Soil October Emmeans
Jonathan Spiess
October 18, 2021
Nutrients
Monthly
Ammonium
What do we do with no significant fixed effects? Just say there were no differences and move on?
The full additive plus interaction model says no significant fixed effects, and there are no TSF differences when following that with a tukey on TSF.
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.92688 0.308959 3 1061.52 1.5524 0.1994
## ESD 0.16528 0.055092 3 1061.53 0.2768 0.8422
## Treatment 0.00410 0.004099 1 72.12 0.0206 0.8863
## TSF:ESD 2.32599 0.258444 9 1059.16 1.2986 0.2331## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(NH4_ppm + 1)
## Chisq Df Pr(>Chisq)
## TSF 11.3489 3 0.009981 **
## ESD 4.4268 3 0.218916
## Treatment 0.0206 1 0.885880
## TSF:ESD 11.6871 9 0.231532
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see ?isSingular## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.86 0.106 4.87 1.59 2.14
## Intermediate 1.84 0.104 4.54 1.56 2.11
## 3 Years Since Fire 1.74 0.118 7.63 1.46 2.01
## Not Yet Burned 1.89 0.107 5.11 1.61 2.16
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate 0.0282 0.0386 1072 0.730 0.8850
## Recently Burned - 3 Years Since Fire 0.1280 0.0681 1078 1.878 0.2380
## Recently Burned - Not Yet Burned -0.0230 0.0461 1076 -0.499 0.9593
## Intermediate - 3 Years Since Fire 0.0998 0.0645 1077 1.547 0.4099
## Intermediate - Not Yet Burned -0.0512 0.0431 1080 -1.186 0.6357
## 3 Years Since Fire - Not Yet Burned -0.1510 0.0741 1084 -2.038 0.1746
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.86 0.106 4.87 1.59 2.14
## Intermediate 1.84 0.104 4.54 1.56 2.11
## 3 Years Since Fire 1.74 0.118 7.63 1.46 2.01
## Not Yet Burned 1.89 0.107 5.11 1.61 2.16
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate 0.0282 0.0386 1072 -0.0711 0.1275
## Recently Burned - 3 Years Since Fire 0.1280 0.0681 1078 -0.0473 0.3034
## Recently Burned - Not Yet Burned -0.0230 0.0461 1076 -0.1416 0.0956
## Intermediate - 3 Years Since Fire 0.0998 0.0645 1077 -0.0662 0.2659
## Intermediate - Not Yet Burned -0.0512 0.0431 1080 -0.1622 0.0598
## 3 Years Since Fire - Not Yet Burned -0.1510 0.0741 1084 -0.3416 0.0396
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.82 0.107 5.18 1.55 2.10
## Loamy 1.87 0.116 7.18 1.60 2.15
## Saline Lowland 1.81 0.108 5.21 1.54 2.08
## Sandy 1.82 0.104 4.55 1.54 2.09
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.04738 0.0682 1076 -0.695 0.8990
## Clayey - Saline Lowland 0.01457 0.0524 1076 0.278 0.9925
## Clayey - Sandy 0.00488 0.0436 1073 0.112 0.9995
## Loamy - Saline Lowland 0.06195 0.0717 1076 0.864 0.8233
## Loamy - Sandy 0.05226 0.0620 1076 0.843 0.8337
## Saline Lowland - Sandy -0.00969 0.0440 1076 -0.220 0.9962
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.82 0.107 5.18 1.55 2.10
## Loamy 1.87 0.116 7.18 1.60 2.15
## Saline Lowland 1.81 0.108 5.21 1.54 2.08
## Sandy 1.82 0.104 4.55 1.54 2.09
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.04738 0.0682 1076 -0.223 0.128
## Clayey - Saline Lowland 0.01457 0.0524 1076 -0.120 0.149
## Clayey - Sandy 0.00488 0.0436 1073 -0.107 0.117
## Loamy - Saline Lowland 0.06195 0.0717 1076 -0.123 0.246
## Loamy - Sandy 0.05226 0.0620 1076 -0.107 0.212
## Saline Lowland - Sandy -0.00969 0.0440 1076 -0.123 0.103
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesThe previous model I was using as the best model for Ammonium (TSF only) does show a significant effect for TSF with recently burned and not yet burned being higher than 3 years since fire.
Nitrate
None again. Previously, additive and the two single term models were better than null
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.49676 0.16559 3 1086.58 0.8732 0.45440
## ESD 1.45867 0.48622 3 1074.33 2.5640 0.05339 .
## Treatment 0.37349 0.37349 1 24.29 1.9696 0.17315
## TSF:ESD 2.56257 0.28473 9 1074.77 1.5015 0.14236
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(NO3_ppm + 1)
## Chisq Df Pr(>Chisq)
## TSF 9.2887 3 0.02569 *
## ESD 9.4251 3 0.02414 *
## Treatment 1.9696 1 0.16049
## TSF:ESD 13.5133 9 0.14072
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.58 0.0549 8.42 1.45 1.71
## Intermediate 1.54 0.0514 6.41 1.42 1.67
## 3 Years Since Fire 1.48 0.0747 30.14 1.33 1.64
## Not Yet Burned 1.54 0.0570 9.85 1.41 1.67
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate 0.03807 0.0376 1079 1.013 0.7421
## Recently Burned - 3 Years Since Fire 0.09653 0.0659 1107 1.465 0.4593
## Recently Burned - Not Yet Burned 0.04121 0.0447 1100 0.922 0.7929
## Intermediate - 3 Years Since Fire 0.05846 0.0625 1105 0.936 0.7856
## Intermediate - Not Yet Burned 0.00314 0.0416 1115 0.075 0.9998
## 3 Years Since Fire - Not Yet Burned -0.05532 0.0709 1119 -0.780 0.8636
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.58 0.0549 8.42 1.45 1.71
## Intermediate 1.54 0.0514 6.41 1.42 1.67
## 3 Years Since Fire 1.48 0.0747 30.14 1.33 1.64
## Not Yet Burned 1.54 0.0570 9.85 1.41 1.67
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate 0.03807 0.0376 1079 -0.0587 0.135
## Recently Burned - 3 Years Since Fire 0.09653 0.0659 1107 -0.0730 0.266
## Recently Burned - Not Yet Burned 0.04121 0.0447 1100 -0.0738 0.156
## Intermediate - 3 Years Since Fire 0.05846 0.0625 1105 -0.1023 0.219
## Intermediate - Not Yet Burned 0.00314 0.0416 1115 -0.1038 0.110
## 3 Years Since Fire - Not Yet Burned -0.05532 0.0709 1119 -0.2379 0.127
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.52 0.0578 10.47 1.39 1.65
## Loamy 1.54 0.0727 25.31 1.39 1.69
## Saline Lowland 1.60 0.0581 10.51 1.47 1.73
## Sandy 1.48 0.0516 6.53 1.36 1.61
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.0179 0.0664 1077 -0.269 0.9932
## Clayey - Saline Lowland -0.0752 0.0510 1073 -1.473 0.4543
## Clayey - Sandy 0.0393 0.0426 1078 0.923 0.7924
## Loamy - Saline Lowland -0.0573 0.0698 993 -0.821 0.8445
## Loamy - Sandy 0.0572 0.0604 1065 0.947 0.7797
## Saline Lowland - Sandy 0.1145 0.0429 1073 2.670 0.0385
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.52 0.0578 10.47 1.39 1.65
## Loamy 1.54 0.0727 25.31 1.39 1.69
## Saline Lowland 1.60 0.0581 10.51 1.47 1.73
## Sandy 1.48 0.0516 6.53 1.36 1.61
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.0179 0.0664 1077 -0.18868 0.1530
