## BurnSB:Year2010 0.02784 0.06347 99.00000 0.439 0.661891
## BurnUB:Year2010 0.08962 0.06347 99.00000 1.412 0.161071
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.582 0.412 0.412
## BrnSB:Y2010 0.412 -0.582 -0.291 -0.707
## BrnUB:Y2010 0.412 -0.291 -0.582 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mg + 1)
## Chisq Df Pr(>Chisq)
## Burn 5.8318 2 0.05415 .
## Year 25.1132 1 5.406e-07 ***
## Burn:Year 2.0892 2 0.35183
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.70 0.0384 13.5 8.62 8.78
## SB 8.61 0.0384 13.5 8.53 8.69
## UB 8.60 0.0384 13.5 8.52 8.69
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.08819 0.0543 13.5 1.624 0.2695
## FB - UB 0.09666 0.0543 13.5 1.780 0.2131
## SB - UB 0.00847 0.0543 13.5 0.156 0.9867
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.70 0.0384 13.5 8.62 8.78
## SB 8.61 0.0384 13.5 8.53 8.69
## UB 8.60 0.0384 13.5 8.52 8.69
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.08819 0.0543 13.5 -0.0545 0.231
## FB - UB 0.09666 0.0543 13.5 -0.0460 0.239
## SB - UB 0.00847 0.0543 13.5 -0.1342 0.151
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.70 0.0258 29.8 8.65 8.76
## 2010 8.57 0.0258 29.8 8.52 8.63
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.13 0.0263 102 4.935 <.0001
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.70 0.0258 29.8 8.65 8.76
## 2010 8.57 0.0258 29.8 8.52 8.63
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.13 0.0263 102 0.0777 0.182
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 8.78 0.0446 29.8 8.69 8.88
## SB 8.68 0.0446 29.8 8.59 8.77
## UB 8.64 0.0446 29.8 8.55 8.73
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 8.62 0.0446 29.8 8.52 8.71
## SB 8.54 0.0446 29.8 8.45 8.63
## UB 8.56 0.0446 29.8 8.47 8.66
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1021 0.0631 29.8 1.617 0.2542
## FB - UB 0.1415 0.0631 29.8 2.241 0.0806
## SB - UB 0.0394 0.0631 29.8 0.623 0.8085
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0743 0.0631 29.8 1.176 0.4762
## FB - UB 0.0519 0.0631 29.8 0.821 0.6930
## SB - UB -0.0224 0.0631 29.8 -0.355 0.9330
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 8.78 0.0446 29.8 8.69 8.88
## SB 8.68 0.0446 29.8 8.59 8.77
## UB 8.64 0.0446 29.8 8.55 8.73
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 8.62 0.0446 29.8 8.52 8.71
## SB 8.54 0.0446 29.8 8.45 8.63
## UB 8.56 0.0446 29.8 8.47 8.66
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1021 0.0631 29.8 -0.0536 0.258
## FB - UB 0.1415 0.0631 29.8 -0.0142 0.297
## SB - UB 0.0394 0.0631 29.8 -0.1163 0.195
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0743 0.0631 29.8 -0.0814 0.230
## FB - UB 0.0519 0.0631 29.8 -0.1038 0.208
## SB - UB -0.0224 0.0631 29.8 -0.1781 0.133
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mg + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -58.5 -37.0 37.2 -74.5 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.7652 -0.5248 0.0160 0.5080 4.6661
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.001351 0.03675
## Residual 0.028297 0.16822
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.92484 0.04497 23.22837 198.458 < 2e-16 ***
## BurnSB -0.20057 0.06360 23.22837 -3.154 0.00441 **
## BurnUB -0.22966 0.06360 23.22837 -3.611 0.00145 **
## Year2010 -0.30106 0.05607 99.00000 -5.369 5.23e-07 ***
## BurnSB:Year2010 0.13970 0.07930 99.00000 1.762 0.08121 .
## BurnUB:Year2010 0.22644 0.07930 99.00000 2.855 0.00524 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.623 0.441 0.441
## BrnSB:Y2010 0.441 -0.623 -0.312 -0.707
## BrnUB:Y2010 0.441 -0.312 -0.623 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mg + 1)
## Chisq Df Pr(>Chisq)
## Burn 8.3179 2 0.01562 *
## Year 30.5782 1 3.207e-08 ***
## Burn:Year 8.3025 2 0.01574 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.77 0.0431 13.5 8.68 8.87
## SB 8.64 0.0431 13.5 8.55 8.74
## UB 8.66 0.0431 13.5 8.57 8.75
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1307 0.0609 13.5 2.146 0.1174
## FB - UB 0.1164 0.0609 13.5 1.912 0.1732
## SB - UB -0.0143 0.0609 13.5 -0.235 0.9702
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 8.77 0.0431 13.5 8.68 8.87
## SB 8.64 0.0431 13.5 8.55 8.74
## UB 8.66 0.0431 13.5 8.57 8.75
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1307 0.0609 13.5 -0.0293 0.291
## FB - UB 0.1164 0.0609 13.5 -0.0436 0.277
## SB - UB -0.0143 0.0609 13.5 -0.1744 0.146
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.78 0.0298 34.3 8.72 8.84
## 2010 8.60 0.0298 34.3 8.54 8.66
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.179 0.0329 102 5.445 <.0001
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.78 0.0298 34.3 8.72 8.84
## 2010 8.60 0.0298 34.3 8.54 8.66
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.179 0.0329 102 0.114 0.244
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 8.92 0.0516 34.3 8.82 9.03
## SB 8.72 0.0516 34.3 8.62 8.83
## UB 8.70 0.0516 34.3 8.59 8.80
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 8.62 0.0516 34.3 8.52 8.73
## SB 8.56 0.0516 34.3 8.46 8.67
## UB 8.62 0.0516 34.3 8.52 8.73
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.20057 0.073 34.3 2.747 0.0251
## FB - UB 0.22966 0.073 34.3 3.146 0.0093
## SB - UB 0.02908 0.073 34.3 0.398 0.9165
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.06087 0.073 34.3 0.834 0.6849
## FB - UB 0.00322 0.073 34.3 0.044 0.9989
## SB - UB -0.05765 0.073 34.3 -0.790 0.7118
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 8.92 0.0516 34.3 8.82 9.03
## SB 8.72 0.0516 34.3 8.62 8.83
## UB 8.70 0.0516 34.3 8.59 8.80
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 8.62 0.0516 34.3 8.52 8.73
## SB 8.56 0.0516 34.3 8.46 8.67
## UB 8.62 0.0516 34.3 8.52 8.73
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.20057 0.073 34.3 0.0217 0.379
## FB - UB 0.22966 0.073 34.3 0.0508 0.408
## SB - UB 0.02908 0.073 34.3 -0.1497 0.208
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.06087 0.073 34.3 -0.1180 0.240
## FB - UB 0.00322 0.073 34.3 -0.1756 0.182
## SB - UB -0.05765 0.073 34.3 -0.2365 0.121
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesMn - manganese
Mn D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mn + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -69.7 -59.7 39.8 -79.7 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.38829 -0.58356 0.00676 0.35014 2.50469
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.006939 0.0833
## Residual 0.010216 0.1011
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.33073 0.05367 9.00000 117.952 1.15e-15 ***
## BurnSB -0.12172 0.07590 9.00000 -1.604 0.143
## BurnUB -0.04005 0.07590 9.00000 -0.528 0.610
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mn + 1)
## Chisq Df Pr(>Chisq)
## Burn 2.6718 2 0.2629## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.33 0.0657 13.5 6.19 6.47
## SB 6.21 0.0657 13.5 6.07 6.35
## UB 6.29 0.0657 13.5 6.15 6.43
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1217 0.093 13.5 1.309 0.4141
## FB - UB 0.0401 0.093 13.5 0.431 0.9035
## SB - UB -0.0817 0.093 13.5 -0.879 0.6624
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.33 0.0657 13.5 6.19 6.47
## SB 6.21 0.0657 13.5 6.07 6.35
## UB 6.29 0.0657 13.5 6.15 6.43
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1217 0.093 13.5 -0.123 0.366
## FB - UB 0.0401 0.093 13.5 -0.204 0.284
## SB - UB -0.0817 0.093 13.5 -0.326 0.163
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesMn D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mn + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -57.8 -47.8 33.9 -67.8 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.9421 -0.6740 -0.1155 0.5464 2.3939
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.003794 0.06159
## Residual 0.014240 0.11933
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.34706 0.04534 9.00000 139.989 2.46e-16 ***
## BurnSB -0.16433 0.06412 9.00000 -2.563 0.0305 *
## BurnUB -0.05859 0.06412 9.00000 -0.914 0.3847
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mn + 1)
## Chisq Df Pr(>Chisq)
## Burn 6.7484 2 0.03425 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.35 0.0555 13.5 6.23 6.47
## SB 6.18 0.0555 13.5 6.06 6.30
## UB 6.29 0.0555 13.5 6.17 6.41
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1643 0.0785 13.5 2.093 0.1287
## FB - UB 0.0586 0.0785 13.5 0.746 0.7410
## SB - UB -0.1057 0.0785 13.5 -1.346 0.3950
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.35 0.0555 13.5 6.23 6.47
## SB 6.18 0.0555 13.5 6.06 6.30
## UB 6.29 0.0555 13.5 6.17 6.41
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1643 0.0785 13.5 -0.0421 0.371
## FB - UB 0.0586 0.0785 13.5 -0.1478 0.265
## SB - UB -0.1057 0.0785 13.5 -0.3121 0.101
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mn + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -139.3 -117.9 77.7 -155.3 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3036 -0.6105 -0.1349 0.7512 2.1119
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.001693 0.04115
## Residual 0.012842 0.11332
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.324643 0.035746 17.088371 176.933 <2e-16 ***
## BurnSB -0.004993 0.050552 17.088371 -0.099 0.922
## BurnUB 0.001446 0.050552 17.088371 0.029 0.978
## Year2010 0.061973 0.037774 99.000000 1.641 0.104
## BurnSB:Year2010 -0.042781 0.053421 99.000000 -0.801 0.425
## BurnUB:Year2010 0.017547 0.053421 99.000000 0.328 0.743
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.528 0.374 0.374
## BrnSB:Y2010 0.374 -0.528 -0.264 -0.707
## BrnUB:Y2010 0.374 -0.264 -0.528 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mn + 1)
## Chisq Df Pr(>Chisq)
## Burn 0.7746 2 0.67888
## Year 6.0317 1 0.01405 *
## Burn:Year 1.3497 2 0.50924
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.36 0.0372 13.5 6.28 6.44
## SB 6.33 0.0372 13.5 6.25 6.41
## UB 6.37 0.0372 13.5 6.29 6.45
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0264 0.0526 13.5 0.502 0.8716
## FB - UB -0.0102 0.0526 13.5 -0.194 0.9794
## SB - UB -0.0366 0.0526 13.5 -0.696 0.7696
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.36 0.0372 13.5 6.28 6.44
## SB 6.33 0.0372 13.5 6.25 6.41
## UB 6.37 0.0372 13.5 6.29 6.45
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0264 0.0526 13.5 -0.112 0.165
## FB - UB -0.0102 0.0526 13.5 -0.148 0.128
## SB - UB -0.0366 0.0526 13.5 -0.175 0.102
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.32 0.0241 25.5 6.27 6.37
## 2010 6.38 0.0241 25.5 6.33 6.43
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.0536 0.0221 102 -2.418 0.0174
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.32 0.0241 25.5 6.27 6.37
## 2010 6.38 0.0241 25.5 6.33 6.43
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.0536 0.0221 102 -0.0975 -0.00963
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 6.32 0.0418 25.5 6.24 6.41
## SB 6.32 0.0418 25.5 6.23 6.41
## UB 6.33 0.0418 25.5 6.24 6.41
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 6.39 0.0418 25.5 6.30 6.47
## SB 6.34 0.0418 25.5 6.25 6.42
## UB 6.41 0.0418 25.5 6.32 6.49
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.00499 0.0592 25.5 0.084 0.9961
## FB - UB -0.00145 0.0592 25.5 -0.024 0.9997
## SB - UB -0.00644 0.0592 25.5 -0.109 0.9935
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.04777 0.0592 25.5 0.808 0.7018
## FB - UB -0.01899 0.0592 25.5 -0.321 0.9449
## SB - UB -0.06677 0.0592 25.5 -1.129 0.5056
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 6.32 0.0418 25.5 6.24 6.41
## SB 6.32 0.0418 25.5 6.23 6.41
## UB 6.33 0.0418 25.5 6.24 6.41
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 6.39 0.0418 25.5 6.30 6.47
## SB 6.34 0.0418 25.5 6.25 6.42
## UB 6.41 0.0418 25.5 6.32 6.49
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.00499 0.0592 25.5 -0.1422 0.1522
## FB - UB -0.00145 0.0592 25.5 -0.1486 0.1457
## SB - UB -0.00644 0.0592 25.5 -0.1536 0.1407
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.04777 0.0592 25.5 -0.0994 0.1949
## FB - UB -0.01899 0.0592 25.5 -0.1662 0.1282
## SB - UB -0.06677 0.0592 25.5 -0.2139 0.0804
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mn + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -85.8 -64.4 50.9 -101.8 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.0606 -0.5372 -0.0329 0.5596 2.4846
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.001648 0.04059
## Residual 0.021602 0.14697
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.39204 0.04182 20.34765 152.831 <2e-16 ***
## BurnSB -0.11672 0.05915 20.34765 -1.973 0.0622 .
## BurnUB -0.05425 0.05915 20.34765 -0.917 0.3698
## Year2010 -0.04682 0.04899 99.00000 -0.956 0.3416
## BurnSB:Year2010 0.08627 0.06928 99.00000 1.245 0.2160
## BurnUB:Year2010 0.11492 0.06928 99.00000 1.659 0.1004
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.586 0.414 0.414
## BrnSB:Y2010 0.414 -0.586 -0.293 -0.707
## BrnUB:Y2010 0.414 -0.293 -0.586 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mn + 1)
## Chisq Df Pr(>Chisq)
## Burn 3.2840 2 0.1936
## Year 0.5124 1 0.4741
## Burn:Year 2.9817 2 0.2252## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.37 0.0415 13.5 6.28 6.46
## SB 6.30 0.0415 13.5 6.21 6.38
## UB 6.37 0.0415 13.5 6.28 6.46
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.07358 0.0587 13.5 1.253 0.4439
## FB - UB -0.00321 0.0587 13.5 -0.055 0.9984
## SB - UB -0.07679 0.0587 13.5 -1.308 0.4149
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.37 0.0415 13.5 6.28 6.46
## SB 6.30 0.0415 13.5 6.21 6.38
## UB 6.37 0.0415 13.5 6.28 6.46
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.07358 0.0587 13.5 -0.0807 0.2279
## FB - UB -0.00321 0.0587 13.5 -0.1575 0.1511
## SB - UB -0.07679 0.0587 13.5 -0.2311 0.0775
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.34 0.0279 30.2 6.28 6.39
## 2010 6.36 0.0279 30.2 6.30 6.41
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.0202 0.0287 102 -0.705 0.4825
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.34 0.0279 30.2 6.28 6.39
## 2010 6.36 0.0279 30.2 6.30 6.41
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.0202 0.0287 102 -0.0772 0.0367
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 6.39 0.0484 30.2 6.29 6.49
## SB 6.28 0.0484 30.2 6.18 6.37
## UB 6.34 0.0484 30.2 6.24 6.44
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 6.35 0.0484 30.2 6.25 6.44
## SB 6.31 0.0484 30.2 6.22 6.41
## UB 6.41 0.0484 30.2 6.31 6.50
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1167 0.0684 30.2 1.705 0.2197
## FB - UB 0.0543 0.0684 30.2 0.793 0.7104
## SB - UB -0.0625 0.0684 30.2 -0.913 0.6366
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0304 0.0684 30.2 0.445 0.8970
## FB - UB -0.0607 0.0684 30.2 -0.886 0.6529
## SB - UB -0.0911 0.0684 30.2 -1.331 0.3894
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 6.39 0.0484 30.2 6.29 6.49
## SB 6.28 0.0484 30.2 6.18 6.37
## UB 6.34 0.0484 30.2 6.24 6.44
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 6.35 0.0484 30.2 6.25 6.44
## SB 6.31 0.0484 30.2 6.22 6.41
## UB 6.41 0.0484 30.2 6.31 6.50
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1167 0.0684 30.2 -0.052 0.2854
## FB - UB 0.0543 0.0684 30.2 -0.114 0.2229
## SB - UB -0.0625 0.0684 30.2 -0.231 0.1062
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0304 0.0684 30.2 -0.138 0.1991
## FB - UB -0.0607 0.0684 30.2 -0.229 0.1080
## SB - UB -0.0911 0.0684 30.2 -0.260 0.0776
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesTP - Total phosphorus
TP D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(TP + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -91.8 -81.8 50.9 -101.8 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.05537 -0.64634 -0.00856 0.53968 2.39429
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.003067 0.05538
## Residual 0.007199 0.08485
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.70596 0.03771 9.00000 177.807 <2e-16 ***
## BurnSB -0.14707 0.05334 9.00000 -2.757 0.0222 *
## BurnUB -0.05467 0.05334 9.00000 -1.025 0.3321
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(TP + 1)
## Chisq Df Pr(>Chisq)
## Burn 7.7695 2 0.02055 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.71 0.0462 13.5 6.61 6.81
## SB 6.56 0.0462 13.5 6.46 6.66
## UB 6.65 0.0462 13.5 6.55 6.75
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1471 0.0653 13.5 2.251 0.0981
## FB - UB 0.0547 0.0653 13.5 0.837 0.6873
## SB - UB -0.0924 0.0653 13.5 -1.414 0.3614
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.71 0.0462 13.5 6.61 6.81
## SB 6.56 0.0462 13.5 6.46 6.66
## UB 6.65 0.0462 13.5 6.55 6.75
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1471 0.0653 13.5 -0.0246 0.3188
## FB - UB 0.0547 0.0653 13.5 -0.1170 0.2264
## SB - UB -0.0924 0.0653 13.5 -0.2641 0.0793
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesTP D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(TP + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -77.2 -67.3 43.6 -87.2 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.6591 -0.5965 0.1123 0.5868 2.3232
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.002374 0.04872
## Residual 0.010052 0.10026
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.64354 0.03674 9.00000 180.837 < 2e-16 ***
## BurnSB -0.19400 0.05195 9.00000 -3.734 0.00467 **
## BurnUB -0.09991 0.05195 9.00000 -1.923 0.08665 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(TP + 1)
## Chisq Df Pr(>Chisq)
## Burn 13.946 2 0.0009367 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.64 0.045 13.5 6.55 6.74
## SB 6.45 0.045 13.5 6.35 6.55
## UB 6.54 0.045 13.5 6.45 6.64
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1940 0.0636 13.5 3.049 0.0229
## FB - UB 0.0999 0.0636 13.5 1.570 0.2915
## SB - UB -0.0941 0.0636 13.5 -1.479 0.3313
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.64 0.045 13.5 6.55 6.74
## SB 6.45 0.045 13.5 6.35 6.55
## UB 6.54 0.045 13.5 6.45 6.64
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1940 0.0636 13.5 0.0267 0.3612
## FB - UB 0.0999 0.0636 13.5 -0.0673 0.2672
## SB - UB -0.0941 0.0636 13.5 -0.2613 0.0732
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(TP + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -170.8 -149.3 93.4 -186.8 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.5848 -0.6408 0.1015 0.6912 2.4176
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.00000 0.0000
## Residual 0.01038 0.1019
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.798896 0.024018 108.000000 283.073 < 2e-16 ***
## BurnSB -0.106347 0.033967 108.000000 -3.131 0.00224 **
## BurnUB -0.111037 0.033967 108.000000 -3.269 0.00145 **
## Year2010 -0.086123 0.033967 108.000000 -2.536 0.01266 *
## BurnSB:Year2010 0.009973 0.048036 108.000000 0.208 0.83593
## BurnUB:Year2010 0.096005 0.048036 108.000000 1.999 0.04816 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.707 0.500 0.500
## BrnSB:Y2010 0.500 -0.707 -0.354 -0.707
## BrnUB:Y2010 0.500 -0.354 -0.707 -0.707 0.500
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(TP + 1)
## Chisq Df Pr(>Chisq)
## Burn 18.1626 2 0.0001138 ***
## Year 6.7095 1 0.0095902 **
## Burn:Year 4.8301 2 0.0893634 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.76 0.0196 10.6 6.71 6.80
## SB 6.65 0.0196 10.6 6.61 6.70
## UB 6.69 0.0196 10.6 6.65 6.74
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1014 0.0277 10.6 3.663 0.0102
## FB - UB 0.0630 0.0277 10.6 2.278 0.1031
## SB - UB -0.0383 0.0277 10.6 -1.385 0.3826
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.76 0.0196 10.6 6.71 6.80
## SB 6.65 0.0196 10.6 6.61 6.70
## UB 6.69 0.0196 10.6 6.65 6.74
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1014 0.0277 10.6 0.0262 0.1765
## FB - UB 0.0630 0.0277 10.6 -0.0122 0.1382
## SB - UB -0.0383 0.0277 10.6 -0.1135 0.0369
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.726 0.0151 38.38 6.696 6.757
## 2010 6.676 0.0151 38.38 6.645 6.706
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0508 0.02 104 2.537 0.0126
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.726 0.0151 38.38 6.696 6.757
## 2010 6.676 0.0151 38.38 6.645 6.706
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0508 0.02 104 0.0111 0.0905
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 6.80 0.0261 38.4 6.75 6.85
## SB 6.69 0.0261 38.4 6.64 6.75
## UB 6.69 0.0261 38.4 6.63 6.74
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 6.71 0.0261 38.4 6.66 6.77
## SB 6.62 0.0261 38.4 6.56 6.67
## UB 6.70 0.0261 38.4 6.64 6.75
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.10635 0.037 38.4 2.877 0.0175
## FB - UB 0.11104 0.037 38.4 3.004 0.0127
## SB - UB 0.00469 0.037 38.4 0.127 0.9912
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.09637 0.037 38.4 2.607 0.0338
## FB - UB 0.01503 0.037 38.4 0.407 0.9131
## SB - UB -0.08134 0.037 38.4 -2.200 0.0839
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 6.80 0.0261 38.4 6.75 6.85
## SB 6.69 0.0261 38.4 6.64 6.75
## UB 6.69 0.0261 38.4 6.63 6.74
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 6.71 0.0261 38.4 6.66 6.77
## SB 6.62 0.0261 38.4 6.56 6.67
## UB 6.70 0.0261 38.4 6.64 6.75
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.10635 0.037 38.4 0.01622 0.19647
## FB - UB 0.11104 0.037 38.4 0.02091 0.20116
## SB - UB 0.00469 0.037 38.4 -0.08544 0.09481
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.09637 0.037 38.4 0.00625 0.18650
## FB - UB 0.01503 0.037 38.4 -0.07509 0.10516
## SB - UB -0.08134 0.037 38.4 -0.17147 0.00878
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(TP + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -64.3 -42.8 40.1 -80.3 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.0412 -0.4588 -0.0453 0.4270 5.9272
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.00000 0.0000
## Residual 0.02785 0.1669
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.69430 0.03933 108.00000 170.196 < 2e-16 ***
## BurnSB -0.21151 0.05562 108.00000 -3.803 0.000238 ***
## BurnUB -0.11680 0.05562 108.00000 -2.100 0.038081 *
## Year2010 -0.16772 0.05562 108.00000 -3.015 0.003202 **
## BurnSB:Year2010 0.13719 0.07867 108.00000 1.744 0.084015 .
## BurnUB:Year2010 0.16117 0.07867 108.00000 2.049 0.042912 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.707 0.500 0.500
## BrnSB:Y2010 0.500 -0.707 -0.354 -0.707
## BrnUB:Y2010 0.500 -0.354 -0.707 -0.707 0.500
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(TP + 1)
## Chisq Df Pr(>Chisq)
## Burn 14.2738 2 0.0007952 ***
## Year 4.5182 1 0.0335355 *
## Burn:Year 4.8877 2 0.0868256 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.61 0.033 11.9 6.54 6.68
## SB 6.47 0.033 11.9 6.40 6.54
## UB 6.57 0.033 11.9 6.50 6.65
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1429 0.0467 11.9 3.061 0.0250
## FB - UB 0.0362 0.0467 11.9 0.776 0.7244
## SB - UB -0.1067 0.0467 11.9 -2.286 0.0970
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 6.61 0.033 11.9 6.54 6.68
## SB 6.47 0.033 11.9 6.40 6.54
## UB 6.57 0.033 11.9 6.50 6.65
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1429 0.0467 11.9 0.0182 0.268
## FB - UB 0.0362 0.0467 11.9 -0.0885 0.161
## SB - UB -0.1067 0.0467 11.9 -0.2314 0.018
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.58 0.0251 42.7 6.53 6.64
## 2010 6.52 0.0251 42.7 6.47 6.57
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0683 0.0327 103 2.087 0.0393
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.58 0.0251 42.7 6.53 6.64
## 2010 6.52 0.0251 42.7 6.47 6.57
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0683 0.0327 103 0.00341 0.133
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 6.69 0.0435 42.7 6.61 6.78
## SB 6.48 0.0435 42.7 6.40 6.57
## UB 6.58 0.0435 42.7 6.49 6.67
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 6.53 0.0435 42.7 6.44 6.61
## SB 6.45 0.0435 42.7 6.36 6.54
## UB 6.57 0.0435 42.7 6.48 6.66
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.2115 0.0615 42.7 3.439 0.0037
## FB - UB 0.1168 0.0615 42.7 1.899 0.1514
## SB - UB -0.0947 0.0615 42.7 -1.540 0.2828
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0743 0.0615 42.7 1.208 0.4548
## FB - UB -0.0444 0.0615 42.7 -0.721 0.7523
## SB - UB -0.1187 0.0615 42.7 -1.930 0.1428
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 6.69 0.0435 42.7 6.61 6.78
## SB 6.48 0.0435 42.7 6.40 6.57
## UB 6.58 0.0435 42.7 6.49 6.67
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 6.53 0.0435 42.7 6.44 6.61
## SB 6.45 0.0435 42.7 6.36 6.54
## UB 6.57 0.0435 42.7 6.48 6.66
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.2115 0.0615 42.7 0.0622 0.3609
## FB - UB 0.1168 0.0615 42.7 -0.0326 0.2662
## SB - UB -0.0947 0.0615 42.7 -0.2441 0.0546
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0743 0.0615 42.7 -0.0750 0.2237
## FB - UB -0.0444 0.0615 42.7 -0.1937 0.1050
## SB - UB -0.1187 0.0615 42.7 -0.2680 0.0307
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesZn - Zinc
Zn D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Zn + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -118.9 -108.9 64.4 -128.9 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.29719 -0.48667 0.01912 0.73087 1.66045
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.001626 0.04032
## Residual 0.004436 0.06660
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.287118 0.028079 9.000000 152.681 < 2e-16 ***
## BurnSB -0.130368 0.039710 9.000000 -3.283 0.00948 **
## BurnUB -0.004573 0.039710 9.000000 -0.115 0.91085
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Zn + 1)
## Chisq Df Pr(>Chisq)
## Burn 13.885 2 0.000966 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 4.29 0.0344 13.5 4.21 4.36
## SB 4.16 0.0344 13.5 4.08 4.23
## UB 4.28 0.0344 13.5 4.21 4.36
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.13037 0.0486 13.5 2.681 0.0454
## FB - UB 0.00457 0.0486 13.5 0.094 0.9951
## SB - UB -0.12580 0.0486 13.5 -2.587 0.0540
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 4.29 0.0344 13.5 4.21 4.36
## SB 4.16 0.0344 13.5 4.08 4.23
## UB 4.28 0.0344 13.5 4.21 4.36
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.13037 0.0486 13.5 0.00254 0.25820
## FB - UB 0.00457 0.0486 13.5 -0.12326 0.13240
## SB - UB -0.12580 0.0486 13.5 -0.25362 0.00203
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesZn D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Zn + 1) ~ Burn + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -115.0 -105.1 62.5 -125.0 49
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.02644 -0.62039 -0.00171 0.60566 2.01807
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.002242 0.04735
## Residual 0.004604 0.06785
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.25525 0.03167 9.00000 134.354 3.56e-16 ***
## BurnSB -0.16561 0.04479 9.00000 -3.697 0.00494 **
## BurnUB -0.02955 0.04479 9.00000 -0.660 0.52596
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB
## BurnSB -0.707
## BurnUB -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Zn + 1)
## Chisq Df Pr(>Chisq)
## Burn 15.557 2 0.0004187 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 4.26 0.0388 13.5 4.17 4.34
## SB 4.09 0.0388 13.5 4.01 4.17
## UB 4.23 0.0388 13.5 4.14 4.31
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1656 0.0549 13.5 3.019 0.0242
## FB - UB 0.0295 0.0549 13.5 0.539 0.8539
## SB - UB -0.1361 0.0549 13.5 -2.480 0.0654
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 4.26 0.0388 13.5 4.17 4.34
## SB 4.09 0.0388 13.5 4.01 4.17
## UB 4.23 0.0388 13.5 4.14 4.31
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1656 0.0549 13.5 0.0214 0.30980
## FB - UB 0.0295 0.0549 13.5 -0.1146 0.17373
## SB - UB -0.1361 0.0549 13.5 -0.2803 0.00812
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOverall Treatment D0
## boundary (singular) fit: see help('isSingular')## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Zn + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -187.9 -166.5 102.0 -203.9 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.09471 -0.59736 -0.03194 0.57783 3.00981
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.000000 0.00000
## Residual 0.008859 0.09412
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.32030 0.02219 108.00000 194.738 < 2e-16 ***
## BurnSB -0.03925 0.03137 108.00000 -1.251 0.21364
## BurnUB -0.03710 0.03137 108.00000 -1.183 0.23955
## Year2010 -0.09779 0.03137 108.00000 -3.117 0.00234 **
## BurnSB:Year2010 -0.03296 0.04437 108.00000 -0.743 0.45919
## BurnUB:Year2010 0.07631 0.04437 108.00000 1.720 0.08833 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.707 0.500 0.500
## BrnSB:Y2010 0.500 -0.707 -0.354 -0.707
## BrnUB:Y2010 0.500 -0.354 -0.707 -0.707 0.500
## optimizer (nloptwrap) convergence code: 0 (OK)
## boundary (singular) fit: see help('isSingular')## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Zn + 1)
## Chisq Df Pr(>Chisq)
## Burn 8.5749 2 0.01374 *
## Year 21.1673 1 4.209e-06 ***
## Burn:Year 6.3827 2 0.04112 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 4.27 0.0176 9.51 4.23 4.31
## SB 4.22 0.0176 9.51 4.18 4.26
## UB 4.27 0.0176 9.51 4.23 4.31
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.05573 0.0249 9.51 2.239 0.1148
## FB - UB -0.00105 0.0249 9.51 -0.042 0.9990
## SB - UB -0.05678 0.0249 9.51 -2.281 0.1075
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 4.27 0.0176 9.51 4.23 4.31
## SB 4.22 0.0176 9.51 4.18 4.26
## UB 4.27 0.0176 9.51 4.23 4.31
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.05573 0.0249 9.51 -0.0131 0.1246
## FB - UB -0.00105 0.0249 9.51 -0.0699 0.0678
## SB - UB -0.05678 0.0249 9.51 -0.1256 0.0120
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.29 0.0138 34.9 4.27 4.32