## Clayey - Saline Lowland -0.0752 0.0510 1073 -0.20649 0.0561
## Clayey - Sandy 0.0393 0.0426 1078 -0.07022 0.1488
## Loamy - Saline Lowland -0.0573 0.0698 993 -0.23696 0.1223
## Loamy - Sandy 0.0572 0.0604 1065 -0.09822 0.2125
## Saline Lowland - Sandy 0.1145 0.0429 1073 0.00417 0.2248
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesMoisture
TSF and ES are significant, but not the interaction
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.7172 0.23906 3 708.56 5.0979 0.001699 **
## ESD 4.6080 1.53599 3 707.24 32.7545 < 2.2e-16 ***
## Treatment 0.0010 0.00099 1 5.96 0.0212 0.889163
## TSF:ESD 0.6950 0.07722 9 707.54 1.6468 0.098323 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Moisture + 1)
## Chisq Df Pr(>Chisq)
## TSF 29.3994 3 1.846e-06 ***
## ESD 146.8851 3 < 2.2e-16 ***
## Treatment 0.0212 1 0.88437
## TSF:ESD 14.8210 9 0.09597 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.53 0.0741 10.73 2.37 2.69
## Intermediate 2.55 0.0727 9.58 2.39 2.72
## 3 Years Since Fire 2.57 0.0772 13.52 2.40 2.73
## Not Yet Burned 2.43 0.0772 13.48 2.27 2.60
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate -0.0235 0.0229 720 -1.023 0.7363
## Recently Burned - 3 Years Since Fire -0.0388 0.0346 725 -1.121 0.6766
## Recently Burned - Not Yet Burned 0.0947 0.0348 726 2.722 0.0335
## Intermediate - 3 Years Since Fire -0.0154 0.0317 726 -0.484 0.9626
## Intermediate - Not Yet Burned 0.1182 0.0314 726 3.768 0.0010
## 3 Years Since Fire - Not Yet Burned 0.1336 0.0429 732 3.110 0.0105
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 2.53 0.0741 10.73 2.37 2.69
## Intermediate 2.55 0.0727 9.58 2.39 2.72
## 3 Years Since Fire 2.57 0.0772 13.52 2.40 2.73
## Not Yet Burned 2.43 0.0772 13.48 2.27 2.60
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate -0.0235 0.0229 720 -0.08256 0.0356
## Recently Burned - 3 Years Since Fire -0.0388 0.0346 725 -0.12797 0.0503
## Recently Burned - Not Yet Burned 0.0947 0.0348 726 0.00512 0.1843
## Intermediate - 3 Years Since Fire -0.0154 0.0317 726 -0.09701 0.0663
## Intermediate - Not Yet Burned 0.1182 0.0314 726 0.03742 0.1990
## 3 Years Since Fire - Not Yet Burned 0.1336 0.0429 732 0.02296 0.2441
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 2.53 0.0749 11.39 2.37 2.70
## Loamy 2.54 0.0797 16.02 2.37 2.71
## Saline Lowland 2.62 0.0743 10.89 2.46 2.78
## Sandy 2.39 0.0730 9.79 2.23 2.56
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.00425 0.0420 724 -0.101 0.9996
## Clayey - Saline Lowland -0.08566 0.0305 724 -2.806 0.0264
## Clayey - Sandy 0.14091 0.0267 721 5.285 <.0001
## Loamy - Saline Lowland -0.08141 0.0425 726 -1.914 0.2229
## Loamy - Sandy 0.14515 0.0375 724 3.869 0.0007
## Saline Lowland - Sandy 0.22657 0.0249 723 9.106 <.0001
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 2.53 0.0749 11.39 2.37 2.70
## Loamy 2.54 0.0797 16.02 2.37 2.71
## Saline Lowland 2.62 0.0743 10.89 2.46 2.78
## Sandy 2.39 0.0730 9.79 2.23 2.56
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.00425 0.0420 724 -0.1123 0.10384
## Clayey - Saline Lowland -0.08566 0.0305 724 -0.1643 -0.00706
## Clayey - Sandy 0.14091 0.0267 721 0.0722 0.20957
## Loamy - Saline Lowland -0.08141 0.0425 726 -0.1909 0.02811
## Loamy - Sandy 0.14515 0.0375 724 0.0486 0.24175
## Saline Lowland - Sandy 0.22657 0.0249 723 0.1625 0.29063
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesSingle
Total C
Only ES
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.21102 0.07034 3 266.841 2.3095 0.07674 .
## ESD 2.19913 0.73304 3 272.518 24.0682 7.562e-14 ***
## Treatment 0.03568 0.03568 1 5.866 1.1715 0.32157
## TSF:ESD 0.12070 0.01341 9 272.748 0.4403 0.91241
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(TotalC_percent + 1)
## Chisq Df Pr(>Chisq)
## TSF 9.8728 3 0.01968 *
## ESD 89.7766 3 < 2e-16 ***
## Treatment 1.1715 1 0.27910
## TSF:ESD 3.9631 9 0.91383
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.046 0.0527 20.4 0.936 1.16
## Loamy 1.116 0.0637 46.8 0.988 1.24
## Saline Lowland 1.193 0.0527 20.2 1.083 1.30
## Sandy 0.926 0.0481 12.8 0.822 1.03
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.0699 0.0542 292 -1.291 0.5695
## Clayey - Saline Lowland -0.1471 0.0417 293 -3.530 0.0027
## Clayey - Sandy 0.1203 0.0349 283 3.446 0.0036
## Loamy - Saline Lowland -0.0772 0.0569 296 -1.357 0.5276
## Loamy - Sandy 0.1903 0.0493 291 3.862 0.0008
## Saline Lowland - Sandy 0.2675 0.0350 290 7.645 <.0001
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.046 0.0527 20.4 0.936 1.16
## Loamy 1.116 0.0637 46.8 0.988 1.24
## Saline Lowland 1.193 0.0527 20.2 1.083 1.30
## Sandy 0.926 0.0481 12.8 0.822 1.03
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.0699 0.0542 292 -0.2099 0.0700
## Clayey - Saline Lowland -0.1471 0.0417 293 -0.2548 -0.0394
## Clayey - Sandy 0.1203 0.0349 283 0.0301 0.2106
## Loamy - Saline Lowland -0.0772 0.0569 296 -0.2242 0.0698
## Loamy - Sandy 0.1903 0.0493 291 0.0630 0.3176
## Saline Lowland - Sandy 0.2675 0.0350 290 0.1771 0.3579
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesTotal N
ES is significant, but not the interaction
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.015620 0.005207 3 273.805 2.6323 0.05035 .
## ESD 0.119864 0.039955 3 269.278 20.1993 7.742e-12 ***
## Treatment 0.000833 0.000833 1 5.873 0.4211 0.54091
## TSF:ESD 0.006790 0.000754 9 271.103 0.3814 0.94350
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: TotalN_percent
## Chisq Df Pr(>Chisq)
## TSF 7.9300 3 0.04748 *
## ESD 79.2383 3 < 2e-16 ***
## Treatment 0.4211 1 0.51638
## TSF:ESD 3.4328 9 0.94465
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 0.208 0.0137 19.9 0.179 0.236
## Loamy 0.210 0.0164 45.1 0.177 0.243
## Saline Lowland 0.236 0.0137 19.8 0.207 0.265
## Sandy 0.173 0.0125 12.6 0.146 0.200
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Clayey - Loamy -0.00255 0.01386 289 -0.184 0.9978
## Clayey - Saline Lowland -0.02816 0.01066 290 -2.641 0.0430
## Clayey - Sandy 0.03487 0.00891 282 3.912 0.0007
## Loamy - Saline Lowland -0.02561 0.01455 293 -1.760 0.2951
## Loamy - Sandy 0.03742 0.01259 289 2.972 0.0168
## Saline Lowland - Sandy 0.06303 0.00894 288 7.050 <.0001
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## ESD emmean SE df lower.CL upper.CL
## Clayey 0.208 0.0137 19.9 0.179 0.236
## Loamy 0.210 0.0164 45.1 0.177 0.243
## Saline Lowland 0.236 0.0137 19.8 0.207 0.265
## Sandy 0.173 0.0125 12.6 0.146 0.200
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Clayey - Loamy -0.00255 0.01386 289 -0.03837 0.033260
## Clayey - Saline Lowland -0.02816 0.01066 290 -0.05572 -0.000609
## Clayey - Sandy 0.03487 0.00891 282 0.01183 0.057902
## Loamy - Saline Lowland -0.02561 0.01455 293 -0.06321 0.011998
## Loamy - Sandy 0.03742 0.01259 289 0.00488 0.069962
## Saline Lowland - Sandy 0.06303 0.00894 288 0.03993 0.086135
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesP
Only ESD is significant
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.7098 0.23661 3 273.317 1.8472 0.1389
## ESD 8.6897 2.89657 3 268.710 22.6133 4.375e-13 ***
## Treatment 0.0012 0.00121 1 5.784 0.0095 0.9257
## TSF:ESD 0.9067 0.10075 9 269.885 0.7865 0.6290
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(P_ppm + 1)
## Chisq Df Pr(>Chisq)
## TSF 4.6979 3 0.1953
## ESD 92.3567 3 <2e-16 ***
## Treatment 0.0095 1 0.9225
## TSF:ESD 7.0787 9 0.6289
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 2.15 0.112 19.7 1.92 2.39
## Loamy 2.06 0.134 44.0 1.79 2.33
## Saline Lowland 2.16 0.112 19.6 1.93 2.39
## Sandy 1.71 0.103 12.6 1.49 1.93
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy 0.08976 0.1116 288 0.804 0.8525
## Clayey - Saline Lowland -0.00766 0.0859 288 -0.089 0.9997
## Clayey - Sandy 0.44260 0.0717 282 6.169 <.0001
## Loamy - Saline Lowland -0.09742 0.1172 292 -0.831 0.8397
## Loamy - Sandy 0.35284 0.1014 288 3.479 0.0032
## Saline Lowland - Sandy 0.45026 0.0720 287 6.253 <.0001
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 2.15 0.112 19.7 1.92 2.39
## Loamy 2.06 0.134 44.0 1.79 2.33
## Saline Lowland 2.16 0.112 19.6 1.93 2.39
## Sandy 1.71 0.103 12.6 1.49 1.93
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy 0.08976 0.1116 288 -0.1987 0.378
## Clayey - Saline Lowland -0.00766 0.0859 288 -0.2296 0.214
## Clayey - Sandy 0.44260 0.0717 282 0.2572 0.628
## Loamy - Saline Lowland -0.09742 0.1172 292 -0.4004 0.206
## Loamy - Sandy 0.35284 0.1014 288 0.0908 0.615
## Saline Lowland - Sandy 0.45026 0.0720 287 0.2642 0.636
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesK
TSF and ESD are significant, not interaction
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 1.3257 0.44189 3 278.188 5.4567 0.001169 **
## ESD 4.4516 1.48388 3 273.355 18.3236 7.32e-11 ***
## Treatment 0.1071 0.10713 1 15.616 1.3228 0.267392
## TSF:ESD 0.2951 0.03279 9 273.855 0.4049 0.931976
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(K_ppm + 1)
## Chisq Df Pr(>Chisq)
## TSF 17.4881 3 0.0005608 ***
## ESD 76.5347 3 < 2.2e-16 ***
## Treatment 1.3228 1 0.2500830
## TSF:ESD 3.6442 9 0.9332330
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see ?isSingular## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 5.84 0.0473 29.9 5.74 5.93
## Intermediate 5.84 0.0401 15.1 5.75 5.92
## 3 Years Since Fire 5.91 0.0821 166.6 5.75 6.07
## Not Yet Burned 5.65 0.0513 39.2 5.54 5.75
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate 0.00042 0.0499 283 0.008 1.0000
## Recently Burned - 3 Years Since Fire -0.07039 0.0873 295 -0.806 0.8514
## Recently Burned - Not Yet Burned 0.18933 0.0592 293 3.201 0.0082
## Intermediate - 3 Years Since Fire -0.07081 0.0830 295 -0.853 0.8287
## Intermediate - Not Yet Burned 0.18891 0.0548 294 3.445 0.0036
## 3 Years Since Fire - Not Yet Burned 0.25972 0.0933 281 2.784 0.0291
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 5.84 0.0473 29.9 5.74 5.93
## Intermediate 5.84 0.0401 15.1 5.75 5.92
## 3 Years Since Fire 5.91 0.0821 166.6 5.75 6.07
## Not Yet Burned 5.65 0.0513 39.2 5.54 5.75
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate 0.00042 0.0499 283 -0.1285 0.129
## Recently Burned - 3 Years Since Fire -0.07039 0.0873 295 -0.2959 0.155
## Recently Burned - Not Yet Burned 0.18933 0.0592 293 0.0365 0.342
## Intermediate - 3 Years Since Fire -0.07081 0.0830 295 -0.2852 0.144
## Intermediate - Not Yet Burned 0.18891 0.0548 294 0.0472 0.331
## 3 Years Since Fire - Not Yet Burned 0.25972 0.0933 281 0.0186 0.501
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 5.85 0.0536 45.1 5.74 5.95
## Loamy 5.90 0.0790 97.5 5.74 6.06
## Saline Lowland 5.91 0.0537 38.8 5.80 6.02
## Sandy 5.58 0.0406 16.3 5.49 5.66
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.0532 0.0884 283 -0.602 0.9315
## Clayey - Saline Lowland -0.0621 0.0680 280 -0.913 0.7979
## Clayey - Sandy 0.2686 0.0570 285 4.714 <.0001
## Loamy - Saline Lowland -0.0089 0.0924 221 -0.096 0.9997
## Loamy - Sandy 0.3218 0.0802 275 4.011 0.0005
## Saline Lowland - Sandy 0.3307 0.0570 282 5.802 <.0001
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 5.85 0.0536 45.1 5.74 5.95
## Loamy 5.90 0.0790 97.5 5.74 6.06
## Saline Lowland 5.91 0.0537 38.8 5.80 6.02
## Sandy 5.58 0.0406 16.3 5.49 5.66
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.0532 0.0884 283 -0.282 0.175
## Clayey - Saline Lowland -0.0621 0.0680 280 -0.238 0.114
## Clayey - Sandy 0.2686 0.0570 285 0.121 0.416
## Loamy - Saline Lowland -0.0089 0.0924 221 -0.248 0.230
## Loamy - Sandy 0.3218 0.0802 275 0.114 0.529
## Saline Lowland - Sandy 0.3307 0.0570 282 0.183 0.478
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesCa
ESD only
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.30693 0.10231 3 270.669 0.4929 0.68750
## ESD 2.12863 0.70954 3 271.249 3.4183 0.01786 *
## Treatment 0.18762 0.18762 1 5.814 0.9039 0.37957
## TSF:ESD 1.81592 0.20177 9 272.647 0.9721 0.46342
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Ca_ppm + 1)
## Chisq Df Pr(>Chisq)
## TSF 3.7560 3 0.289044
## ESD 14.0493 3 0.002839 **
## Treatment 0.9039 1 0.341747
## TSF:ESD 8.7485 9 0.460805
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 7.32 0.150 17.9 7.00 7.63
## Loamy 7.67 0.177 37.9 7.31 8.03
## Saline Lowland 7.46 0.151 17.8 7.15 7.78
## Sandy 7.56 0.140 12.1 7.26 7.87
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.3560 0.1416 291 -2.513 0.0599
## Clayey - Saline Lowland -0.1485 0.1090 291 -1.363 0.5236
## Clayey - Sandy -0.2483 0.0912 283 -2.722 0.0346
## Loamy - Saline Lowland 0.2074 0.1487 294 1.395 0.5037
## Loamy - Sandy 0.1077 0.1288 290 0.836 0.8370
## Saline Lowland - Sandy -0.0997 0.0914 289 -1.091 0.6954
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 7.32 0.150 17.9 7.00 7.63
## Loamy 7.67 0.177 37.9 7.31 8.03
## Saline Lowland 7.46 0.151 17.8 7.15 7.78
## Sandy 7.56 0.140 12.1 7.26 7.87
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.3560 0.1416 291 -0.722 0.0100