## 2010 4.21 0.0138 34.9 4.18 4.24
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0833 0.0185 105 4.498 <.0001
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.29 0.0138 34.9 4.27 4.32
## 2010 4.21 0.0138 34.9 4.18 4.24
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0833 0.0185 105 0.0466 0.12
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 4.32 0.0238 34.9 4.27 4.37
## SB 4.28 0.0238 34.9 4.23 4.33
## UB 4.28 0.0238 34.9 4.23 4.33
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 4.22 0.0238 34.9 4.17 4.27
## SB 4.15 0.0238 34.9 4.10 4.20
## UB 4.26 0.0238 34.9 4.21 4.31
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.03925 0.0337 34.9 1.165 0.4815
## FB - UB 0.03710 0.0337 34.9 1.101 0.5196
## SB - UB -0.00214 0.0337 34.9 -0.064 0.9978
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.07221 0.0337 34.9 2.144 0.0957
## FB - UB -0.03920 0.0337 34.9 -1.164 0.4823
## SB - UB -0.11141 0.0337 34.9 -3.307 0.0061
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 4.32 0.0238 34.9 4.27 4.37
## SB 4.28 0.0238 34.9 4.23 4.33
## UB 4.28 0.0238 34.9 4.23 4.33
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 4.22 0.0238 34.9 4.17 4.27
## SB 4.15 0.0238 34.9 4.10 4.20
## UB 4.26 0.0238 34.9 4.21 4.31
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.03925 0.0337 34.9 -0.0432 0.1217
## FB - UB 0.03710 0.0337 34.9 -0.0453 0.1196
## SB - UB -0.00214 0.0337 34.9 -0.0846 0.0803
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.07221 0.0337 34.9 -0.0102 0.1547
## FB - UB -0.03920 0.0337 34.9 -0.1217 0.0432
## SB - UB -0.11141 0.0337 34.9 -0.1939 -0.0290
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesOVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Zn + 1) ~ Burn + Year + Burn * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -125.8 -104.4 70.9 -141.8 100
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.1992 -0.4647 -0.0321 0.4204 3.5784
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0004611 0.02147
## Residual 0.0153462 0.12388
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.26707 0.03172 25.82361 134.516 < 2e-16 ***
## BurnSB -0.10883 0.04486 25.82361 -2.426 0.022563 *
## BurnUB -0.04853 0.04486 25.82361 -1.082 0.289384
## Year2010 -0.14738 0.04129 99.00000 -3.569 0.000554 ***
## BurnSB:Year2010 0.05904 0.05840 99.00000 1.011 0.314444
## BurnUB:Year2010 0.13240 0.05840 99.00000 2.267 0.025548 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) BurnSB BurnUB Yr2010 BSB:Y2
## BurnSB -0.707
## BurnUB -0.707 0.500
## Year2010 -0.651 0.460 0.460
## BrnSB:Y2010 0.460 -0.651 -0.325 -0.707
## BrnUB:Y2010 0.460 -0.325 -0.651 -0.707 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Zn + 1)
## Chisq Df Pr(>Chisq)
## Burn 9.2004 2 0.0100499 *
## Year 12.2858 1 0.0004564 ***
## Burn:Year 5.1606 2 0.0757527 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 4.19 0.0295 13.5 4.13 4.26
## SB 4.11 0.0295 13.5 4.05 4.18
## UB 4.21 0.0295 13.5 4.15 4.27
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0793 0.0417 13.5 1.901 0.1762
## FB - UB -0.0177 0.0417 13.5 -0.424 0.9064
## SB - UB -0.0970 0.0417 13.5 -2.325 0.0862
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Burn emmean SE df lower.CL upper.CL
## FB 4.19 0.0295 13.5 4.13 4.26
## SB 4.11 0.0295 13.5 4.05 4.18
## UB 4.21 0.0295 13.5 4.15 4.27
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0793 0.0417 13.5 -0.0303 0.1889
## FB - UB -0.0177 0.0417 13.5 -0.1273 0.0920
## SB - UB -0.0970 0.0417 13.5 -0.2066 0.0127
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.21 0.0209 37.9 4.17 4.26
## 2010 4.13 0.0209 37.9 4.09 4.17
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0836 0.0242 102 3.452 0.0008
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.21 0.0209 37.9 4.17 4.26
## 2010 4.13 0.0209 37.9 4.09 4.17
##
## Results are averaged over the levels of: Burn
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0836 0.0242 102 0.0355 0.132
##
## Results are averaged over the levels of: Burn
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 4.27 0.0362 37.9 4.19 4.34
## SB 4.16 0.0362 37.9 4.08 4.23
## UB 4.22 0.0362 37.9 4.15 4.29
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 4.12 0.0362 37.9 4.05 4.19
## SB 4.07 0.0362 37.9 4.00 4.14
## UB 4.20 0.0362 37.9 4.13 4.28
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.1088 0.0512 37.9 2.127 0.0979
## FB - UB 0.0485 0.0512 37.9 0.948 0.6136
## SB - UB -0.0603 0.0512 37.9 -1.178 0.4732
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## FB - SB 0.0498 0.0512 37.9 0.973 0.5983
## FB - UB -0.0839 0.0512 37.9 -1.639 0.2421
## SB - UB -0.1337 0.0512 37.9 -2.612 0.0336
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## $emmeans
## Year = 2009:
## Burn emmean SE df lower.CL upper.CL
## FB 4.27 0.0362 37.9 4.19 4.34
## SB 4.16 0.0362 37.9 4.08 4.23
## UB 4.22 0.0362 37.9 4.15 4.29
##
## Year = 2010:
## Burn emmean SE df lower.CL upper.CL
## FB 4.12 0.0362 37.9 4.05 4.19
## SB 4.07 0.0362 37.9 4.00 4.14
## UB 4.20 0.0362 37.9 4.13 4.28
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.1088 0.0512 37.9 -0.0160 0.23365
## FB - UB 0.0485 0.0512 37.9 -0.0763 0.17335
## SB - UB -0.0603 0.0512 37.9 -0.1851 0.06452
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## FB - SB 0.0498 0.0512 37.9 -0.0750 0.17461
## FB - UB -0.0839 0.0512 37.9 -0.2087 0.04095
## SB - UB -0.1337 0.0512 37.9 -0.2585 -0.00884
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates#Spacing and Depth ## NH4 Ammonium
## Warning: Removed 2 rows containing non-finite outside the scale range
## (`stat_boxplot()`).
Pretreatment - 2008 Depth 0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NH4 + 1) ~ sampleID + (1 | Site)
## Data: N_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 32.6 40.6 -12.3 24.6 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.6760 -0.7224 0.1038 0.6145 2.3050
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.11334 0.3367
## Residual 0.06093 0.2468
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.89039 0.12186 10.52663 15.513 1.37e-08 ***
## sampleIDS -0.07262 0.06718 45.00000 -1.081 0.285
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.276## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NH4 + 1)
## Chisq Df Pr(>Chisq)
## sampleID 1.1685 1 0.2797## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.89 0.129 11.8 1.61 2.17
## S 1.82 0.129 11.8 1.54 2.10
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.0726 0.0679 46 1.069 0.2907
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.89 0.129 11.8 1.61 2.17
## S 1.82 0.129 11.8 1.54 2.10
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0726 0.0679 46 -0.0641 0.209
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Pretreatment - 2008 Depth 5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NH4 + 1) ~ sampleID + (1 | Site)
## Data: N_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 14.6 22.6 -3.3 6.6 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8858 -0.5318 0.1476 0.6473 2.1184
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.12147 0.3485
## Residual 0.04051 0.2013
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.48768 0.12246 9.96735 12.148 2.69e-07 ***
## sampleIDS 0.04013 0.05478 45.00000 0.733 0.468
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.224## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NH4 + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.5366 1 0.4638## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.49 0.13 11.2 1.20 1.77
## S 1.53 0.13 11.2 1.24 1.81
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0401 0.0554 46 -0.724 0.4725
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.49 0.13 11.2 1.20 1.77
## S 1.53 0.13 11.2 1.24 1.81
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0401 0.0554 46 -0.152 0.0714
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NH4 + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(N_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 276.0 309.7 -128.0 256.0 205
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3232 -0.6643 -0.0074 0.6625 2.7843
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.01222 0.1106
## Residual 0.18508 0.4302
## Number of obs: 215, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 3.69745 0.09062 93.61682 40.800 < 2e-16 ***
## sampleIDS 0.66817 0.11709 206.02112 5.707 3.97e-08 ***
## Year2010 -2.24092 0.11709 206.02112 -19.139 < 2e-16 ***
## Year2011 -2.08755 0.11709 206.02112 -17.829 < 2e-16 ***
## Year2012 -1.53524 0.11823 206.14198 -12.985 < 2e-16 ***
## sampleIDS:Year2010 -0.23468 0.16559 206.02112 -1.417 0.1579
## sampleIDS:Year2011 -0.78661 0.16559 206.02112 -4.750 3.80e-06 ***
## sampleIDS:Year2012 -0.40868 0.16640 206.08223 -2.456 0.0149 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010 Yr2011 Yr2012 sIDS:Y2010 sIDS:Y2011
## sampleIDS -0.646
## Year2010 -0.646 0.500
## Year2011 -0.646 0.500 0.500
## Year2012 -0.640 0.495 0.495 0.495
## smIDS:Y2010 0.457 -0.707 -0.707 -0.354 -0.350
## smIDS:Y2011 0.457 -0.707 -0.354 -0.707 -0.350 0.500
## smIDS:Y2012 0.455 -0.704 -0.352 -0.352 -0.711 0.498 0.498## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NH4 + 1)
## Chisq Df Pr(>Chisq)
## sampleID 28.071 1 1.169e-07 ***
## Year 1144.404 3 < 2.2e-16 ***
## sampleID:Year 24.042 3 2.448e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.23 0.0583 19.5 2.11 2.35
## S 2.54 0.0581 19.3 2.42 2.66
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.311 0.0597 213 -5.203 <.0001
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.23 0.0583 19.5 2.11 2.35
## S 2.54 0.0581 19.3 2.42 2.66
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.311 0.0597 213 -0.428 -0.193
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.03 0.0718 44.3 3.89 4.18
## 2010 1.67 0.0718 44.3 1.53 1.82
## 2011 1.55 0.0718 44.3 1.41 1.70
## 2012 2.29 0.0723 45.3 2.15 2.44
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 2.358 0.0842 213 27.996 <.0001
## Year2009 - Year2011 2.481 0.0842 213 29.451 <.0001
## Year2009 - Year2012 1.740 0.0847 213 20.549 <.0001
## Year2010 - Year2011 0.123 0.0842 213 1.455 0.4664
## Year2010 - Year2012 -0.619 0.0847 213 -7.308 <.0001
## Year2011 - Year2012 -0.741 0.0847 213 -8.757 <.0001
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.03 0.0718 44.3 3.89 4.18
## 2010 1.67 0.0718 44.3 1.53 1.82
## 2011 1.55 0.0718 44.3 1.41 1.70
## 2012 2.29 0.0723 45.3 2.15 2.44
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 2.358 0.0842 213 2.1401 2.576
## Year2009 - Year2011 2.481 0.0842 213 2.2627 2.699
## Year2009 - Year2012 1.740 0.0847 213 1.5204 1.959
## Year2010 - Year2011 0.123 0.0842 213 -0.0955 0.341
## Year2010 - Year2012 -0.619 0.0847 213 -0.8379 -0.399
## Year2011 - Year2012 -0.741 0.0847 213 -0.9605 -0.522
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 3.70 0.0933 103 3.51 3.88
## S 4.37 0.0933 103 4.18 4.55
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 1.46 0.0933 103 1.27 1.64
## S 1.89 0.0933 103 1.71 2.08
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 1.61 0.0933 103 1.42 1.79
## S 1.49 0.0933 103 1.31 1.68
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 2.16 0.0948 107 1.97 2.35
## S 2.42 0.0933 103 2.24 2.61
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.668 0.119 213 -5.609 <.0001
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.433 0.119 213 -3.639 0.0003
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## I - S 0.118 0.119 213 0.994 0.3212
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## I - S -0.259 0.120 213 -2.157 0.0321
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 3.70 0.0933 103 3.51 3.88
## S 4.37 0.0933 103 4.18 4.55
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 1.46 0.0933 103 1.27 1.64
## S 1.89 0.0933 103 1.71 2.08
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 1.61 0.0933 103 1.42 1.79
## S 1.49 0.0933 103 1.31 1.68
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 2.16 0.0948 107 1.97 2.35
## S 2.42 0.0933 103 2.24 2.61
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.668 0.119 213 -0.903 -0.4334
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.433 0.119 213 -0.668 -0.1987
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.118 0.119 213 -0.116 0.3533
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.259 0.120 213 -0.497 -0.0224
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NH4 + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(N_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 218.3 252.0 -99.1 198.3 205
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.3631 -0.6826 0.0647 0.6916 3.2566
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.01526 0.1236
## Residual 0.13954 0.3735
## Number of obs: 215, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 3.20313 0.08285 65.95415 38.662 <2e-16 ***
## sampleIDS 0.25193 0.10167 205.92700 2.478 0.0140 *
## Year2010 -1.46481 0.10167 205.92700 -14.408 <2e-16 ***
## Year2011 -1.83632 0.10267 206.01482 -17.886 <2e-16 ***
## Year2012 -1.18189 0.10167 205.92700 -11.625 <2e-16 ***
## sampleIDS:Year2010 -0.29672 0.14378 205.92700 -2.064 0.0403 *
## sampleIDS:Year2011 -0.08048 0.14449 205.97139 -0.557 0.5781
## sampleIDS:Year2012 -0.20119 0.14378 205.92700 -1.399 0.1632
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010 Yr2011 Yr2012 sIDS:Y2010 sIDS:Y2011
## sampleIDS -0.614
## Year2010 -0.614 0.500
## Year2011 -0.608 0.495 0.495
## Year2012 -0.614 0.500 0.500 0.495
## smIDS:Y2010 0.434 -0.707 -0.707 -0.350 -0.354
## smIDS:Y2011 0.432 -0.704 -0.352 -0.711 -0.352 0.498
## smIDS:Y2012 0.434 -0.707 -0.354 -0.350 -0.707 0.500 0.498## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NH4 + 1)
## Chisq Df Pr(>Chisq)
## sampleID 4.4107 1 0.03571 *
## Year 799.2246 3 < 2e-16 ***
## sampleID:Year 4.9615 3 0.17464
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.08 0.0576 16.5 1.96 2.20
## S 2.19 0.0575 16.4 2.07 2.31
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.107 0.0518 213 -2.070 0.0396
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.08 0.0576 16.5 1.96 2.20
## S 2.19 0.0575 16.4 2.07 2.31
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.107 0.0518 213 -0.21 -0.00513
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 3.33 0.0681 32.7 3.19 3.47
## 2010 1.72 0.0681 32.7 1.58 1.85
## 2011 1.45 0.0685 33.4 1.31 1.59
## 2012 2.05 0.0681 32.7 1.91 2.19
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 1.613 0.0731 213 22.055 <.0001
## Year2009 - Year2011 1.877 0.0735 213 25.530 <.0001
## Year2009 - Year2012 1.282 0.0731 213 17.534 <.0001
## Year2010 - Year2011 0.263 0.0735 213 3.583 0.0024
## Year2010 - Year2012 -0.331 0.0731 213 -4.521 0.0001
## Year2011 - Year2012 -0.594 0.0735 213 -8.082 <.0001
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 3.33 0.0681 32.7 3.19 3.47
## 2010 1.72 0.0681 32.7 1.58 1.85
## 2011 1.45 0.0685 33.4 1.31 1.59
## 2012 2.05 0.0681 32.7 1.91 2.19
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 1.613 0.0731 213 1.4238 1.803
## Year2009 - Year2011 1.877 0.0735 213 1.6862 2.067
## Year2009 - Year2012 1.282 0.0731 213 1.0931 1.472
## Year2010 - Year2011 0.263 0.0735 213 0.0731 0.454
## Year2010 - Year2012 -0.331 0.0731 213 -0.5201 -0.141
## Year2011 - Year2012 -0.594 0.0735 213 -0.7844 -0.404
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 3.20 0.0855 73.8 3.03 3.37
## S 3.46 0.0855 73.8 3.28 3.63
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 1.74 0.0855 73.8 1.57 1.91
## S 1.69 0.0855 73.8 1.52 1.86
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 1.37 0.0868 77.1 1.19 1.54
## S 1.54 0.0855 73.8 1.37 1.71
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 2.02 0.0855 73.8 1.85 2.19
## S 2.07 0.0855 73.8 1.90 2.24
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.2519 0.103 213 -2.436 0.0157
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S 0.0448 0.103 213 0.433 0.6655
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## I - S -0.1714 0.104 213 -1.641 0.1022
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## I - S -0.0507 0.103 213 -0.490 0.6243
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 3.20 0.0855 73.8 3.03 3.37
## S 3.46 0.0855 73.8 3.28 3.63
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 1.74 0.0855 73.8 1.57 1.91
## S 1.69 0.0855 73.8 1.52 1.86
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 1.37 0.0868 77.1 1.19 1.54
## S 1.54 0.0855 73.8 1.37 1.71
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 2.02 0.0855 73.8 1.85 2.19
## S 2.07 0.0855 73.8 1.90 2.24
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.2519 0.103 213 -0.456 -0.0480
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0448 0.103 213 -0.159 0.2487
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.1714 0.104 213 -0.377 0.0345
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0507 0.103 213 -0.255 0.1532
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95N03 Nitrate
Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NO3 + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(N_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 246.4 280.1 -113.2 226.4 205
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.8711 -0.4561 0.1094 0.4614 2.6516