## Clayey - Saline Lowland -0.1485 0.1090 291 -0.430 0.1330
## Clayey - Sandy -0.2483 0.0912 283 -0.484 -0.0125
## Loamy - Saline Lowland 0.2074 0.1487 294 -0.177 0.5918
## Loamy - Sandy 0.1077 0.1288 290 -0.225 0.4404
## Saline Lowland - Sandy -0.0997 0.0914 289 -0.336 0.1365
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesMg
ESD only, interaction borderline
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.12304 0.04101 3 273.55 0.3996 0.75337
## ESD 0.99569 0.33190 3 268.53 3.2340 0.02282 *
## Treatment 0.00554 0.00554 1 5.60 0.0540 0.82448
## TSF:ESD 1.75811 0.19535 9 270.99 1.9034 0.05155 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Mg_ppm + 1)
## Chisq Df Pr(>Chisq)
## TSF 4.1508 3 0.2456291
## ESD 18.7579 3 0.0003068 ***
## Treatment 0.0540 1 0.8162228
## TSF:ESD 17.1309 9 0.0467048 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 5.81 0.0790 34.3 5.65 5.97
## Loamy 5.80 0.1029 87.8 5.59 6.00
## Saline Lowland 5.86 0.0793 33.2 5.70 6.02
## Sandy 5.68 0.0685 17.0 5.54 5.83
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy 0.0111 0.0998 291 0.111 0.9995
## Clayey - Saline Lowland -0.0509 0.0768 292 -0.662 0.9112
## Clayey - Sandy 0.1220 0.0642 284 1.900 0.2303
## Loamy - Saline Lowland -0.0619 0.1048 292 -0.591 0.9348
## Loamy - Sandy 0.1109 0.0907 291 1.223 0.6127
## Saline Lowland - Sandy 0.1728 0.0644 290 2.684 0.0383
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 5.81 0.0790 34.3 5.65 5.97
## Loamy 5.80 0.1029 87.8 5.59 6.00
## Saline Lowland 5.86 0.0793 33.2 5.70 6.02
## Sandy 5.68 0.0685 17.0 5.54 5.83
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy 0.0111 0.0998 291 -0.24694 0.269
## Clayey - Saline Lowland -0.0509 0.0768 292 -0.24934 0.148
## Clayey - Sandy 0.1220 0.0642 284 -0.04393 0.288
## Loamy - Saline Lowland -0.0619 0.1048 292 -0.33273 0.209
## Loamy - Sandy 0.1109 0.0907 291 -0.12343 0.345
## Saline Lowland - Sandy 0.1728 0.0644 290 0.00644 0.339
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesDecomp
ESD only, interaction borderline
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 2883.97 961.32 3 232.42 5.6547 0.0009349 ***
## ESD 1711.08 570.36 3 237.91 3.3550 0.0196276 *
## Treatment 63.57 63.57 1 237.85 0.3740 0.5414380
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Decomp
## Chisq Df Pr(>Chisq)
## TSF 16.964 3 0.0007188 ***
## ESD 10.065 3 0.0180218 *
## Treatment 0.374 1 0.5408540
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 54.4 4.19 7.05 44.5 64.3
## Intermediate 60.6 4.06 5.55 50.5 70.8
## 3 Years Since Fire 57.8 4.77 15.12 47.6 67.9
## Not Yet Burned 51.4 4.63 12.86 41.3 61.4
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -6.24 2.07 246 -3.016 0.0149
## Recently Burned - 3 Years Since Fire -3.36 3.24 249 -1.037 0.7278
## Recently Burned - Not Yet Burned 3.03 3.02 249 1.003 0.7475
## Intermediate - 3 Years Since Fire 2.88 3.18 249 0.907 0.8009
## Intermediate - Not Yet Burned 9.28 2.77 249 3.354 0.0051
## 3 Years Since Fire - Not Yet Burned 6.39 4.09 246 1.564 0.4010
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 54.4 4.19 7.05 44.5 64.3
## Intermediate 60.6 4.06 5.55 50.5 70.8
## 3 Years Since Fire 57.8 4.77 15.12 47.6 67.9
## Not Yet Burned 51.4 4.63 12.86 41.3 61.4
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -6.24 2.07 246 -11.60 -0.889
## Recently Burned - 3 Years Since Fire -3.36 3.24 249 -11.74 5.020
## Recently Burned - Not Yet Burned 3.03 3.02 249 -4.79 10.854
## Intermediate - 3 Years Since Fire 2.88 3.18 249 -5.33 11.098
## Intermediate - Not Yet Burned 9.28 2.77 249 2.12 16.431
## 3 Years Since Fire - Not Yet Burned 6.39 4.09 246 -4.18 16.968
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 53.1 4.46 10.90 43.3 62.9
## Loamy 61.4 4.54 12.19 51.5 71.3
## Saline Lowland 56.2 4.21 7.27 46.3 66.1
## Sandy 53.5 4.09 5.94 43.4 63.5
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Clayey - Loamy -8.279 3.30 245 -2.512 0.0605
## Clayey - Saline Lowland -3.066 2.81 245 -1.091 0.6954
## Clayey - Sandy -0.357 2.67 245 -0.134 0.9991
## Loamy - Saline Lowland 5.213 2.84 245 1.838 0.2580
## Loamy - Sandy 7.922 2.70 245 2.932 0.0192
## Saline Lowland - Sandy 2.709 2.09 245 1.293 0.5682
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 53.1 4.46 10.90 43.3 62.9
## Loamy 61.4 4.54 12.19 51.5 71.3
## Saline Lowland 56.2 4.21 7.27 46.3 66.1
## Sandy 53.5 4.09 5.94 43.4 63.5
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Clayey - Loamy -8.279 3.30 245 -16.804 0.246
## Clayey - Saline Lowland -3.066 2.81 245 -10.335 4.204
## Clayey - Sandy -0.357 2.67 245 -7.260 6.546
## Loamy - Saline Lowland 5.213 2.84 245 -2.123 12.549
## Loamy - Sandy 7.922 2.70 245 0.933 14.911
## Saline Lowland - Sandy 2.709 2.09 245 -2.710 8.127
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = Decomp ~ TSF + ESD + Treatment + (1 | Year), data = LitBag,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 6.243 2.034 3.069 0.01102
## 3 Years Since Fire - Recently Burned == 0 3.361 3.151 1.067 0.69929
## Not Yet Burned - Recently Burned == 0 -3.034 2.919 -1.039 0.71588
## 3 Years Since Fire - Intermediate == 0 -2.883 3.058 -0.942 0.77308
## Not Yet Burned - Intermediate == 0 -9.277 2.689 -3.451 0.00278
## Not Yet Burned - 3 Years Since Fire == 0 -6.395 3.871 -1.652 0.33715
##
## Intermediate - Recently Burned == 0 *
## 3 Years Since Fire - Recently Burned == 0
## Not Yet Burned - Recently Burned == 0
## 3 Years Since Fire - Intermediate == 0
## Not Yet Burned - Intermediate == 0 **
## Not Yet Burned - 3 Years Since Fire == 0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)##
## Simultaneous Confidence Intervals
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = Decomp ~ TSF + ESD + Treatment + (1 | Year), data = LitBag,
## REML = FALSE)
##
## Quantile = 2.5447
## 95% family-wise confidence level
##
##
## Linear Hypotheses:
## Estimate lwr upr
## Intermediate - Recently Burned == 0 6.2432 1.0672 11.4192
## 3 Years Since Fire - Recently Burned == 0 3.3607 -4.6577 11.3791
## Not Yet Burned - Recently Burned == 0 -3.0340 -10.4612 4.3933
## 3 Years Since Fire - Intermediate == 0 -2.8825 -10.6652 4.9002
## Not Yet Burned - Intermediate == 0 -9.2772 -16.1186 -2.4358
## Not Yet Burned - 3 Years Since Fire == 0 -6.3947 -16.2462 3.4568##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = Decomp ~ TSF + ESD + Treatment + (1 | Year), data = LitBag,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 8.2789 3.2472 2.550 0.0509 .