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.02305 0.1518
## Residual 0.15755 0.3969
## Number of obs: 215, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.316411 0.091634 53.007748 14.366 < 2e-16 ***
## sampleIDS 0.206908 0.108030 206.018573 1.915 0.0568 .
## Year2010 0.858559 0.108030 206.018573 7.947 1.23e-13 ***
## Year2011 -0.521272 0.108030 206.018573 -4.825 2.72e-06 ***
## Year2012 -0.228656 0.109096 206.088770 -2.096 0.0373 *
## sampleIDS:Year2010 0.130802 0.152778 206.018573 0.856 0.3929
## sampleIDS:Year2011 -0.005959 0.152778 206.018573 -0.039 0.9689
## sampleIDS:Year2012 -0.184288 0.153533 206.054046 -1.200 0.2314
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010 Yr2011 Yr2012 sIDS:Y2010 sIDS:Y2011
## sampleIDS -0.589
## Year2010 -0.589 0.500
## Year2011 -0.589 0.500 0.500
## Year2012 -0.584 0.495 0.495 0.495
## smIDS:Y2010 0.417 -0.707 -0.707 -0.354 -0.350
## smIDS:Y2011 0.417 -0.707 -0.354 -0.707 -0.350 0.500
## smIDS:Y2012 0.415 -0.704 -0.352 -0.352 -0.711 0.498 0.498## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NO3 + 1)
## Chisq Df Pr(>Chisq)
## sampleID 12.6881 1 0.000368 ***
## Year 421.1551 3 < 2.2e-16 ***
## sampleID:Year 4.2554 3 0.235175
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.34 0.0669 15.2 1.20 1.49
## S 1.54 0.0668 15.0 1.39 1.68
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.192 0.0551 213 -3.486 0.0006
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.34 0.0669 15.2 1.20 1.49
## S 1.54 0.0668 15.0 1.39 1.68
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.192 0.0551 213 -0.301 -0.0834
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 1.420 0.0772 27.4 1.261 1.58
## 2010 2.344 0.0772 27.4 2.185 2.50
## 2011 0.896 0.0772 27.4 0.737 1.05
## 2012 1.099 0.0776 28.0 0.940 1.26
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.924 0.0777 213 -11.888 <.0001
## Year2009 - Year2011 0.524 0.0777 213 6.745 <.0001
## Year2009 - Year2012 0.321 0.0781 213 4.107 0.0003
## Year2010 - Year2011 1.448 0.0777 213 18.633 <.0001
## Year2010 - Year2012 1.245 0.0781 213 15.937 <.0001
## Year2011 - Year2012 -0.203 0.0781 213 -2.605 0.0480
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 1.420 0.0772 27.4 1.261 1.58
## 2010 2.344 0.0772 27.4 2.185 2.50
## 2011 0.896 0.0772 27.4 0.737 1.05
## 2012 1.099 0.0776 28.0 0.940 1.26
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.924 0.0777 213 -1.125 -0.7227
## Year2009 - Year2011 0.524 0.0777 213 0.323 0.7255
## Year2009 - Year2012 0.321 0.0781 213 0.119 0.5231
## Year2010 - Year2011 1.448 0.0777 213 1.247 1.6495
## Year2010 - Year2012 1.245 0.0781 213 1.043 1.4470
## Year2011 - Year2012 -0.203 0.0781 213 -0.406 -0.0012
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 1.316 0.0948 59.0 1.127 1.506
## S 1.523 0.0948 59.0 1.334 1.713
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 2.175 0.0948 59.0 1.985 2.365
## S 2.513 0.0948 59.0 2.323 2.702
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 0.795 0.0948 59.0 0.605 0.985
## S 0.996 0.0948 59.0 0.806 1.186
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 1.088 0.0961 61.7 0.896 1.280
## S 1.110 0.0948 59.0 0.921 1.300
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.2069 0.110 213 -1.882 0.0611
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.3377 0.110 213 -3.072 0.0024
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## I - S -0.2009 0.110 213 -1.828 0.0689
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## I - S -0.0226 0.111 213 -0.204 0.8387
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 1.316 0.0948 59.0 1.127 1.506
## S 1.523 0.0948 59.0 1.334 1.713
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 2.175 0.0948 59.0 1.985 2.365
## S 2.513 0.0948 59.0 2.323 2.702
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 0.795 0.0948 59.0 0.605 0.985
## S 0.996 0.0948 59.0 0.806 1.186
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 1.088 0.0961 61.7 0.896 1.280
## S 1.110 0.0948 59.0 0.921 1.300
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.2069 0.110 213 -0.424 0.00975
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.3377 0.110 213 -0.554 -0.12105
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.2009 0.110 213 -0.418 0.01571
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0226 0.111 213 -0.241 0.19619
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NO3 + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(N_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 198.8 232.5 -89.4 178.8 205
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.4786 -0.5488 0.0429 0.5980 2.9408
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.03591 0.1895
## Residual 0.12330 0.3511
## Number of obs: 215, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.89063 0.09250 30.63051 9.628 8.88e-11 ***
## sampleIDS 0.01736 0.09557 206.00482 0.182 0.856
## Year2010 0.74355 0.09557 206.00482 7.780 3.43e-13 ***
## Year2011 -0.13697 0.09651 206.04483 -1.419 0.157
## Year2012 0.12975 0.09557 206.00482 1.358 0.176
## sampleIDS:Year2010 -0.06952 0.13515 206.00482 -0.514 0.608
## sampleIDS:Year2011 0.21260 0.13582 206.02503 1.565 0.119
## sampleIDS:Year2012 0.02486 0.13515 206.00482 0.184 0.854
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010 Yr2011 Yr2012 sIDS:Y2010 sIDS:Y2011
## sampleIDS -0.517
## Year2010 -0.517 0.500
## Year2011 -0.512 0.495 0.495
## Year2012 -0.517 0.500 0.500 0.495
## smIDS:Y2010 0.365 -0.707 -0.707 -0.350 -0.354
## smIDS:Y2011 0.363 -0.704 -0.352 -0.711 -0.352 0.498
## smIDS:Y2012 0.365 -0.707 -0.354 -0.350 -0.707 0.500 0.498## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NO3 + 1)
## Chisq Df Pr(>Chisq)
## sampleID 1.4917 1 0.2219
## Year 154.8100 3 <2e-16 ***
## sampleID:Year 4.7114 3 0.1942
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.07 0.0757 12.8 0.911 1.24
## S 1.13 0.0756 12.8 0.970 1.30
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0593 0.0487 213 -1.218 0.2247
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.07 0.0757 12.8 0.911 1.24
## S 1.13 0.0756 12.8 0.970 1.30
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0593 0.0487 213 -0.155 0.0367
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.899 0.0831 19.0 0.725 1.07
## 2010 1.608 0.0831 19.0 1.434 1.78
## 2011 0.869 0.0834 19.3 0.694 1.04
## 2012 1.041 0.0831 19.0 0.868 1.22
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.7088 0.0688 213 -10.309 <.0001
## Year2009 - Year2011 0.0307 0.0691 213 0.444 0.9707
## Year2009 - Year2012 -0.1422 0.0688 213 -2.068 0.1670
## Year2010 - Year2011 0.7395 0.0691 213 10.702 <.0001
## Year2010 - Year2012 0.5666 0.0688 213 8.241 <.0001
## Year2011 - Year2012 -0.1728 0.0691 213 -2.502 0.0625
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.899 0.0831 19.0 0.725 1.07
## 2010 1.608 0.0831 19.0 1.434 1.78
## 2011 0.869 0.0834 19.3 0.694 1.04
## 2012 1.041 0.0831 19.0 0.868 1.22
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.7088 0.0688 213 -0.887 -0.53076
## Year2009 - Year2011 0.0307 0.0691 213 -0.148 0.20959
## Year2009 - Year2012 -0.1422 0.0688 213 -0.320 0.03586
## Year2010 - Year2011 0.7395 0.0691 213 0.561 0.91838
## Year2010 - Year2012 0.5666 0.0688 213 0.389 0.74465
## Year2011 - Year2012 -0.1728 0.0691 213 -0.352 0.00607
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 0.891 0.0963 34.3 0.695 1.086
## S 0.908 0.0963 34.3 0.712 1.104
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 1.634 0.0963 34.3 1.439 1.830
## S 1.582 0.0963 34.3 1.386 1.778
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 0.754 0.0972 35.7 0.556 0.951
## S 0.984 0.0963 34.3 0.788 1.179
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 1.020 0.0963 34.3 0.825 1.216
## S 1.063 0.0963 34.3 0.867 1.258
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.0174 0.0972 213 -0.179 0.8585
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S 0.0522 0.0972 213 0.537 0.5922
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## I - S -0.2300 0.0982 213 -2.342 0.0201
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## I - S -0.0422 0.0972 213 -0.434 0.6646
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 0.891 0.0963 34.3 0.695 1.086
## S 0.908 0.0963 34.3 0.712 1.104
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 1.634 0.0963 34.3 1.439 1.830
## S 1.582 0.0963 34.3 1.386 1.778
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 0.754 0.0972 35.7 0.556 0.951
## S 0.984 0.0963 34.3 0.788 1.179
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 1.020 0.0963 34.3 0.825 1.216
## S 1.063 0.0963 34.3 0.867 1.258
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0174 0.0972 213 -0.209 0.1743
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0522 0.0972 213 -0.139 0.2438
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.2300 0.0982 213 -0.424 -0.0364
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0422 0.0972 213 -0.234 0.1494
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NO3 + 1) ~ sampleID + (1 | Site)
## Data: N_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -5.4 2.6 6.7 -13.4 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.64258 -0.70748 -0.04394 0.61386 2.79805
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.009408 0.09699
## Residual 0.039424 0.19855
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.01255 0.05005 17.33766 20.229 1.68e-13 ***
## sampleIDS -0.27858 0.05404 45.00000 -5.155 5.48e-06 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.540## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NO3 + 1)
## Chisq Df Pr(>Chisq)
## sampleID 26.575 1 2.536e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.013 0.0524 19.4 0.903 1.122
## S 0.734 0.0524 19.4 0.625 0.843
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.279 0.0547 46 5.097 <.0001
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 1.013 0.0524 19.4 0.903 1.122
## S 0.734 0.0524 19.4 0.625 0.843
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.279 0.0547 46 0.169 0.389
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Pretreatment - 2008 Depth 5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(N_NO3 + 1) ~ sampleID + (1 | Site)
## Data: N_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -72.5 -64.5 40.2 -80.5 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.6652 -0.6168 -0.1175 0.5174 3.0771
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.015825 0.12580
## Residual 0.008734 0.09346
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.56354 0.04563 10.56515 12.35 1.3e-07 ***
## sampleIDS -0.03128 0.02544 45.00000 -1.23 0.225
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.279## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(N_NO3 + 1)
## Chisq Df Pr(>Chisq)
## sampleID 1.5125 1 0.2188## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.564 0.0482 11.9 0.458 0.669
## S 0.532 0.0482 11.9 0.427 0.637
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.0313 0.0257 46 1.216 0.2301
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.564 0.0482 11.9 0.458 0.669
## S 0.532 0.0482 11.9 0.427 0.637
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0313 0.0257 46 -0.0205 0.0831
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95TN Total Nitrogen
2008 pretreatment TN D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TN ~ sampleID + (1 | Site)
## Data: WNC_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -197.8 -189.9 102.9 -205.8 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.47837 -0.76511 -0.01516 0.47874 2.84785
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0003162 0.01778
## Residual 0.0010948 0.03309
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.210741 0.008699 16.354174 24.225 3.03e-14 ***
## sampleIDS 0.031111 0.009005 45.000000 3.455 0.00121 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.518## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TN
## Chisq Df Pr(>Chisq)
## sampleID 11.935 1 0.0005509 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.211 0.00911 18.4 0.192 0.230
## S 0.242 0.00911 18.4 0.223 0.261
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0311 0.00911 46 -3.416 0.0013
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.211 0.00911 18.4 0.192 0.230
## S 0.242 0.00911 18.4 0.223 0.261
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0311 0.00911 46 -0.0494 -0.0128
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95TN D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TN ~ sampleID + (1 | Site)
## Data: WNC_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -229.8 -221.8 118.9 -237.8 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.65155 -0.77559 -0.04164 0.62503 3.03126
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 5.649e-05 0.007516
## Residual 6.689e-04 0.025863
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.172963 0.005572 22.894107 31.040 <2e-16 ***
## sampleIDS 0.018889 0.007039 45.000000 2.683 0.0102 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.632## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TN
## Chisq Df Pr(>Chisq)
## sampleID 7.201 1 0.007286 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.173 0.0058 25.6 0.161 0.185
## S 0.192 0.0058 25.6 0.180 0.204
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0189 0.00712 46 -2.653 0.0109
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.173 0.0058 25.6 0.161 0.185
## S 0.192 0.0058 25.6 0.180 0.204
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0189 0.00712 46 -0.0332 -0.00456
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TN ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(WNC_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -689.6 -655.9 354.8 -709.6 206
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.6000 -0.6458 -0.0918 0.6394 4.8367
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0007596 0.02756
## Residual 0.0019896 0.04461
## Number of obs: 216, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 0.25556 0.01257 25.15004 20.325 < 2e-16 ***
## sampleIDS 0.08074 0.01214 207.00000 6.651 2.55e-10 ***
## Year2010 -0.03111 0.01214 207.00000 -2.563 0.0111 *
## Year2011 -0.02111 0.01214 207.00000 -1.739 0.0835 .
## Year2012 -0.02778 0.01214 207.00000 -2.288 0.0231 *
## sampleIDS:Year2010 0.01667 0.01717 207.00000 0.971 0.3328
## sampleIDS:Year2011 -0.02815 0.01717 207.00000 -1.640 0.1026
## sampleIDS:Year2012 -0.03148 0.01717 207.00000 -1.834 0.0681 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010 Yr2011 Yr2012 sIDS:Y2010 sIDS:Y2011
## sampleIDS -0.483
## Year2010 -0.483 0.500
## Year2011 -0.483 0.500 0.500
## Year2012 -0.483 0.500 0.500 0.500
## smIDS:Y2010 0.341 -0.707 -0.707 -0.354 -0.354
## smIDS:Y2011 0.341 -0.707 -0.354 -0.707 -0.354 0.500
## smIDS:Y2012 0.341 -0.707 -0.354 -0.354 -0.707 0.500 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TN
## Chisq Df Pr(>Chisq)
## sampleID 132.989 1 < 2.2e-16 ***
## Year 29.205 3 2.028e-06 ***
## sampleID:Year 10.854 3 0.01254 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.236 0.0107 12.2 0.212 0.259
## S 0.306 0.0107 12.2 0.282 0.329
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.07 0.00618 214 -11.335 <.0001
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.236 0.0107 12.2 0.212 0.259
## S 0.306 0.0107 12.2 0.282 0.329
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.07 0.00618 214 -0.0822 -0.0578
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.296 0.0116 16.9 0.272 0.320
## 2010 0.273 0.0116 16.9 0.249 0.298
## 2011 0.261 0.0116 16.9 0.236 0.285
## 2012 0.252 0.0116 16.9 0.228 0.277
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.02278 0.00873 214 2.608 0.0476
## Year2009 - Year2011 0.03519 0.00873 214 4.029 0.0004
## Year2009 - Year2012 0.04352 0.00873 214 4.983 <.0001
## Year2010 - Year2011 0.01241 0.00873 214 1.421 0.4878
## Year2010 - Year2012 0.02074 0.00873 214 2.375 0.0850
## Year2011 - Year2012 0.00833 0.00873 214 0.954 0.7755
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.296 0.0116 16.9 0.272 0.320
## 2010 0.273 0.0116 16.9 0.249 0.298
## 2011 0.261 0.0116 16.9 0.236 0.285
## 2012 0.252 0.0116 16.9 0.228 0.277
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.02278 0.00873 214 0.000165 0.0454
## Year2009 - Year2011 0.03519 0.00873 214 0.012572 0.0578
## Year2009 - Year2012 0.04352 0.00873 214 0.020905 0.0661
## Year2010 - Year2011 0.01241 0.00873 214 -0.010206 0.0350
## Year2010 - Year2012 0.02074 0.00873 214 -0.001872 0.0434
## Year2011 - Year2012 0.00833 0.00873 214 -0.014280 0.0309
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 0.256 0.0131 28.2 0.229 0.282
## S 0.336 0.0131 28.2 0.309 0.363
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 0.224 0.0131 28.2 0.198 0.251
## S 0.322 0.0131 28.2 0.295 0.349
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 0.234 0.0131 28.2 0.208 0.261
## S 0.287 0.0131 28.2 0.260 0.314
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 0.228 0.0131 28.2 0.201 0.255
## S 0.277 0.0131 28.2 0.250 0.304
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.0807 0.0124 214 -6.537 <.0001
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.0974 0.0124 214 -7.887 <.0001
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## I - S -0.0526 0.0124 214 -4.258 <.0001
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## I - S -0.0493 0.0124 214 -3.988 0.0001
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 0.256 0.0131 28.2 0.229 0.282
## S 0.336 0.0131 28.2 0.309 0.363
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 0.224 0.0131 28.2 0.198 0.251
## S 0.322 0.0131 28.2 0.295 0.349
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 0.234 0.0131 28.2 0.208 0.261
## S 0.287 0.0131 28.2 0.260 0.314
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 0.228 0.0131 28.2 0.201 0.255
## S 0.277 0.0131 28.2 0.250 0.304
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0807 0.0124 214 -0.1051 -0.0564
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0974 0.0124 214 -0.1218 -0.0731
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0526 0.0124 214 -0.0769 -0.0282
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0493 0.0124 214 -0.0736 -0.0249
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TN ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(WNC_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -946.1 -912.3 483.0 -966.1 206
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.8574 -0.6119 -0.0775 0.5642 6.9125
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0001393 0.01180
## Residual 0.0006188 0.02487
## Number of obs: 216, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 1.807e-01 6.197e-03 3.748e+01 29.167 <2e-16 ***
## sampleIDS 1.407e-02 6.770e-03 2.070e+02 2.079 0.0389 *
## Year2010 2.222e-03 6.770e-03 2.070e+02 0.328 0.7431
## Year2011 9.259e-03 6.770e-03 2.070e+02 1.368 0.1729
## Year2012 -2.222e-03 6.770e-03 2.070e+02 -0.328 0.7431
## sampleIDS:Year2010 3.704e-04 9.574e-03 2.070e+02 0.039 0.9692
## sampleIDS:Year2011 2.593e-03 9.574e-03 2.070e+02 0.271 0.7868
## sampleIDS:Year2012 1.852e-03 9.574e-03 2.070e+02 0.193 0.8468
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010 Yr2011 Yr2012 sIDS:Y2010 sIDS:Y2011
## sampleIDS -0.546
## Year2010 -0.546 0.500
## Year2011 -0.546 0.500 0.500
## Year2012 -0.546 0.500 0.500 0.500
## smIDS:Y2010 0.386 -0.707 -0.707 -0.354 -0.354
## smIDS:Y2011 0.386 -0.707 -0.354 -0.707 -0.354 0.500
## smIDS:Y2012 0.386 -0.707 -0.354 -0.354 -0.707 0.500 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TN
## Chisq Df Pr(>Chisq)
## sampleID 20.3703 1 6.381e-06 ***
## Year 7.4066 3 0.06001 .
## sampleID:Year 0.0980 3 0.99207
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.183 0.00486 13.5 0.173 0.194
## S 0.198 0.00486 13.5 0.188 0.209
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0153 0.00344 214 -4.436 <.0001
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 0.183 0.00486 13.5 0.173 0.194
## S 0.198 0.00486 13.5 0.188 0.209
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0153 0.00344 214 -0.0221 -0.00849
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.188 0.00543 21.6 0.176 0.199
## 2010 0.190 0.00543 21.6 0.179 0.201
## 2011 0.198 0.00543 21.6 0.187 0.210
## 2012 0.186 0.00543 21.6 0.175 0.198
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.00241 0.00487 214 -0.494 0.9603
## Year2009 - Year2011 -0.01056 0.00487 214 -2.167 0.1357
## Year2009 - Year2012 0.00130 0.00487 214 0.266 0.9934
## Year2010 - Year2011 -0.00815 0.00487 214 -1.673 0.3405
## Year2010 - Year2012 0.00370 0.00487 214 0.760 0.8721
## Year2011 - Year2012 0.01185 0.00487 214 2.434 0.0739
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 0.188 0.00543 21.6 0.176 0.199
## 2010 0.190 0.00543 21.6 0.179 0.201
## 2011 0.198 0.00543 21.6 0.187 0.210
## 2012 0.186 0.00543 21.6 0.175 0.198
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.00241 0.00487 214 -0.015018 0.01020
## Year2009 - Year2011 -0.01056 0.00487 214 -0.023166 0.00205
## Year2009 - Year2012 0.00130 0.00487 214 -0.011314 0.01391
## Year2010 - Year2011 -0.00815 0.00487 214 -0.020759 0.00446
## Year2010 - Year2012 0.00370 0.00487 214 -0.008907 0.01631
## Year2011 - Year2012 0.01185 0.00487 214 -0.000759 0.02446
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 0.181 0.00643 42 0.168 0.194
## S 0.195 0.00643 42 0.182 0.208
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 0.183 0.00643 42 0.170 0.196
## S 0.197 0.00643 42 0.184 0.210
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 0.190 0.00643 42 0.177 0.203
## S 0.207 0.00643 42 0.194 0.220
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 0.179 0.00643 42 0.166 0.192
## S 0.194 0.00643 42 0.181 0.207
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.0141 0.00689 214 -2.043 0.0422
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.0144 0.00689 214 -2.097 0.0371
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## I - S -0.0167 0.00689 214 -2.420 0.0164
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## I - S -0.0159 0.00689 214 -2.312 0.0217
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 0.181 0.00643 42 0.168 0.194
## S 0.195 0.00643 42 0.182 0.208
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 0.183 0.00643 42 0.170 0.196
## S 0.197 0.00643 42 0.184 0.210
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 0.190 0.00643 42 0.177 0.203
## S 0.207 0.00643 42 0.194 0.220
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 0.179 0.00643 42 0.166 0.192
## S 0.194 0.00643 42 0.181 0.207
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0141 0.00689 214 -0.0277 -0.000498
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0144 0.00689 214 -0.0280 -0.000869
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0167 0.00689 214 -0.0302 -0.003091
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0159 0.00689 214 -0.0295 -0.002350
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95TC Total Carbon
2008 pretreatment TC D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TC ~ sampleID + (1 | Site)
## Data: WNC_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 83.3 91.3 -37.7 75.3 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.55640 -0.70223 -0.05129 0.53585 2.81394
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.03702 0.1924
## Residual 0.20943 0.4576
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 2.5607 0.1089 18.9622 23.504 1.74e-15 ***
## sampleIDS 0.5341 0.1246 45.0000 4.288 9.41e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.572## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TC
## Chisq Df Pr(>Chisq)
## sampleID 18.387 1 1.803e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.56 0.114 21.2 2.32 2.80
## S 3.09 0.114 21.2 2.86 3.33
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.534 0.126 46 -4.240 0.0001
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.56 0.114 21.2 2.32 2.80
## S 3.09 0.114 21.2 2.86 3.33
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.534 0.126 46 -0.788 -0.281
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95TC D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TC ~ sampleID + (1 | Site)
## Data: WNC_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 55.8 63.8 -23.9 47.8 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.5152 -0.6572 -0.0512 0.5059 3.2894
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.001334 0.03652
## Residual 0.140711 0.37511
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 2.06704 0.07321 28.91213 28.23 < 2e-16 ***
## sampleIDS 0.28889 0.10209 45.00000 2.83 0.00694 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.697## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TC
## Chisq Df Pr(>Chisq)
## sampleID 8.0069 1 0.00466 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.07 0.0759 32 1.91 2.22
## S 2.36 0.0759 32 2.20 2.51
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.289 0.103 46 -2.798 0.0075
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.07 0.0759 32 1.91 2.22
## S 2.36 0.0759 32 2.20 2.51
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.289 0.103 46 -0.497 -0.0811
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TC ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(WNC_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 462.8 496.5 -221.4 442.8 206
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.9056 -0.6339 -0.0902 0.7433 4.3518
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.1044 0.3230
## Residual 0.4194 0.6476
## Number of obs: 216, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 3.2111 0.1647 34.6284 19.496 < 2e-16 ***
## sampleIDS 1.2581 0.1763 207.0000 7.138 1.57e-11 ***
## Year2010 -0.4296 0.1763 207.0000 -2.438 0.0156 *
## Year2011 -0.3307 0.1763 207.0000 -1.876 0.0620 .
## Year2012 -0.3311 0.1763 207.0000 -1.879 0.0617 .
## sampleIDS:Year2010 0.2196 0.2493 207.0000 0.881 0.3793
## sampleIDS:Year2011 -0.4385 0.2493 207.0000 -1.759 0.0800 .
## sampleIDS:Year2012 -0.4830 0.2493 207.0000 -1.938 0.0540 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010 Yr2011 Yr2012 sIDS:Y2010 sIDS:Y2011
## sampleIDS -0.535
## Year2010 -0.535 0.500
## Year2011 -0.535 0.500 0.500
## Year2012 -0.535 0.500 0.500 0.500
## smIDS:Y2010 0.378 -0.707 -0.707 -0.354 -0.354
## smIDS:Y2011 0.378 -0.707 -0.354 -0.707 -0.354 0.500
## smIDS:Y2012 0.378 -0.707 -0.354 -0.354 -0.707 0.500 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TC
## Chisq Df Pr(>Chisq)
## sampleID 150.927 1 < 2.2e-16 ***
## Year 27.361 3 4.944e-06 ***
## sampleID:Year 11.287 3 0.01027 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.94 0.131 13.2 2.66 3.22
## S 4.02 0.131 13.2 3.74 4.30
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -1.08 0.0897 214 -12.076 <.0001
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.94 0.131 13.2 2.66 3.22
## S 4.02 0.131 13.2 3.74 4.30
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -1.08 0.0897 214 -1.26 -0.906
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 3.84 0.146 20.5 3.54 4.14
## 2010 3.52 0.146 20.5 3.22 3.82
## 2011 3.29 0.146 20.5 2.99 3.59
## 2012 3.27 0.146 20.5 2.96 3.57
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.3198 0.127 214 2.522 0.0593
## Year2009 - Year2011 0.5500 0.127 214 4.338 0.0001
## Year2009 - Year2012 0.5726 0.127 214 4.516 0.0001
## Year2010 - Year2011 0.2302 0.127 214 1.815 0.2689
## Year2010 - Year2012 0.2528 0.127 214 1.994 0.1936
## Year2011 - Year2012 0.0226 0.127 214 0.178 0.9980
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 3.84 0.146 20.5 3.54 4.14
## 2010 3.52 0.146 20.5 3.22 3.82
## 2011 3.29 0.146 20.5 2.99 3.59
## 2012 3.27 0.146 20.5 2.96 3.57
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.3198 0.127 214 -0.0085 0.648
## Year2009 - Year2011 0.5500 0.127 214 0.2217 0.878
## Year2009 - Year2012 0.5726 0.127 214 0.2443 0.901
## Year2010 - Year2011 0.2302 0.127 214 -0.0981 0.558
## Year2010 - Year2012 0.2528 0.127 214 -0.0755 0.581
## Year2011 - Year2012 0.0226 0.127 214 -0.3057 0.351
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 3.21 0.171 38.8 2.86 3.56
## S 4.47 0.171 38.8 4.12 4.82
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 2.78 0.171 38.8 2.44 3.13
## S 4.26 0.171 38.8 3.91 4.61
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 2.88 0.171 38.8 2.53 3.23
## S 3.70 0.171 38.8 3.35 4.05
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 2.88 0.171 38.8 2.53 3.23
## S 3.66 0.171 38.8 3.31 4.00
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -1.258 0.179 214 -7.016 <.0001
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -1.478 0.179 214 -8.241 <.0001
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## I - S -0.820 0.179 214 -4.571 <.0001
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## I - S -0.775 0.179 214 -4.323 <.0001
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 3.21 0.171 38.8 2.86 3.56
## S 4.47 0.171 38.8 4.12 4.82
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 2.78 0.171 38.8 2.44 3.13
## S 4.26 0.171 38.8 3.91 4.61
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 2.88 0.171 38.8 2.53 3.23
## S 3.70 0.171 38.8 3.35 4.05
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 2.88 0.171 38.8 2.53 3.23
## S 3.66 0.171 38.8 3.31 4.00
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -1.258 0.179 214 -1.61 -0.905
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -1.478 0.179 214 -1.83 -1.124
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.820 0.179 214 -1.17 -0.466
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.775 0.179 214 -1.13 -0.422
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: TC ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(WNC_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 224.8 258.6 -102.4 204.8 206
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.7515 -0.5951 -0.1175 0.4362 7.1768
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0154 0.1241
## Residual 0.1433 0.3786
## Number of obs: 216, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 2.133e+00 8.378e-02 6.743e+01 25.455 <2e-16 ***
## sampleIDS 2.352e-01 1.030e-01 2.070e+02 2.283 0.0235 *
## Year2010 4.519e-02 1.030e-01 2.070e+02 0.439 0.6614
## Year2011 9.519e-02 1.030e-01 2.070e+02 0.924 0.3567
## Year2012 6.148e-02 1.030e-01 2.070e+02 0.597 0.5514
## sampleIDS:Year2010 2.037e-02 1.457e-01 2.070e+02 0.140 0.8890
## sampleIDS:Year2011 4.963e-02 1.457e-01 2.070e+02 0.341 0.7337
## sampleIDS:Year2012 1.111e-03 1.457e-01 2.070e+02 0.008 0.9939
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010 Yr2011 Yr2012 sIDS:Y2010 sIDS:Y2011
## sampleIDS -0.615
## Year2010 -0.615 0.500
## Year2011 -0.615 0.500 0.500
## Year2012 -0.615 0.500 0.500 0.500
## smIDS:Y2010 0.435 -0.707 -0.707 -0.354 -0.354
## smIDS:Y2011 0.435 -0.707 -0.354 -0.707 -0.354 0.500
## smIDS:Y2012 0.435 -0.707 -0.354 -0.354 -0.707 0.500 0.500## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TC
## Chisq Df Pr(>Chisq)
## sampleID 24.1109 1 9.094e-07 ***
## Year 2.7219 3 0.4365
## sampleID:Year 0.1521 3 0.9849
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.18 0.0579 16.5 2.06 2.31
## S 2.44 0.0579 16.5 2.31 2.56
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.253 0.0524 214 -4.827 <.0001
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 2.18 0.0579 16.5 2.06 2.31
## S 2.44 0.0579 16.5 2.31 2.56
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.253 0.0524 214 -0.356 -0.15
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 2.25 0.0688 33.1 2.11 2.39
## 2010 2.31 0.0688 33.1 2.17 2.45
## 2011 2.37 0.0688 33.1 2.23 2.51
## 2012 2.31 0.0688 33.1 2.17 2.45
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.05537 0.0741 214 -0.747 0.8779
## Year2009 - Year2011 -0.12000 0.0741 214 -1.619 0.3701
## Year2009 - Year2012 -0.06204 0.0741 214 -0.837 0.8368
## Year2010 - Year2011 -0.06463 0.0741 214 -0.872 0.8194
## Year2010 - Year2012 -0.00667 0.0741 214 -0.090 0.9997
## Year2011 - Year2012 0.05796 0.0741 214 0.782 0.8626
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 2.25 0.0688 33.1 2.11 2.39
## 2010 2.31 0.0688 33.1 2.17 2.45
## 2011 2.37 0.0688 33.1 2.23 2.51
## 2012 2.31 0.0688 33.1 2.17 2.45
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.05537 0.0741 214 -0.247 0.1365
## Year2009 - Year2011 -0.12000 0.0741 214 -0.312 0.0719
## Year2009 - Year2012 -0.06204 0.0741 214 -0.254 0.1299
## Year2010 - Year2011 -0.06463 0.0741 214 -0.257 0.1273
## Year2010 - Year2012 -0.00667 0.0741 214 -0.199 0.1853
## Year2011 - Year2012 0.05796 0.0741 214 -0.134 0.2499
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 2.13 0.0865 74.9 1.96 2.30
## S 2.37 0.0865 74.9 2.20 2.54
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 2.18 0.0865 74.9 2.01 2.35
## S 2.43 0.0865 74.9 2.26 2.61
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 2.23 0.0865 74.9 2.06 2.40
## S 2.51 0.0865 74.9 2.34 2.68
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 2.19 0.0865 74.9 2.02 2.37
## S 2.43 0.0865 74.9 2.26 2.60
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.235 0.105 214 -2.244 0.0259