## Saline Lowland - Clayey == 0 3.0658 2.7686 1.107 0.6797
## Sandy - Clayey == 0 0.3572 2.6293 0.136 0.9991
## Saline Lowland - Loamy == 0 -5.2131 2.7931 -1.866 0.2375
## Sandy - Loamy == 0 -7.9217 2.6619 -2.976 0.0151 *
## Sandy - Saline Lowland == 0 -2.7086 2.0635 -1.313 0.5486
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)##
## Simultaneous Confidence Intervals
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = Decomp ~ TSF + ESD + Treatment + (1 | Year), data = LitBag,
## REML = FALSE)
##
## Quantile = 2.5575
## 95% family-wise confidence level
##
##
## Linear Hypotheses:
## Estimate lwr upr
## Loamy - Clayey == 0 8.2789 -0.0258 16.5836
## Saline Lowland - Clayey == 0 3.0658 -4.0149 10.1465
## Sandy - Clayey == 0 0.3572 -6.3673 7.0817
## Saline Lowland - Loamy == 0 -5.2131 -12.3564 1.9301
## Sandy - Loamy == 0 -7.9217 -14.7295 -1.1139
## Sandy - Saline Lowland == 0 -2.7086 -7.9860 2.5688pH
ES, TSF, and interaction
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 4.2821 2.14105 2 370.15 7.5277 0.0006245 ***
## ESD 3.8088 1.26962 3 373.30 4.4638 0.0042742 **
## Treatment 0.0053 0.00528 1 5.78 0.0186 0.8962392
## TSF:ESD 7.3079 1.21799 6 372.31 4.2823 0.0003446 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: pH
## Chisq Df Pr(>Chisq)
## TSF 23.4800 2 7.969e-06 ***
## ESD 21.2182 3 9.484e-05 ***
## Treatment 0.0186 1 0.8916147
## TSF:ESD 25.6939 6 0.0002539 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see ?isSingular## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.52 0.147 16.1 6.21 6.83
## Intermediate 6.81 0.139 11.5 6.50 7.11
## 3 Years Since Fire 6.81 0.148 16.4 6.50 7.13
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.28908 0.0804 363 -3.595 0.0011
## Recently Burned - 3 Years Since Fire -0.29557 0.0946 363 -3.124 0.0055
## Intermediate - 3 Years Since Fire -0.00649 0.0817 363 -0.079 0.9965
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.52 0.147 16.1 6.21 6.83
## Intermediate 6.81 0.139 11.5 6.50 7.11
## 3 Years Since Fire 6.81 0.148 16.4 6.50 7.13
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.28908 0.0804 363 -0.478 -0.0999
## Recently Burned - 3 Years Since Fire -0.29557 0.0946 363 -0.518 -0.0729
## Intermediate - 3 Years Since Fire -0.00649 0.0817 363 -0.199 0.1858
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 6.49 0.148 16.6 6.18 6.80
## Loamy 6.85 0.173 34.3 6.50 7.20
## Saline Lowland 6.74 0.146 15.1 6.43 7.05
## Sandy 6.76 0.139 11.6 6.46 7.07
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Clayey - Loamy -0.3650 0.1337 371 -2.729 0.0335
## Clayey - Saline Lowland -0.2544 0.0972 369 -2.619 0.0452
## Clayey - Sandy -0.2744 0.0848 367 -3.238 0.0072
## Loamy - Saline Lowland 0.1106 0.1387 371 0.797 0.8556
## Loamy - Sandy 0.0905 0.1201 371 0.754 0.8749
## Saline Lowland - Sandy -0.0200 0.0807 369 -0.248 0.9946
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 6.49 0.148 16.6 6.18 6.80
## Loamy 6.85 0.173 34.3 6.50 7.20
## Saline Lowland 6.74 0.146 15.1 6.43 7.05
## Sandy 6.76 0.139 11.6 6.46 7.07
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Clayey - Loamy -0.3650 0.1337 371 -0.710 -0.0199
## Clayey - Saline Lowland -0.2544 0.0972 369 -0.505 -0.0037
## Clayey - Sandy -0.2744 0.0848 367 -0.493 -0.0557
## Loamy - Saline Lowland 0.1106 0.1387 371 -0.247 0.4684
## Loamy - Sandy 0.0905 0.1201 371 -0.219 0.4005
## Saline Lowland - Sandy -0.0200 0.0807 369 -0.228 0.1882
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular## $emmeans
## ESD = Clayey:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.34 0.188 52.8 5.96 6.72
## Intermediate 6.31 0.168 31.6 5.97 6.65
## 3 Years Since Fire 6.82 0.173 35.8 6.47 7.17
##
## ESD = Loamy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.60 0.244 134.5 6.12 7.09
## Intermediate 6.99 0.174 37.4 6.63 7.34
## 3 Years Since Fire 6.97 0.244 134.5 6.49 7.45
##
## ESD = Saline Lowland:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.44 0.164 27.8 6.11 6.78
## Intermediate 7.06 0.148 16.6 6.75 7.38
## 3 Years Since Fire 6.72 0.194 58.9 6.34 7.11
##
## ESD = Sandy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.69 0.159 24.1 6.36 7.01
## Intermediate 6.87 0.148 16.6 6.55 7.18
## 3 Years Since Fire 6.74 0.152 19.4 6.42 7.06
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## ESD = Clayey:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 0.0302 0.170 371 0.178 0.9827
## Recently Burned - 3 Years Since Fire -0.4818 0.175 374 -2.761 0.0166
## Intermediate - 3 Years Since Fire -0.5121 0.153 366 -3.345 0.0026
##
## ESD = Loamy:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.3846 0.230 365 -1.671 0.2176
## Recently Burned - 3 Years Since Fire -0.3663 0.271 362 -1.353 0.3668
## Intermediate - 3 Years Since Fire 0.0183 0.230 365 0.080 0.9965
##
## ESD = Saline Lowland:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.6214 0.119 364 -5.234 <.0001
## Recently Burned - 3 Years Since Fire -0.2805 0.170 365 -1.651 0.2259
## Intermediate - 3 Years Since Fire 0.3409 0.156 365 2.192 0.0739
##
## ESD = Sandy:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.1806 0.113 364 -1.594 0.2493
## Recently Burned - 3 Years Since Fire -0.0537 0.119 363 -0.450 0.8946
## Intermediate - 3 Years Since Fire 0.1269 0.105 363 1.214 0.4459
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 3 estimates## boundary (singular) fit: see ?isSingular## $emmeans
## ESD = Clayey:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.34 0.188 52.8 5.96 6.72
## Intermediate 6.31 0.168 31.6 5.97 6.65
## 3 Years Since Fire 6.82 0.173 35.8 6.47 7.17
##
## ESD = Loamy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.60 0.244 134.5 6.12 7.09
## Intermediate 6.99 0.174 37.4 6.63 7.34
## 3 Years Since Fire 6.97 0.244 134.5 6.49 7.45
##
## ESD = Saline Lowland:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.44 0.164 27.8 6.11 6.78
## Intermediate 7.06 0.148 16.6 6.75 7.38
## 3 Years Since Fire 6.72 0.194 58.9 6.34 7.11
##
## ESD = Sandy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.69 0.159 24.1 6.36 7.01
## Intermediate 6.87 0.148 16.6 6.55 7.18
## 3 Years Since Fire 6.74 0.152 19.4 6.42 7.06
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## ESD = Clayey:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 0.0302 0.170 371 -0.3696 0.4300
## Recently Burned - 3 Years Since Fire -0.4818 0.175 374 -0.8925 -0.0712
## Intermediate - 3 Years Since Fire -0.5121 0.153 366 -0.8723 -0.1518
##
## ESD = Loamy:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.3846 0.230 365 -0.9260 0.1569
## Recently Burned - 3 Years Since Fire -0.3663 0.271 362 -1.0032 0.2707
## Intermediate - 3 Years Since Fire 0.0183 0.230 365 -0.5231 0.5597
##
## ESD = Saline Lowland:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.6214 0.119 364 -0.9008 -0.3420
## Recently Burned - 3 Years Since Fire -0.2805 0.170 365 -0.6805 0.1194
## Intermediate - 3 Years Since Fire 0.3409 0.156 365 -0.0251 0.7068
##
## ESD = Sandy:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.1806 0.113 364 -0.4471 0.0860
## Recently Burned - 3 Years Since Fire -0.0537 0.119 363 -0.3345 0.2272
## Intermediate - 3 Years Since Fire 0.1269 0.105 363 -0.1192 0.3730
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimatesEC
ESD and TSF, no interaction
## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 3.5251 1.76256 2 370.40 3.8418 0.022315 *
## ESD 5.4455 1.81515 3 363.62 3.9564 0.008502 **
## Treatment 0.0149 0.01488 1 5.62 0.0324 0.863384
## TSF:ESD 5.3452 0.89086 6 373.91 1.9418 0.073211 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(EC + 1)
## Chisq Df Pr(>Chisq)
## TSF 15.6211 2 0.0004054 ***
## ESD 20.7851 3 0.0001167 ***
## Treatment 0.0324 1 0.8570705
## TSF:ESD 11.6507 6 0.0702314 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## boundary (singular) fit: see ?isSingular## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 5.08 0.142 26.0 4.79 5.37
## Intermediate 5.36 0.127 14.4 5.08 5.63
## 3 Years Since Fire 5.23 0.143 26.9 4.94 5.53
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate -0.277 0.102 364 -2.710 0.0192
## Recently Burned - 3 Years Since Fire -0.156 0.120 363 -1.300 0.3963
## Intermediate - 3 Years Since Fire 0.121 0.104 363 1.162 0.4768
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 3 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 5.08 0.142 26.0 4.79 5.37
## Intermediate 5.36 0.127 14.4 5.08 5.63
## 3 Years Since Fire 5.23 0.143 26.9 4.94 5.53
##
## Results are averaged over the levels of: ESD, Treatment
## 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
## Recently Burned - Intermediate -0.277 0.102 364 -0.517 -0.0364
## Recently Burned - 3 Years Since Fire -0.156 0.120 363 -0.439 0.1266
## Intermediate - 3 Years Since Fire 0.121 0.104 363 -0.124 0.3648
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 3 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 5.04 0.144 27.4 4.74 5.33
## Loamy 5.40 0.183 67.4 5.04 5.77
## Saline Lowland 5.34 0.140 22.9 5.05 5.63
## Sandy 5.11 0.128 14.7 4.83 5.38
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.3667 0.170 372 -2.160 0.1365
## Clayey - Saline Lowland -0.3043 0.123 372 -2.467 0.0668
## Clayey - Sandy -0.0680 0.108 369 -0.632 0.9218
## Loamy - Saline Lowland 0.0624 0.176 355 0.354 0.9847
## Loamy - Sandy 0.2987 0.152 371 1.959 0.2054
## Saline Lowland - Sandy 0.2363 0.102 372 2.307 0.0983
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimates## boundary (singular) fit: see ?isSingular
## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 5.04 0.144 27.4 4.74 5.33
## Loamy 5.40 0.183 67.4 5.04 5.77
## Saline Lowland 5.34 0.140 22.9 5.05 5.63
## Sandy 5.11 0.128 14.7 4.83 5.38
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.3667 0.170 372 -0.8048 0.0714
## Clayey - Saline Lowland -0.3043 0.123 372 -0.6226 0.0140
## Clayey - Sandy -0.0680 0.108 369 -0.3458 0.2098
## Loamy - Saline Lowland 0.0624 0.176 355 -0.3918 0.5165
## Loamy - Sandy 0.2987 0.152 371 -0.0947 0.6921
## Saline Lowland - Sandy 0.2363 0.102 372 -0.0280 0.5007
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesMicrobes
Total Abundance
ES only, TSF and interaction are close
anova(BioFull)## Analysis of Variance Table
## npar Sum Sq Mean Sq F value
## TSF 3 0.63197 0.21066 2.9866
## ESD 3 1.80748 0.60249 8.5419
## Treatment 1 0.00763 0.00763 0.1082
## TSF:ESD 9 0.82040 0.09116 1.2924car::Anova(BioFull)## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: Total_Biomass + 0.001
## Chisq Df Pr(>Chisq)
## TSF 7.7858 3 0.05065 .
## ESD 31.2966 3 7.362e-07 ***
## Treatment 0.0261 1 0.87167
## TSF:ESD 14.8351 9 0.09557 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1#emmeans(BioFull, pairwise ~ TSF)
emmeans(BioFull, pairwise ~ ESD)## NOTE: Results may be misleading due to involvement in interactions## Note: Use 'contrast(regrid(object), ...)' to obtain contrasts of back-transformed estimates## $emmeans
## ESD emmean SE df asymp.LCL asymp.UCL
## Clayey 0.00861 0.000811 Inf 0.00702 0.0102
## Loamy 0.00850 0.000912 Inf 0.00672 0.0103
## Saline Lowland 0.00817 0.000782 Inf 0.00664 0.0097
## Sandy 0.01001 0.000765 Inf 0.00851 0.0115
##
## Results are averaged over the levels of: TSF, Treatment
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df z.ratio p.value
## Clayey - Loamy 0.000109 0.000712 Inf 0.153 0.9987
## Clayey - Saline Lowland 0.000444 0.000548 Inf 0.811 0.8493
## Clayey - Sandy -0.001395 0.000515 Inf -2.709 0.0341
## Loamy - Saline Lowland 0.000335 0.000709 Inf 0.473 0.9650
## Loamy - Sandy -0.001503 0.000639 Inf -2.352 0.0866
## Saline Lowland - Sandy -0.001839 0.000477 Inf -3.855 0.0007
##
## Results are averaged over the levels of: TSF, Treatment
## Note: contrasts are still on the inverse scale
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(BioFull, pairwise ~ ESD))## NOTE: Results may be misleading due to involvement in interactions
## Note: Use 'contrast(regrid(object), ...)' to obtain contrasts of back-transformed estimates## $emmeans
## ESD emmean SE df asymp.LCL asymp.UCL
## Clayey 0.00861 0.000811 Inf 0.00702 0.0102
## Loamy 0.00850 0.000912 Inf 0.00672 0.0103
## Saline Lowland 0.00817 0.000782 Inf 0.00664 0.0097
## Sandy 0.01001 0.000765 Inf 0.00851 0.0115
##
## Results are averaged over the levels of: TSF, Treatment
## Results are given on the inverse (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df asymp.LCL asymp.UCL
## Clayey - Loamy 0.000109 0.000712 Inf -0.001722 1.94e-03
## Clayey - Saline Lowland 0.000444 0.000548 Inf -0.000963 1.85e-03
## Clayey - Sandy -0.001395 0.000515 Inf -0.002717 -7.21e-05
## Loamy - Saline Lowland 0.000335 0.000709 Inf -0.001485 2.16e-03
## Loamy - Sandy -0.001503 0.000639 Inf -0.003145 1.39e-04
## Saline Lowland - Sandy -0.001839 0.000477 Inf -0.003064 -6.13e-04
##
## Results are averaged over the levels of: TSF, Treatment
## Note: contrasts are still on the inverse scale
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates#emmeans(BioFull, pairwise ~ TSF | ESD)
AMF
ESD, TSF, and interaction. Loamy higher than sandy; Only tsf differences in saline lowland sites, RB and intermediate higher than 3 year since fire
anova(AMFull)## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 23.833 7.9443 3 163.449 2.0143 0.11397
## ESD 40.570 13.5232 3 164.866 3.4289 0.01849 *
## Treatment 3.607 3.6070 1 9.643 0.9146 0.36226
## TSF:ESD 75.296 8.3663 9 163.301 2.1213 0.03043 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1car::Anova(AMFull)## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: AM_bio
## Chisq Df Pr(>Chisq)
## TSF 10.5931 3 0.0141426 *
## ESD 16.5484 3 0.0008751 ***
## Treatment 0.9146 1 0.3389044
## TSF:ESD 19.0920 9 0.0244223 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1emmeans(AMFull, pairwise ~ ESD)## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 6.12 0.595 10.69 4.80 7.43
## Loamy 7.74 0.772 25.85 6.15 9.33
## Saline Lowland 6.08 0.568 8.73 4.79 7.37
## Sandy 5.63 0.505 5.67 4.38 6.88
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Clayey - Loamy -1.6270 0.763 165 -2.133 0.1470
## Clayey - Saline Lowland 0.0377 0.556 165 0.068 0.9999
## Clayey - Sandy 0.4870 0.485 162 1.005 0.7468
## Loamy - Saline Lowland 1.6647 0.771 165 2.158 0.1394
## Loamy - Sandy 2.1140 0.680 165 3.107 0.0118
## Saline Lowland - Sandy 0.4493 0.451 165 0.996 0.7517
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(AMFull, pairwise ~ ESD))## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 6.12 0.595 10.69 4.80 7.43
## Loamy 7.74 0.772 25.85 6.15 9.33
## Saline Lowland 6.08 0.568 8.73 4.79 7.37
## Sandy 5.63 0.505 5.67 4.38 6.88
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Clayey - Loamy -1.6270 0.763 165 -3.607 0.353
## Clayey - Saline Lowland 0.0377 0.556 165 -1.404 1.480
## Clayey - Sandy 0.4870 0.485 162 -0.771 1.745
## Loamy - Saline Lowland 1.6647 0.771 165 -0.337 3.667
## Loamy - Sandy 2.1140 0.680 165 0.348 3.880
## Saline Lowland - Sandy 0.4493 0.451 165 -0.721 1.620
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesemmeans(AMFull, pairwise ~ TSF | ESD)## $emmeans
## ESD = Clayey:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.74 0.857 39.61 5.01 8.47
## Intermediate 5.88 0.675 17.34 4.45 7.30
## 3 Years Since Fire 6.75 0.960 56.89 4.83 8.67
## Not Yet Burned 5.10 1.138 88.15 2.84 7.36
##
## ESD = Loamy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.46 1.146 86.74 4.19 8.74
## Intermediate 7.72 0.753 24.61 6.17 9.27
## 3 Years Since Fire 10.06 1.565 137.79 6.97 13.16
## Not Yet Burned 6.73 1.567 137.82 3.63 9.83
##
## ESD = Saline Lowland:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.94 0.670 16.81 5.52 8.35
## Intermediate 7.73 0.581 9.56 6.43 9.04
## 3 Years Since Fire 3.71 1.145 86.97 1.44 5.99
## Not Yet Burned 5.93 0.858 40.29 4.20 7.67
##
## ESD = Sandy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 5.38 0.625 13.10 4.03 6.73
## Intermediate 6.37 0.556 8.26 5.09 7.64
## 3 Years Since Fire 6.06 0.738 24.31 4.54 7.59
## Not Yet Burned 4.71 0.788 30.48 3.10 6.31
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## ESD = Clayey:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 0.8638 0.903 165 0.956 0.7744
## Recently Burned - 3 Years Since Fire -0.0127 1.128 164 -0.011 1.0000
## Recently Burned - Not Yet Burned 1.6411 1.274 164 1.288 0.5718
## Intermediate - 3 Years Since Fire -0.8764 1.000 164 -0.877 0.8170
## Intermediate - Not Yet Burned 0.7773 1.169 164 0.665 0.9101
## 3 Years Since Fire - Not Yet Burned 1.6537 1.374 165 1.204 0.6253
##
## ESD = Loamy:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -1.2571 1.220 165 -1.030 0.7321
## Recently Burned - 3 Years Since Fire -3.5973 1.760 162 -2.044 0.1763
## Recently Burned - Not Yet Burned -0.2617 1.851 166 -0.141 0.9990
## Intermediate - 3 Years Since Fire -2.3402 1.604 165 -1.459 0.4645
## Intermediate - Not Yet Burned 0.9954 1.571 163 0.634 0.9210
## 3 Years Since Fire - Not Yet Burned 3.3356 2.133 165 1.564 0.4022
##
## ESD = Saline Lowland:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.7965 0.623 162 -1.278 0.5781
## Recently Burned - 3 Years Since Fire 3.2262 1.161 164 2.778 0.0308
## Recently Burned - Not Yet Burned 1.0042 0.893 164 1.124 0.6753
## Intermediate - 3 Years Since Fire 4.0226 1.108 164 3.630 0.0021
## Intermediate - Not Yet Burned 1.8006 0.830 165 2.169 0.1363
## 3 Years Since Fire - Not Yet Burned -2.2220 1.313 166 -1.693 0.3308
##
## ESD = Sandy:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.9848 0.566 162 -1.740 0.3064
## Recently Burned - 3 Years Since Fire -0.6804 0.747 163 -0.911 0.7990
## Recently Burned - Not Yet Burned 0.6756 0.796 164 0.848 0.8312
## Intermediate - 3 Years Since Fire 0.3044 0.692 164 0.440 0.9715
## Intermediate - Not Yet Burned 1.6604 0.740 164 2.245 0.1156
## 3 Years Since Fire - Not Yet Burned 1.3560 0.918 166 1.478 0.4533
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(AMFull, pairwise ~ TSF | ESD))## $emmeans