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.256 0.105 214 -2.438 0.0156
##
## Year = 2011:
## contrast estimate SE df t.ratio p.value
## I - S -0.285 0.105 214 -2.717 0.0071
##
## Year = 2012:
## contrast estimate SE df t.ratio p.value
## I - S -0.236 0.105 214 -2.254 0.0252
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 2.13 0.0865 74.9 1.96 2.30
## S 2.37 0.0865 74.9 2.20 2.54
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 2.18 0.0865 74.9 2.01 2.35
## S 2.43 0.0865 74.9 2.26 2.61
##
## Year = 2011:
## sampleID emmean SE df lower.CL upper.CL
## I 2.23 0.0865 74.9 2.06 2.40
## S 2.51 0.0865 74.9 2.34 2.68
##
## Year = 2012:
## sampleID emmean SE df lower.CL upper.CL
## I 2.19 0.0865 74.9 2.02 2.37
## S 2.43 0.0865 74.9 2.26 2.60
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.235 0.105 214 -0.442 -0.0286
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.256 0.105 214 -0.462 -0.0489
##
## Year = 2011:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.285 0.105 214 -0.491 -0.0782
##
## Year = 2012:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.236 0.105 214 -0.443 -0.0297
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Al -Aluminum
Al D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Al ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 945.9 953.8 -468.9 937.9 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.91636 -0.53003 -0.02591 0.61209 2.12533
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 1115627 1056
## Residual 1545869 1243
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 21691.26 425.69 12.61 50.955 5.59e-16 ***
## sampleIDS -557.15 338.39 45.00 -1.646 0.107
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.397## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Al
## Chisq Df Pr(>Chisq)
## sampleID 2.7108 1 0.09967 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 21691 448 14.2 20731 22652
## S 21134 448 14.2 20174 22094
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 557 342 46 1.628 0.1103
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 21691 448 14.2 20731 22652
## S 21134 448 14.2 20174 22094
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 557 342 46 -132 1246
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Al D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Al ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 948.9 956.9 -470.5 940.9 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.42917 -0.63836 0.04205 0.60135 1.95460
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 1697651 1303
## Residual 1541631 1242
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 22493.81 495.71 11.48 45.377 2.58e-14 ***
## sampleIDS 44.19 337.93 45.00 0.131 0.897
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.341## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Al
## Chisq Df Pr(>Chisq)
## sampleID 0.0171 1 0.896## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 22494 523 12.9 21363 23624
## S 22538 523 12.9 21407 23669
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -44.2 342 46 -0.129 0.8977
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 22494 523 12.9 21363 23624
## S 22538 523 12.9 21407 23669
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -44.2 342 46 -732 644
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Al ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 1888.0 1904.1 -938.0 1876.0 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.61881 -0.68721 -0.02567 0.72688 1.87568
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 1532912 1238
## Residual 1664185 1290
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 20962.81 481.62 13.96 43.525 2.61e-16 ***
## sampleIDS -1060.78 351.10 99.00 -3.021 0.0032 **
## Year2010 1531.96 351.10 99.00 4.363 3.15e-05 ***
## sampleIDS:Year2010 -584.48 496.53 99.00 -1.177 0.2420
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.364
## Year2010 -0.364 0.500
## smIDS:Y2010 0.258 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Al
## Chisq Df Pr(>Chisq)
## sampleID 29.7009 1 5.041e-08 ***
## Year 24.9351 1 5.929e-07 ***
## sampleID:Year 1.3856 1 0.2391
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 21729 474 11.9 20694 22763
## S 20376 474 11.9 19341 21410
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 1353 252 102 5.367 <.0001
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 21729 474 11.9 20694 22763
## S 20376 474 11.9 19341 21410
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 1353 252 102 853 1853
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 20432 474 11.9 19398 21467
## 2010 21672 474 11.9 20638 22707
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -1240 252 102 -4.917 <.0001
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 20432 474 11.9 19398 21467
## 2010 21672 474 11.9 20638 22707
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -1240 252 102 -1740 -740
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 20963 507 15.7 19887 22038
## S 19902 507 15.7 18826 20978
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 22495 507 15.7 21419 23570
## S 20850 507 15.7 19774 21925
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 1061 357 102 2.975 0.0037
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S 1645 357 102 4.614 <.0001
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 20963 507 15.7 19887 22038
## S 19902 507 15.7 18826 20978
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 22495 507 15.7 21419 23570
## S 20850 507 15.7 19774 21925
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 1061 357 102 354 1768
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S 1645 357 102 938 2352
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Al ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 1998.8 2014.9 -993.4 1986.8 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.7512 -0.4013 -0.0295 0.4274 6.3285
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 1328679 1153
## Residual 5077686 2253
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 22319.04 579.39 25.55 38.522 <2e-16 ***
## sampleIDS -691.15 613.29 99.00 -1.127 0.262
## Year2010 198.70 613.29 99.00 0.324 0.747
## sampleIDS:Year2010 1083.59 867.32 99.00 1.249 0.214
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.529
## Year2010 -0.529 0.500
## smIDS:Y2010 0.374 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Al
## Chisq Df Pr(>Chisq)
## sampleID 0.1186 1 0.73055
## Year 2.9157 1 0.08772 .
## sampleID:Year 1.5609 1 0.21154
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 22418 517 15.5 21319 23518
## S 22269 517 15.5 21170 23368
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 149 440 102 0.339 0.7352
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 22418 517 15.5 21319 23518
## S 22269 517 15.5 21170 23368
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 149 440 102 -724 1023
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 21973 517 15.5 20874 23073
## 2010 22714 517 15.5 21615 23813
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -740 440 102 -1.681 0.0957
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 21973 517 15.5 20874 23073
## 2010 22714 517 15.5 21615 23813
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -740 440 102 -1614 133
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 22319 604 28.6 21084 23554
## S 21628 604 28.6 20393 22863
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 22518 604 28.6 21282 23753
## S 22910 604 28.6 21675 24146
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 691 623 102 1.110 0.2697
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -392 623 102 -0.630 0.5300
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 22319 604 28.6 21084 23554
## S 21628 604 28.6 20393 22863
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 22518 604 28.6 21282 23753
## S 22910 604 28.6 21675 24146
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 691 623 102 -544 1926
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -392 623 102 -1628 843
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Ca -Calcium
Ca D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Ca + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 69.5 77.5 -30.7 61.5 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.5759 -0.6194 -0.2550 0.3865 2.9120
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.04145 0.2036
## Residual 0.15600 0.3950
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.6876 0.1019 16.7768 85.255 <2e-16 ***
## sampleIDS -0.1166 0.1075 45.0000 -1.085 0.284
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.527## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Ca + 1)
## Chisq Df Pr(>Chisq)
## sampleID 1.1772 1 0.2779## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.69 0.107 18.8 8.46 8.91
## S 8.57 0.107 18.8 8.35 8.79
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.117 0.109 46 1.073 0.2889
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.69 0.107 18.8 8.46 8.91
## S 8.57 0.107 18.8 8.35 8.79
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.117 0.109 46 -0.102 0.335
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Ca D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Ca + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 76.6 84.6 -34.3 68.6 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.5048 -0.5758 -0.1332 0.4771 2.8981
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.05837 0.2416
## Residual 0.17352 0.4166
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.8766 0.1136 15.6088 78.117 <2e-16 ***
## sampleIDS -0.1262 0.1134 45.0000 -1.113 0.272
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.499## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Ca + 1)
## Chisq Df Pr(>Chisq)
## sampleID 1.2383 1 0.2658## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.88 0.119 17.5 8.63 9.13
## S 8.75 0.119 17.5 8.50 9.00
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.126 0.115 46 1.100 0.2769
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.88 0.119 17.5 8.63 9.13
## S 8.75 0.119 17.5 8.50 9.00
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.126 0.115 46 -0.105 0.357
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Ca + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 105.0 121.1 -46.5 93.0 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4018 -0.5057 -0.1049 0.4155 3.2482
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.05916 0.2432
## Residual 0.11772 0.3431
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.76277 0.10456 18.02164 83.804 <2e-16 ***
## sampleIDS 0.02959 0.09338 99.00000 0.317 0.752
## Year2010 -0.08985 0.09338 99.00000 -0.962 0.338
## sampleIDS:Year2010 -0.01812 0.13206 99.00000 -0.137 0.891
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.447
## Year2010 -0.447 0.500
## smIDS:Y2010 0.316 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Ca + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.0966 1 0.7559
## Year 2.2440 1 0.1341
## sampleID:Year 0.0188 1 0.8908## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.72 0.0987 13.2 8.50 8.93
## S 8.74 0.0987 13.2 8.53 8.95
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0205 0.0671 102 -0.306 0.7602
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.72 0.0987 13.2 8.50 8.93
## S 8.74 0.0987 13.2 8.53 8.95
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0205 0.0671 102 -0.154 0.112
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.78 0.0987 13.2 8.56 8.99
## 2010 8.68 0.0987 13.2 8.47 8.89
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0989 0.0671 102 1.475 0.1433
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.78 0.0987 13.2 8.56 8.99
## 2010 8.68 0.0987 13.2 8.47 8.89
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0989 0.0671 102 -0.0341 0.232
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 8.76 0.11 20.2 8.53 8.99
## S 8.79 0.11 20.2 8.56 9.02
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 8.67 0.11 20.2 8.44 8.90
## S 8.68 0.11 20.2 8.46 8.91
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.0296 0.0948 102 -0.312 0.7557
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.0115 0.0948 102 -0.121 0.9040
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 8.76 0.11 20.2 8.53 8.99
## S 8.79 0.11 20.2 8.56 9.02
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 8.67 0.11 20.2 8.44 8.90
## S 8.68 0.11 20.2 8.46 8.91
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0296 0.0948 102 -0.218 0.159
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0115 0.0948 102 -0.200 0.177
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Ca + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 165.1 181.2 -76.5 153.1 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -3.1819 -0.5439 -0.1401 0.4323 3.8484
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.07627 0.2762
## Residual 0.21009 0.4584
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.84082 0.12750 21.29646 69.340 <2e-16 ***
## sampleIDS -0.01623 0.12475 99.00000 -0.130 0.897
## Year2010 -0.12749 0.12475 99.00000 -1.022 0.309
## sampleIDS:Year2010 0.10895 0.17642 99.00000 0.618 0.538
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.489
## Year2010 -0.489 0.500
## smIDS:Y2010 0.346 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Ca + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.1880 1 0.6646
## Year 0.6851 1 0.4078
## sampleID:Year 0.3814 1 0.5369## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.78 0.117 14.2 8.53 9.03
## S 8.82 0.117 14.2 8.56 9.07
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0382 0.0896 102 -0.427 0.6703
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.78 0.117 14.2 8.53 9.03
## S 8.82 0.117 14.2 8.56 9.07
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0382 0.0896 102 -0.216 0.139
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.83 0.117 14.2 8.58 9.08
## 2010 8.76 0.117 14.2 8.51 9.01
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.073 0.0896 102 0.815 0.4169
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.83 0.117 14.2 8.58 9.08
## 2010 8.76 0.117 14.2 8.51 9.01
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.073 0.0896 102 -0.105 0.251
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 8.84 0.133 23.9 8.57 9.12
## S 8.82 0.133 23.9 8.55 9.10
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 8.71 0.133 23.9 8.44 8.99
## S 8.81 0.133 23.9 8.53 9.08
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 0.0162 0.127 102 0.128 0.8983
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.0927 0.127 102 -0.732 0.4659
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 8.84 0.133 23.9 8.57 9.12
## S 8.82 0.133 23.9 8.55 9.10
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 8.71 0.133 23.9 8.44 8.99
## S 8.81 0.133 23.9 8.53 9.08
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0162 0.127 102 -0.235 0.267
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0927 0.127 102 -0.344 0.159
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Fe - Iron
Fe D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Fe ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 1011.0 1019.0 -501.5 1003.0 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4140 -0.3907 -0.0578 0.2811 3.9170
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 5585823 2363
## Residual 4834093 2199
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 23811.37 894.25 11.38 26.627 1.32e-11 ***
## sampleIDS -546.52 598.40 45.00 -0.913 0.366
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.335## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Fe
## Chisq Df Pr(>Chisq)
## sampleID 0.8341 1 0.3611## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 23811 944 12.8 21769 25853
## S 23265 944 12.8 21223 25307
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 547 605 46 0.903 0.3712
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 23811 944 12.8 21769 25853
## S 23265 944 12.8 21223 25307
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 547 605 46 -672 1765
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Fe D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Fe ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 1024.8 1032.7 -508.4 1016.8 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.0853 -0.4441 -0.0960 0.3075 4.4199
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 5245585 2290
## Residual 6573372 2564
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 24467.56 909.01 12.31 26.917 2.61e-12 ***
## sampleIDS -500.93 697.79 45.00 -0.718 0.477
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.384## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Fe
## Chisq Df Pr(>Chisq)
## sampleID 0.5153 1 0.4728## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 24468 958 13.8 22411 26524
## S 23967 958 13.8 21910 26023
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 501 706 46 0.710 0.4814
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 24468 958 13.8 22411 26524
## S 23967 958 13.8 21910 26023
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 501 706 46 -920 1921
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Fe ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 1909.8 1925.9 -948.9 1897.8 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.7178 -0.6151 0.0076 0.7362 1.9567
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 524924 724.5
## Residual 2241785 1497.3
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 23104.89 375.97 27.22 61.454 < 2e-16 ***
## sampleIDS -1122.22 407.50 99.00 -2.754 0.00701 **
## Year2010 1795.26 407.50 99.00 4.406 2.68e-05 ***
## sampleIDS:Year2010 -323.81 576.30 99.00 -0.562 0.57546
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.542
## Year2010 -0.542 0.500
## smIDS:Y2010 0.383 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Fe
## Chisq Df Pr(>Chisq)
## sampleID 19.8604 1 8.331e-06 ***
## Year 32.1314 1 1.441e-08 ***
## sampleID:Year 0.3157 1 0.5742
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 24003 332 16 23298 24707
## S 22718 332 16 22014 23423
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 1284 293 102 4.388 <.0001
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 24003 332 16 23298 24707
## S 22718 332 16 22014 23423
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 1284 293 102 704 1865
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 22544 332 16 21840 23248
## 2010 24177 332 16 23473 24881
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -1633 293 102 -5.582 <.0001
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 22544 332 16 21840 23248
## 2010 24177 332 16 23473 24881
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -1633 293 102 -2214 -1053
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 23105 391 30.5 22306 23904
## S 21983 391 30.5 21184 22781
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 24900 391 30.5 24101 25699
## S 23454 391 30.5 22655 24253
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 1122 414 102 2.712 0.0079
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S 1446 414 102 3.494 0.0007