## ESD = Clayey:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.74 0.857 39.61 5.01 8.47
## Intermediate 5.88 0.675 17.34 4.45 7.30
## 3 Years Since Fire 6.75 0.960 56.89 4.83 8.67
## Not Yet Burned 5.10 1.138 88.15 2.84 7.36
##
## ESD = Loamy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.46 1.146 86.74 4.19 8.74
## Intermediate 7.72 0.753 24.61 6.17 9.27
## 3 Years Since Fire 10.06 1.565 137.79 6.97 13.16
## Not Yet Burned 6.73 1.567 137.82 3.63 9.83
##
## ESD = Saline Lowland:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 6.94 0.670 16.81 5.52 8.35
## Intermediate 7.73 0.581 9.56 6.43 9.04
## 3 Years Since Fire 3.71 1.145 86.97 1.44 5.99
## Not Yet Burned 5.93 0.858 40.29 4.20 7.67
##
## ESD = Sandy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 5.38 0.625 13.10 4.03 6.73
## Intermediate 6.37 0.556 8.26 5.09 7.64
## 3 Years Since Fire 6.06 0.738 24.31 4.54 7.59
## Not Yet Burned 4.71 0.788 30.48 3.10 6.31
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## ESD = Clayey:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 0.8638 0.903 165 -1.481 3.208
## Recently Burned - 3 Years Since Fire -0.0127 1.128 164 -2.941 2.915
## Recently Burned - Not Yet Burned 1.6411 1.274 164 -1.666 4.948
## Intermediate - 3 Years Since Fire -0.8764 1.000 164 -3.472 1.719
## Intermediate - Not Yet Burned 0.7773 1.169 164 -2.256 3.811
## 3 Years Since Fire - Not Yet Burned 1.6537 1.374 165 -1.912 5.219
##
## ESD = Loamy:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -1.2571 1.220 165 -4.424 1.910
## Recently Burned - 3 Years Since Fire -3.5973 1.760 162 -8.166 0.971
## Recently Burned - Not Yet Burned -0.2617 1.851 166 -5.066 4.543
## Intermediate - 3 Years Since Fire -2.3402 1.604 165 -6.502 1.822
## Intermediate - Not Yet Burned 0.9954 1.571 163 -3.082 5.072
## 3 Years Since Fire - Not Yet Burned 3.3356 2.133 165 -2.201 8.872
##
## ESD = Saline Lowland:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.7965 0.623 162 -2.414 0.821
## Recently Burned - 3 Years Since Fire 3.2262 1.161 164 0.212 6.240
## Recently Burned - Not Yet Burned 1.0042 0.893 164 -1.315 3.323
## Intermediate - 3 Years Since Fire 4.0226 1.108 164 1.146 6.899
## Intermediate - Not Yet Burned 1.8006 0.830 165 -0.354 3.956
## 3 Years Since Fire - Not Yet Burned -2.2220 1.313 166 -5.629 1.185
##
## ESD = Sandy:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.9848 0.566 162 -2.454 0.484
## Recently Burned - 3 Years Since Fire -0.6804 0.747 163 -2.619 1.258
## Recently Burned - Not Yet Burned 0.6756 0.796 164 -1.391 2.742
## Intermediate - 3 Years Since Fire 0.3044 0.692 164 -1.493 2.102
## Intermediate - Not Yet Burned 1.6604 0.740 164 -0.259 3.580
## 3 Years Since Fire - Not Yet Burned 1.3560 0.918 166 -1.025 3.737
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesFungi
only Interaction. No ecologicial sites sig different from each other, and no tsf differences within individual ES. RB almost lower than 3yr for sandy and loamy
anova(FungiFull)## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.26143 0.08714 3 162.605 0.6541 0.581493
## ESD 1.18904 0.39635 3 163.501 2.9748 0.033317 *
## Treatment 0.00338 0.00338 1 9.805 0.0254 0.876705
## TSF:ESD 3.04612 0.33846 9 162.413 2.5403 0.009387 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1car::Anova(FungiFull)## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Fungi_bio + 1)
## Chisq Df Pr(>Chisq)
## TSF 2.6657 3 0.446096
## ESD 4.7759 3 0.188959
## Treatment 0.0254 1 0.873472
## TSF:ESD 22.8631 9 0.006511 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1emmeans(FungiFull, pairwise ~ ESD)## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.79 0.130 7.60 1.48 2.09
## Loamy 1.92 0.159 15.70 1.59 2.26
## Saline Lowland 1.56 0.126 6.65 1.25 1.86
## Sandy 1.68 0.117 4.95 1.38 1.98
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.138 0.1402 164 -0.983 0.7594
## Clayey - Saline Lowland 0.230 0.1021 163 2.249 0.1146
## Clayey - Sandy 0.106 0.0891 162 1.187 0.6362
## Loamy - Saline Lowland 0.368 0.1418 165 2.591 0.0506
## Loamy - Sandy 0.244 0.1251 164 1.947 0.2127
## Saline Lowland - Sandy -0.124 0.0829 163 -1.495 0.4427
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(FungiFull, pairwise ~ ESD))## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.79 0.130 7.60 1.48 2.09
## Loamy 1.92 0.159 15.70 1.59 2.26
## Saline Lowland 1.56 0.126 6.65 1.25 1.86
## Sandy 1.68 0.117 4.95 1.38 1.98
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.138 0.1402 164 -0.501805 0.2262
## Clayey - Saline Lowland 0.230 0.1021 163 -0.035422 0.4948
## Clayey - Sandy 0.106 0.0891 162 -0.125567 0.3370
## Loamy - Saline Lowland 0.368 0.1418 165 -0.000644 0.7356
## Loamy - Sandy 0.244 0.1251 164 -0.081113 0.5682
## Saline Lowland - Sandy -0.124 0.0829 163 -0.339170 0.0912
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesemmeans(FungiFull, pairwise ~ TSF | ESD)## $emmeans
## ESD = Clayey:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.93 0.173 22.16 1.567 2.28
## Intermediate 1.62 0.143 10.92 1.309 1.94
## 3 Years Since Fire 1.82 0.190 31.38 1.433 2.21
## Not Yet Burned 1.78 0.221 51.30 1.332 2.22
##
## ESD = Loamy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.74 0.222 51.44 1.292 2.18
## Intermediate 1.83 0.156 14.77 1.495 2.16
## 3 Years Since Fire 2.53 0.296 103.10 1.938 3.11
## Not Yet Burned 1.61 0.297 103.25 1.017 2.19
##
## ESD = Saline Lowland:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.66 0.142 10.67 1.344 1.97
## Intermediate 1.67 0.128 7.08 1.365 1.97
## 3 Years Since Fire 1.18 0.222 51.43 0.733 1.63
## Not Yet Burned 1.72 0.173 22.39 1.363 2.08
##
## ESD = Sandy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.49 0.135 8.79 1.184 1.80
## Intermediate 1.65 0.124 6.35 1.351 1.95
## 3 Years Since Fire 1.83 0.153 14.28 1.500 2.16
## Not Yet Burned 1.75 0.161 17.33 1.413 2.09
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## ESD = Clayey:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate 0.30120 0.166 163 1.813 0.2708