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 23105 391 30.5 22306 23904
## S 21983 391 30.5 21184 22781
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 24900 391 30.5 24101 25699
## S 23454 391 30.5 22655 24253
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 1122 414 102 301 1943
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S 1446 414 102 625 2267
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: Fe ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 2001.0 2017.1 -994.5 1989.0 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.9032 -0.5240 0.0059 0.5585 3.8875
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 513126 716.3
## Residual 5476006 2340.1
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 24089.78 509.73 44.33 47.259 <2e-16 ***
## sampleIDS -386.56 636.89 99.00 -0.607 0.545
## Year2010 609.85 636.89 99.00 0.958 0.341
## sampleIDS:Year2010 825.22 900.70 99.00 0.916 0.362
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.625
## Year2010 -0.625 0.500
## smIDS:Y2010 0.442 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Fe
## Chisq Df Pr(>Chisq)
## sampleID 0.0033 1 0.95386
## Year 5.1546 1 0.02318 *
## sampleID:Year 0.8394 1 0.35956
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 24395 416 21.4 23530 25260
## S 24421 416 21.4 23556 25286
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -26.1 457 102 -0.057 0.9547
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 24395 416 21.4 23530 25260
## S 24421 416 21.4 23556 25286
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -26.1 457 102 -933 881
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 23897 416 21.4 23031 24762
## 2010 24919 416 21.4 24054 25784
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -1022 457 102 -2.236 0.0275
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 23897 416 21.4 23031 24762
## 2010 24919 416 21.4 24054 25784
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -1022 457 102 -1930 -115
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 24090 527 49.2 23030 25149
## S 23703 527 49.2 22644 24763
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 24700 527 49.2 23640 25759
## S 25138 527 49.2 24079 26198
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 387 647 102 0.598 0.5514
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -439 647 102 -0.678 0.4991
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 24090 527 49.2 23030 25149
## S 23703 527 49.2 22644 24763
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 24700 527 49.2 23640 25759
## S 25138 527 49.2 24079 26198
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 387 647 102 -896 1669
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -439 647 102 -1722 844
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95K - Potassium normal dist
K D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: K ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## 818 826 -405 810 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.86229 -0.74572 -0.07081 0.53856 2.14722
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 117226 342.4
## Residual 142195 377.1
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4891.519 135.246 12.212 36.167 8.55e-14 ***
## sampleIDS -4.556 102.630 45.000 -0.044 0.965
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.379## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: K
## Chisq Df Pr(>Chisq)
## sampleID 0.002 1 0.9646## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4892 143 13.7 4585 5198
## S 4887 143 13.7 4581 5193
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 4.56 104 46 0.044 0.9652
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4892 143 13.7 4585 5198
## S 4887 143 13.7 4581 5193
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 4.56 104 46 -204 213
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95K D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: K ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## 832.2 840.1 -412.1 824.2 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.02994 -0.66837 0.01344 0.65919 2.32561
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 101889 319.2
## Residual 196634 443.4
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4798.74 136.40 13.75 35.183 7.2e-15 ***
## sampleIDS 144.44 120.69 45.00 1.197 0.238
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.442## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: K
## Chisq Df Pr(>Chisq)
## sampleID 1.4324 1 0.2314## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4799 143 15.4 4494 5104
## S 4943 143 15.4 4638 5248
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -144 122 46 -1.183 0.2427
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4799 143 15.4 4494 5104
## S 4943 143 15.4 4638 5248
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -144 122 46 -390 101
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: K ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## 1665.3 1681.4 -826.6 1653.3 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.34745 -0.58555 -0.03805 0.51400 2.79932
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 42976 207.3
## Residual 236490 486.3
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 5298.04 116.34 31.44 45.541 < 2e-16 ***
## sampleIDS 148.48 132.35 99.00 1.122 0.26464
## Year2010 423.22 132.35 99.00 3.198 0.00186 **
## sampleIDS:Year2010 -221.59 187.18 99.00 -1.184 0.23930
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.569
## Year2010 -0.569 0.500
## smIDS:Y2010 0.402 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: K
## Chisq Df Pr(>Chisq)
## sampleID 0.1621 1 0.687193
## Year 11.1441 1 0.000843 ***
## sampleID:Year 1.4015 1 0.236468
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 5510 100 17.3 5298 5721
## S 5547 100 17.3 5336 5759
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -37.7 95 102 -0.397 0.6925
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 5510 100 17.3 5298 5721
## S 5547 100 17.3 5336 5759
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -37.7 95 102 -226 151
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 5372 100 17.3 5161 5584
## 2010 5685 100 17.3 5473 5896
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -312 95 102 -3.287 0.0014
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 5372 100 17.3 5161 5584
## 2010 5685 100 17.3 5473 5896
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -312 95 102 -501 -124
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 5298 121 35.1 5053 5543
## S 5447 121 35.1 5201 5692
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 5721 121 35.1 5476 5967
## S 5648 121 35.1 5403 5893
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -148.5 134 102 -1.105 0.2719
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S 73.1 134 102 0.544 0.5877
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 5298 121 35.1 5053 5543
## S 5447 121 35.1 5201 5692
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 5721 121 35.1 5476 5967
## S 5648 121 35.1 5403 5893
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -148.5 134 102 -415 118
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S 73.1 134 102 -193 340
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: K ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## 1746.3 1762.4 -867.1 1734.3 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.2180 -0.4426 -0.0081 0.5441 6.2536
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 59186 243.3
## Residual 512971 716.2
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 5339.15 159.92 40.12 33.386 <2e-16 ***
## sampleIDS 34.19 194.93 99.00 0.175 0.861
## Year2010 141.93 194.93 99.00 0.728 0.468
## sampleIDS:Year2010 306.70 275.67 99.00 1.113 0.269
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.609
## Year2010 -0.609 0.500
## smIDS:Y2010 0.431 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: K
## Chisq Df Pr(>Chisq)
## sampleID 1.8512 1 0.17365
## Year 4.5892 1 0.03217 *
## sampleID:Year 1.2378 1 0.26590
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 5410 133 20.1 5133 5687
## S 5598 133 20.1 5321 5875
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -188 140 102 -1.340 0.1833
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 5410 133 20.1 5133 5687
## S 5598 133 20.1 5321 5875
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -188 140 102 -465 90.1
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 5356 133 20.1 5079 5633
## 2010 5652 133 20.1 5375 5929
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -295 140 102 -2.110 0.0373
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 5356 133 20.1 5079 5633
## 2010 5652 133 20.1 5375 5929
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -295 140 102 -573 -17.6
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 5339 166 44.6 5005 5673
## S 5373 166 44.6 5040 5707
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 5481 166 44.6 5147 5815
## S 5822 166 44.6 5488 6156
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -34.2 198 102 -0.173 0.8632
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -340.9 198 102 -1.722 0.0881
##
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 5339 166 44.6 5005 5673
## S 5373 166 44.6 5040 5707
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 5481 166 44.6 5147 5815
## S 5822 166 44.6 5488 6156
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -34.2 198 102 -427 358.4
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -340.9 198 102 -734 51.7
##
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Mg - Magnesium
Mg D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mg + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -56.3 -48.3 32.1 -64.3 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.8687 -0.5071 0.1104 0.4644 1.9118
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.01860 0.1364
## Residual 0.01209 0.1099
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.51994 0.05014 10.82426 169.917 <2e-16 ***
## sampleIDS -0.01502 0.02992 45.00000 -0.502 0.618
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.298## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mg + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.2521 1 0.6156## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.52 0.053 12.2 8.40 8.64
## S 8.50 0.053 12.2 8.39 8.62
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.015 0.0303 46 0.496 0.6219
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.52 0.053 12.2 8.40 8.64
## S 8.50 0.053 12.2 8.39 8.62
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.015 0.0303 46 -0.0459 0.0759
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Mg D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mg + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -85.4 -77.4 46.7 -93.4 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.83485 -0.73843 0.02808 0.67087 2.08702
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.016998 0.13038
## Residual 0.006498 0.08061
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.58855 0.04614 10.10317 186.122 <2e-16 ***
## sampleIDS -0.02531 0.02194 45.00000 -1.154 0.255
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.238## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mg + 1)
## Chisq Df Pr(>Chisq)
## sampleID 1.3313 1 0.2486## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.59 0.0488 11.4 8.48 8.70
## S 8.56 0.0488 11.4 8.46 8.67
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.0253 0.0222 46 1.141 0.2598
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.59 0.0488 11.4 8.48 8.70
## S 8.56 0.0488 11.4 8.46 8.67
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0253 0.0222 46 -0.0193 0.07
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mg + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -103.4 -87.3 57.7 -115.4 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.4121 -0.6381 -0.1191 0.6577 2.6557
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.003337 0.05777
## Residual 0.018258 0.13512
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.71984 0.03236 31.33995 269.488 < 2e-16 ***
## sampleIDS -0.03238 0.03678 99.00000 -0.881 0.380691
## Year2010 -0.13182 0.03678 99.00000 -3.585 0.000526 ***
## sampleIDS:Year2010 0.00394 0.05201 99.00000 0.076 0.939771
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.568
## Year2010 -0.568 0.500
## smIDS:Y2010 0.402 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mg + 1)
## Chisq Df Pr(>Chisq)
## sampleID 1.3678 1 0.2422
## Year 24.9354 1 5.928e-07 ***
## sampleID:Year 0.0057 1 0.9396
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.65 0.028 17.3 8.60 8.71
## S 8.62 0.028 17.3 8.56 8.68
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.0304 0.0264 102 1.152 0.2521
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.65 0.028 17.3 8.60 8.71
## S 8.62 0.028 17.3 8.56 8.68
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0304 0.0264 102 -0.022 0.0828
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.70 0.028 17.3 8.64 8.76
## 2010 8.57 0.028 17.3 8.51 8.63
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.13 0.0264 102 4.917 <.0001
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.70 0.028 17.3 8.64 8.76
## 2010 8.57 0.028 17.3 8.51 8.63
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.13 0.0264 102 0.0775 0.182
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 8.72 0.0336 35 8.65 8.79
## S 8.69 0.0336 35 8.62 8.76
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 8.59 0.0336 35 8.52 8.66
## S 8.56 0.0336 35 8.49 8.63
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 0.0324 0.0373 102 0.867 0.3879
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S 0.0284 0.0373 102 0.762 0.4480
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 8.72 0.0336 35 8.65 8.79
## S 8.69 0.0336 35 8.62 8.76
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 8.59 0.0336 35 8.52 8.66
## S 8.56 0.0336 35 8.49 8.63
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0324 0.0373 102 -0.0417 0.106
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0284 0.0373 102 -0.0456 0.103
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mg + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -49.8 -33.7 30.9 -61.8 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.6870 -0.5060 0.0383 0.4636 4.9462
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.004613 0.06792
## Residual 0.030288 0.17404
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 8.78777 0.04043 34.67961 217.374 < 2e-16 ***
## sampleIDS -0.01268 0.04737 99.00000 -0.268 0.789
## Year2010 -0.21106 0.04737 99.00000 -4.456 2.2e-05 ***
## sampleIDS:Year2010 0.06407 0.06699 99.00000 0.957 0.341
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.586
## Year2010 -0.586 0.500
## smIDS:Y2010 0.414 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mg + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.334 1 0.5633
## Year 28.568 1 9.046e-08 ***
## sampleID:Year 0.915 1 0.3388
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.68 0.0344 18.3 8.61 8.75
## S 8.70 0.0344 18.3 8.63 8.77
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0194 0.034 102 -0.569 0.5705
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 8.68 0.0344 18.3 8.61 8.75
## S 8.70 0.0344 18.3 8.63 8.77
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0194 0.034 102 -0.0868 0.0481
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.78 0.0344 18.3 8.71 8.85
## 2010 8.60 0.0344 18.3 8.53 8.67
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.179 0.034 102 5.263 <.0001
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 8.78 0.0344 18.3 8.71 8.85
## 2010 8.60 0.0344 18.3 8.53 8.67
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.179 0.034 102 0.112 0.246
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 8.79 0.0419 38.7 8.70 8.87
## S 8.78 0.0419 38.7 8.69 8.86
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 8.58 0.0419 38.7 8.49 8.66
## S 8.63 0.0419 38.7 8.54 8.71
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 0.0127 0.0481 102 0.264 0.7926
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.0514 0.0481 102 -1.068 0.2878
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 8.79 0.0419 38.7 8.70 8.87
## S 8.78 0.0419 38.7 8.69 8.86
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 8.58 0.0419 38.7 8.49 8.66
## S 8.63 0.0419 38.7 8.54 8.71
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0127 0.0481 102 -0.0827 0.108
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0514 0.0481 102 -0.1468 0.044
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Mn - manganese
Mn D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mn + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -69.4 -61.4 38.7 -77.4 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.30308 -0.52708 0.03479 0.38226 2.28742
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.009506 0.0975
## Residual 0.010208 0.1010
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.279446 0.037873 11.884960 165.805 <2e-16 ***
## sampleIDS -0.005291 0.027498 45.000000 -0.192 0.848
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.363## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mn + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.037 1 0.8474## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.28 0.0399 13.4 6.19 6.37
## S 6.27 0.0399 13.4 6.19 6.36
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.00529 0.0278 46 0.190 0.8499
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.28 0.0399 13.4 6.19 6.37
## S 6.27 0.0399 13.4 6.19 6.36
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.00529 0.0278 46 -0.0507 0.0613
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Mn D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mn + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -54.7 -46.8 31.4 -62.7 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.68427 -0.63988 0.01132 0.47355 2.43295
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.008418 0.09175
## Residual 0.014236 0.11932
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.274620 0.038245 13.264585 164.065 <2e-16 ***
## sampleIDS -0.003729 0.032474 45.000002 -0.115 0.909
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.425## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mn + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.0132 1 0.9086## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.27 0.0402 14.9 6.19 6.36
## S 6.27 0.0402 14.9 6.19 6.36
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.00373 0.0328 46 0.114 0.9101
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.27 0.0402 14.9 6.19 6.36
## S 6.27 0.0402 14.9 6.19 6.36
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.00373 0.0328 46 -0.0624 0.0698
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mn + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -144.4 -128.3 78.2 -156.4 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.2237 -0.6152 -0.1134 0.6446 1.9014
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.00195 0.04416
## Residual 0.01261 0.11228
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.342042 0.026147 34.384135 242.557 <2e-16 ***
## sampleIDS -0.037163 0.030559 99.000000 -1.216 0.2268
## Year2010 0.055134 0.030559 99.000000 1.804 0.0742 .
## sampleIDS:Year2010 -0.003145 0.043217 99.000000 -0.073 0.9421
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.584
## Year2010 -0.584 0.500
## smIDS:Y2010 0.413 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mn + 1)
## Chisq Df Pr(>Chisq)
## sampleID 3.2134 1 0.07304 .
## Year 6.1440 1 0.01319 *
## sampleID:Year 0.0053 1 0.94199
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.37 0.0223 18.2 6.32 6.42
## S 6.33 0.0223 18.2 6.28 6.38
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.0387 0.0219 102 1.765 0.0805
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.37 0.0223 18.2 6.32 6.42
## S 6.33 0.0223 18.2 6.28 6.38
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0387 0.0219 102 -0.00479 0.0823
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.32 0.0223 18.2 6.28 6.37
## 2010 6.38 0.0223 18.2 6.33 6.42
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.0536 0.0219 102 -2.441 0.0164
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.32 0.0223 18.2 6.28 6.37
## 2010 6.38 0.0223 18.2 6.33 6.42
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.0536 0.0219 102 -0.0971 -0.01
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 6.34 0.0271 38.4 6.29 6.40
## S 6.30 0.0271 38.4 6.25 6.36
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 6.40 0.0271 38.4 6.34 6.45
## S 6.36 0.0271 38.4 6.30 6.41
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 0.0372 0.031 102 1.198 0.2339
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S 0.0403 0.031 102 1.299 0.1969
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 6.34 0.0271 38.4 6.29 6.40
## S 6.30 0.0271 38.4 6.25 6.36
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 6.40 0.0271 38.4 6.34 6.45
## S 6.36 0.0271 38.4 6.30 6.41
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0372 0.031 102 -0.0244 0.0987
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0403 0.031 102 -0.0212 0.1019
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Mn + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -85.4 -69.3 48.7 -97.4 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.9352 -0.5281 -0.0708 0.5922 2.7882
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.002875 0.05362
## Residual 0.021963 0.14820
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.34645 0.03366 37.60182 188.551 <2e-16 ***
## sampleIDS -0.02279 0.04033 99.00000 -0.565 0.573
## Year2010 -0.01117 0.04033 99.00000 -0.277 0.782
## sampleIDS:Year2010 0.06284 0.05704 99.00000 1.102 0.273
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.599
## Year2010 -0.599 0.500
## smIDS:Y2010 0.424 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mn + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.0917 1 0.7621
## Year 0.5040 1 0.4777
## sampleID:Year 1.2138 1 0.2706## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.34 0.0282 19.2 6.28 6.40
## S 6.35 0.0282 19.2 6.29 6.41
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.00864 0.029 102 -0.298 0.7662
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.34 0.0282 19.2 6.28 6.40
## S 6.35 0.0282 19.2 6.29 6.41
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.00864 0.029 102 -0.0661 0.0488
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.34 0.0282 19.2 6.28 6.39
## 2010 6.36 0.0282 19.2 6.30 6.41
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 -0.0202 0.029 102 -0.699 0.4861
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.34 0.0282 19.2 6.28 6.39
## 2010 6.36 0.0282 19.2 6.30 6.41
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 -0.0202 0.029 102 -0.0777 0.0372
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 6.35 0.0349 41.9 6.28 6.42
## S 6.32 0.0349 41.9 6.25 6.39
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 6.34 0.0349 41.9 6.26 6.41
## S 6.38 0.0349 41.9 6.30 6.45
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 0.0228 0.041 102 0.556 0.5792
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.0401 0.041 102 -0.978 0.3304
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 6.35 0.0349 41.9 6.28 6.42
## S 6.32 0.0349 41.9 6.25 6.39
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 6.34 0.0349 41.9 6.26 6.41
## S 6.38 0.0349 41.9 6.30 6.45
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0228 0.041 102 -0.0585 0.1040
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0401 0.041 102 -0.1213 0.0412
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95TP - Total phosphorus
TP D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(TP + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -91.5 -83.5 49.7 -99.5 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.72127 -0.64089 -0.02622 0.71330 1.98753
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.006836 0.08268
## Residual 0.006688 0.08178
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.61809 0.03174 11.65458 208.523 <2e-16 ***
## sampleIDS 0.04126 0.02226 45.00000 1.854 0.0703 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.351## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(TP + 1)
## Chisq Df Pr(>Chisq)
## sampleID 3.4368 1 0.06376 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.62 0.0335 13.1 6.55 6.69
## S 6.66 0.0335 13.1 6.59 6.73
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0413 0.0225 46 -1.833 0.0733
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.62 0.0335 13.1 6.55 6.69
## S 6.66 0.0335 13.1 6.59 6.73
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0413 0.0225 46 -0.0866 0.00405
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95TP D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(TP + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -73.0 -65.0 40.5 -81.0 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.2322 -0.5619 0.1041 0.5715 1.8923
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.008728 0.09342
## Residual 0.009571 0.09783
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.52555 0.03639 11.93926 179.321 <2e-16 ***
## sampleIDS 0.04004 0.02663 45.00000 1.504 0.14
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.366## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(TP + 1)
## Chisq Df Pr(>Chisq)
## sampleID 2.2618 1 0.1326## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.53 0.0384 13.4 6.44 6.61
## S 6.57 0.0384 13.4 6.48 6.65
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.04 0.0269 46 -1.487 0.1438
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.53 0.0384 13.4 6.44 6.61
## S 6.57 0.0384 13.4 6.48 6.65
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.04 0.0269 46 -0.0942 0.0142
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(TP + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -178.9 -162.8 95.4 -190.9 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.3662 -0.5701 0.1238 0.6381 1.8893
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.001758 0.04193
## Residual 0.009044 0.09510
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.68691 0.02303 30.26647 290.372 <2e-16 ***
## sampleIDS 0.07905 0.02588 99.00000 3.054 0.0029 **
## Year2010 -0.05624 0.02588 99.00000 -2.173 0.0322 *
## sampleIDS:Year2010 0.01088 0.03660 99.00000 0.297 0.7670
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.562
## Year2010 -0.562 0.500
## smIDS:Y2010 0.397 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(TP + 1)
## Chisq Df Pr(>Chisq)
## sampleID 21.3086 1 3.91e-06 ***
## Year 7.7031 1 0.005513 **
## sampleID:Year 0.0883 1 0.766360
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.66 0.02 17 6.62 6.70
## S 6.74 0.02 17 6.70 6.79
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0845 0.0186 102 -4.546 <.0001
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.66 0.02 17 6.62 6.70
## S 6.74 0.02 17 6.70 6.79
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0845 0.0186 102 -0.121 -0.0476
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.73 0.02 17 6.68 6.77
## 2010 6.68 0.02 17 6.63 6.72
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0508 0.0186 102 2.733 0.0074
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.73 0.02 17 6.68 6.77
## 2010 6.68 0.02 17 6.63 6.72
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0508 0.0186 102 0.0139 0.0877
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 6.69 0.0239 33.8 6.64 6.74
## S 6.77 0.0239 33.8 6.72 6.81
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 6.63 0.0239 33.8 6.58 6.68
## S 6.72 0.0239 33.8 6.67 6.77
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.0790 0.0263 102 -3.007 0.0033
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.0899 0.0263 102 -3.421 0.0009
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 6.69 0.0239 33.8 6.64 6.74
## S 6.77 0.0239 33.8 6.72 6.81
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 6.63 0.0239 33.8 6.58 6.68
## S 6.72 0.0239 33.8 6.67 6.77
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0790 0.0263 102 -0.131 -0.0269
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0899 0.0263 102 -0.142 -0.0378
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(TP + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -56.6 -40.5 34.3 -68.6 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -4.1247 -0.4424 -0.0857 0.4779 6.0278
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.00346 0.05882
## Residual 0.02880 0.16971
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 6.59353 0.03809 39.31082 173.087 <2e-16 ***
## sampleIDS -0.01733 0.04619 99.00000 -0.375 0.7083
## Year2010 -0.10821 0.04619 99.00000 -2.343 0.0211 *
## sampleIDS:Year2010 0.07988 0.06532 99.00000 1.223 0.2243
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.606
## Year2010 -0.606 0.500
## smIDS:Y2010 0.429 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(TP + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.4792 1 0.48879
## Year 4.3685 1 0.03661 *
## sampleID:Year 1.4955 1 0.22136
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.54 0.0317 19.8 6.47 6.61
## S 6.56 0.0317 19.8 6.50 6.63
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0226 0.0332 102 -0.682 0.4970
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 6.54 0.0317 19.8 6.47 6.61
## S 6.56 0.0317 19.8 6.50 6.63
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0226 0.0332 102 -0.0884 0.0432
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.58 0.0317 19.8 6.52 6.65
## 2010 6.52 0.0317 19.8 6.45 6.58
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0683 0.0332 102 2.058 0.0421
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 6.58 0.0317 19.8 6.52 6.65
## 2010 6.52 0.0317 19.8 6.45 6.58
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0683 0.0332 102 0.00248 0.134
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 6.59 0.0395 43.7 6.51 6.67
## S 6.58 0.0395 43.7 6.50 6.66
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 6.49 0.0395 43.7 6.41 6.56
## S 6.55 0.0395 43.7 6.47 6.63
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 0.0173 0.0469 102 0.370 0.7125
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.0625 0.0469 102 -1.334 0.1853
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 6.59 0.0395 43.7 6.51 6.67
## S 6.58 0.0395 43.7 6.50 6.66
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 6.49 0.0395 43.7 6.41 6.56
## S 6.55 0.0395 43.7 6.47 6.63
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0173 0.0469 102 -0.0757 0.1104
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0625 0.0469 102 -0.1556 0.0305
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Zn - Zinc
Zn D0 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Zn + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_0_PreStudy
##
## AIC BIC logLik deviance df.resid
## -114.1 -106.1 61.0 -122.1 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.12168 -0.48152 0.04097 0.70626 1.70375
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.005301 0.07281
## Residual 0.004280 0.06542
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.23073 0.02734 11.22970 154.742 <2e-16 ***
## sampleIDS 0.02281 0.01780 45.00000 1.281 0.207
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.326## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Zn + 1)
## Chisq Df Pr(>Chisq)
## sampleID 1.6419 1 0.2001## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4.23 0.0289 12.6 4.17 4.29
## S 4.25 0.0289 12.6 4.19 4.32
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0228 0.018 46 -1.267 0.2115
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4.23 0.0289 12.6 4.17 4.29
## S 4.25 0.0289 12.6 4.19 4.32
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0228 0.018 46 -0.0591 0.0134
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Zn D5 2008
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Zn + 1) ~ sampleID + (1 | Site)
## Data: Mins_SheepSoil_5_PreStudy
##
## AIC BIC logLik deviance df.resid
## -108.3 -100.4 58.2 -116.3 50
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.87505 -0.58628 -0.08556 0.70633 2.29720
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.007449 0.08631
## Residual 0.004571 0.06761
## Number of obs: 54, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.18495 0.03157 10.72911 132.540 <2e-16 ***
## sampleIDS 0.01051 0.01840 45.00000 0.571 0.571
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr)
## sampleIDS -0.291## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Zn + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.326 1 0.568## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4.18 0.0334 12.1 4.11 4.26
## S 4.20 0.0334 12.1 4.12 4.27
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.0105 0.0186 46 -0.565 0.5751
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4.18 0.0334 12.1 4.11 4.26
## S 4.20 0.0334 12.1 4.12 4.27
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0105 0.0186 46 -0.048 0.027
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95Overall Treatment D0
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Zn + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_0_Study)
##
## AIC BIC logLik deviance df.resid
## -179.3 -163.3 95.7 -191.3 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -2.08013 -0.59157 -0.07712 0.60690 2.73894
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.0005281 0.02298
## Residual 0.0095418 0.09768
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.290341 0.020300 54.575585 211.352 < 2e-16 ***
## sampleIDS 0.009020 0.026586 99.000000 0.339 0.73511
## Year2010 -0.082372 0.026586 99.000000 -3.098 0.00253 **
## sampleIDS:Year2010 -0.001936 0.037598 99.000000 -0.051 0.95904
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.655
## Year2010 -0.655 0.500
## smIDS:Y2010 0.463 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Zn + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.1835 1 0.6684
## Year 19.6533 1 9.284e-06 ***
## sampleID:Year 0.0027 1 0.9589
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4.25 0.016 25.1 4.22 4.28
## S 4.26 0.016 25.1 4.22 4.29
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S -0.00805 0.0191 102 -0.422 0.6741
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4.25 0.016 25.1 4.22 4.28
## S 4.26 0.016 25.1 4.22 4.29
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S -0.00805 0.0191 102 -0.0459 0.0298
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.29 0.016 25.1 4.26 4.33
## 2010 4.21 0.016 25.1 4.18 4.24
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0833 0.0191 102 4.366 <.0001
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.29 0.016 25.1 4.26 4.33
## 2010 4.21 0.016 25.1 4.18 4.24
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0833 0.0191 102 0.0455 0.121
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 4.29 0.0209 60.1 4.25 4.33
## S 4.30 0.0209 60.1 4.26 4.34
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 4.21 0.0209 60.1 4.17 4.25
## S 4.22 0.0209 60.1 4.17 4.26
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S -0.00902 0.027 102 -0.334 0.7390
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.00708 0.027 102 -0.262 0.7935
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 4.29 0.0209 60.1 4.25 4.33
## S 4.30 0.0209 60.1 4.26 4.34
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 4.21 0.0209 60.1 4.17 4.25
## S 4.22 0.0209 60.1 4.17 4.26
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.00902 0.027 102 -0.0626 0.0445
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.00708 0.027 102 -0.0606 0.0465
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95OVerall Treatment D5
## Linear mixed model fit by maximum likelihood . t-tests use Satterthwaite's
## method [lmerModLmerTest]
## Formula: log(Zn + 1) ~ sampleID + Year + sampleID * Year + (1 | Site)
## Data: subset(Mins_SheepSoil_5_Study)
##
## AIC BIC logLik deviance df.resid
## -120.2 -104.1 66.1 -132.2 102
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -5.0784 -0.4557 0.0475 0.4961 3.8071
##
## Random effects:
## Groups Name Variance Std.Dev.
## Site (Intercept) 0.002196 0.04686
## Residual 0.015869 0.12597
## Number of obs: 108, groups: Site, 9
##
## Fixed effects:
## Estimate Std. Error df t value Pr(>|t|)
## (Intercept) 4.23134 0.02884 36.51525 146.717 < 2e-16 ***
## sampleIDS -0.03345 0.03428 99.00000 -0.976 0.33165
## Year2010 -0.11543 0.03428 99.00000 -3.367 0.00108 **
## sampleIDS:Year2010 0.06372 0.04849 99.00000 1.314 0.19179
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) smpIDS Yr2010
## sampleIDS -0.594
## Year2010 -0.594 0.500
## smIDS:Y2010 0.420 -0.707 -0.707## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Zn + 1)
## Chisq Df Pr(>Chisq)
## sampleID 0.0043 1 0.947863
## Year 11.8813 1 0.000567 ***
## sampleID:Year 1.7274 1 0.188749
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4.17 0.0243 18.9 4.12 4.22
## S 4.17 0.0243 18.9 4.12 4.22
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## I - S 0.00159 0.0246 102 0.064 0.9488
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## sampleID emmean SE df lower.CL upper.CL
## I 4.17 0.0243 18.9 4.12 4.22
## S 4.17 0.0243 18.9 4.12 4.22
##
## Results are averaged over the levels of: Year
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## I - S 0.00159 0.0246 102 -0.0472 0.0504
##
## Results are averaged over the levels of: Year
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.21 0.0243 18.9 4.16 4.27
## 2010 4.13 0.0243 18.9 4.08 4.18
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Year2009 - Year2010 0.0836 0.0246 102 3.394 0.0010
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## Year emmean SE df lower.CL upper.CL
## 2009 4.21 0.0243 18.9 4.16 4.27
## 2010 4.13 0.0243 18.9 4.08 4.18
##
## Results are averaged over the levels of: sampleID
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Year2009 - Year2010 0.0836 0.0246 102 0.0347 0.132
##
## Results are averaged over the levels of: sampleID
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 4.23 0.0299 40.7 4.17 4.29
## S 4.20 0.0299 40.7 4.14 4.26
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 4.12 0.0299 40.7 4.06 4.18
## S 4.15 0.0299 40.7 4.09 4.21
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df t.ratio p.value
## I - S 0.0334 0.0348 102 0.961 0.3390
##
## Year = 2010:
## contrast estimate SE df t.ratio p.value
## I - S -0.0303 0.0348 102 -0.870 0.3865
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger## $emmeans
## Year = 2009:
## sampleID emmean SE df lower.CL upper.CL
## I 4.23 0.0299 40.7 4.17 4.29
## S 4.20 0.0299 40.7 4.14 4.26
##
## Year = 2010:
## sampleID emmean SE df lower.CL upper.CL
## I 4.12 0.0299 40.7 4.06 4.18
## S 4.15 0.0299 40.7 4.09 4.21
##
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## Year = 2009:
## contrast estimate SE df lower.CL upper.CL
## I - S 0.0334 0.0348 102 -0.0356 0.1025
##
## Year = 2010:
## contrast estimate SE df lower.CL upper.CL
## I - S -0.0303 0.0348 102 -0.0993 0.0388
##
## Note: contrasts are still on the log(mu + 1) scale. Consider using
## regrid() if you want contrasts of back-transformed estimates.
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95