## Recently Burned - 3 Years Since Fire 0.10391 0.207 163 0.501 0.9587
## Recently Burned - Not Yet Burned 0.15003 0.234 163 0.640 0.9188
## Intermediate - 3 Years Since Fire -0.19730 0.184 163 -1.073 0.7066
## Intermediate - Not Yet Burned -0.15117 0.215 163 -0.703 0.8956
## 3 Years Since Fire - Not Yet Burned 0.04612 0.253 164 0.183 0.9978
##
## ESD = Loamy:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.08853 0.224 164 -0.394 0.9791
## Recently Burned - 3 Years Since Fire -0.78784 0.324 162 -2.435 0.0746
## Recently Burned - Not Yet Burned 0.13250 0.341 164 0.389 0.9799
## Intermediate - 3 Years Since Fire -0.69931 0.295 163 -2.371 0.0868
## Intermediate - Not Yet Burned 0.22103 0.289 162 0.765 0.8699
## 3 Years Since Fire - Not Yet Burned 0.92034 0.393 164 2.345 0.0923
##
## ESD = Saline Lowland:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.00873 0.115 162 -0.076 0.9998
## Recently Burned - 3 Years Since Fire 0.47934 0.214 163 2.245 0.1157
## Recently Burned - Not Yet Burned -0.06320 0.164 163 -0.385 0.9806
## Intermediate - 3 Years Since Fire 0.48806 0.204 163 2.395 0.0821
## Intermediate - Not Yet Burned -0.05447 0.153 163 -0.357 0.9844
## 3 Years Since Fire - Not Yet Burned -0.54253 0.242 164 -2.246 0.1154
##
## ESD = Sandy:
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.16071 0.104 161 -1.545 0.4133
## Recently Burned - 3 Years Since Fire -0.33734 0.137 162 -2.456 0.0709
## Recently Burned - Not Yet Burned -0.26263 0.146 163 -1.793 0.2802
## Intermediate - 3 Years Since Fire -0.17663 0.127 163 -1.387 0.5093
## Intermediate - Not Yet Burned -0.10192 0.136 163 -0.749 0.8768
## 3 Years Since Fire - Not Yet Burned 0.07472 0.169 164 0.442 0.9710
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(FungiFull, pairwise ~ TSF | ESD))## $emmeans
## ESD = Clayey:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.93 0.173 22.16 1.567 2.28
## Intermediate 1.62 0.143 10.92 1.309 1.94
## 3 Years Since Fire 1.82 0.190 31.38 1.433 2.21
## Not Yet Burned 1.78 0.221 51.30 1.332 2.22
##
## ESD = Loamy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.74 0.222 51.44 1.292 2.18
## Intermediate 1.83 0.156 14.77 1.495 2.16
## 3 Years Since Fire 2.53 0.296 103.10 1.938 3.11
## Not Yet Burned 1.61 0.297 103.25 1.017 2.19
##
## ESD = Saline Lowland:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.66 0.142 10.67 1.344 1.97
## Intermediate 1.67 0.128 7.08 1.365 1.97
## 3 Years Since Fire 1.18 0.222 51.43 0.733 1.63
## Not Yet Burned 1.72 0.173 22.39 1.363 2.08
##
## ESD = Sandy:
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 1.49 0.135 8.79 1.184 1.80
## Intermediate 1.65 0.124 6.35 1.351 1.95
## 3 Years Since Fire 1.83 0.153 14.28 1.500 2.16
## Not Yet Burned 1.75 0.161 17.33 1.413 2.09
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log(mu + 1) (not the response) scale.
## Confidence level used: 0.95
##
## $contrasts
## ESD = Clayey:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate 0.30120 0.166 163 -0.1300 0.7324
## Recently Burned - 3 Years Since Fire 0.10391 0.207 163 -0.4345 0.6423
## Recently Burned - Not Yet Burned 0.15003 0.234 163 -0.4581 0.7582
## Intermediate - 3 Years Since Fire -0.19730 0.184 163 -0.6747 0.2801
## Intermediate - Not Yet Burned -0.15117 0.215 163 -0.7090 0.4067
## 3 Years Since Fire - Not Yet Burned 0.04612 0.253 164 -0.6098 0.7020
##
## ESD = Loamy:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.08853 0.224 164 -0.6712 0.4942
## Recently Burned - 3 Years Since Fire -0.78784 0.324 162 -1.6276 0.0520
## Recently Burned - Not Yet Burned 0.13250 0.341 164 -0.7515 1.0165
## Intermediate - 3 Years Since Fire -0.69931 0.295 163 -1.4650 0.0663
## Intermediate - Not Yet Burned 0.22103 0.289 162 -0.5286 0.9707
## 3 Years Since Fire - Not Yet Burned 0.92034 0.393 164 -0.0985 1.9392
##
## ESD = Saline Lowland:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.00873 0.115 162 -0.3061 0.2886
## Recently Burned - 3 Years Since Fire 0.47934 0.214 163 -0.0750 1.0337
## Recently Burned - Not Yet Burned -0.06320 0.164 163 -0.4897 0.3634
## Intermediate - 3 Years Since Fire 0.48806 0.204 163 -0.0410 1.0171
## Intermediate - Not Yet Burned -0.05447 0.153 163 -0.4509 0.3419
## 3 Years Since Fire - Not Yet Burned -0.54253 0.242 164 -1.1695 0.0845
##
## ESD = Sandy:
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.16071 0.104 161 -0.4308 0.1093
## Recently Burned - 3 Years Since Fire -0.33734 0.137 162 -0.6939 0.0192
## Recently Burned - Not Yet Burned -0.26263 0.146 163 -0.6427 0.1175
## Intermediate - 3 Years Since Fire -0.17663 0.127 163 -0.5072 0.1539
## Intermediate - Not Yet Burned -0.10192 0.136 163 -0.4550 0.2511
## 3 Years Since Fire - Not Yet Burned 0.07472 0.169 164 -0.3636 0.5131
##
## Results are averaged over the levels of: Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesEuk
ESD only, loamy larger than sandy
anova(EukFull)## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.29304 0.09768 3 162.699 0.9059 0.43962
## ESD 1.24604 0.41535 3 163.689 3.8521 0.01069 *
## Treatment 0.00482 0.00482 1 9.716 0.0447 0.83692
## TSF:ESD 0.99432 0.11048 9 162.503 1.0246 0.42256
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1car::Anova(EukFull)## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Euk_bio + 1)
## Chisq Df Pr(>Chisq)
## TSF 2.9844 3 0.3940
## ESD 11.1982 3 0.0107 *
## Treatment 0.0447 1 0.8326
## TSF:ESD 9.2218 9 0.4171
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1emmeans(EukFull, pairwise ~ ESD)## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.55 0.113 8.06 1.29 1.81
## Loamy 1.66 0.139 17.26 1.36 1.95
## Saline Lowland 1.47 0.109 6.97 1.21 1.73
## Sandy 1.36 0.100 5.06 1.10 1.61
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.1107 0.1261 164 -0.877 0.8166
## Clayey - Saline Lowland 0.0729 0.0919 164 0.794 0.8573
## Clayey - Sandy 0.1907 0.0801 162 2.379 0.0852
## Loamy - Saline Lowland 0.1836 0.1276 165 1.439 0.4771
## Loamy - Sandy 0.3013 0.1125 164 2.678 0.0403
## Saline Lowland - Sandy 0.1177 0.0746 164 1.579 0.3936
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(EukFull, pairwise ~ ESD))## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 1.55 0.113 8.06 1.29 1.81
## Loamy 1.66 0.139 17.26 1.36 1.95
## Saline Lowland 1.47 0.109 6.97 1.21 1.73
## Sandy 1.36 0.100 5.06 1.10 1.61
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.1107 0.1261 164 -0.43809 0.217
## Clayey - Saline Lowland 0.0729 0.0919 164 -0.16556 0.311
## Clayey - Sandy 0.1907 0.0801 162 -0.01739 0.399
## Loamy - Saline Lowland 0.1836 0.1276 165 -0.14758 0.515
## Loamy - Sandy 0.3013 0.1125 164 0.00929 0.593
## Saline Lowland - Sandy 0.1177 0.0746 164 -0.07584 0.311
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates#emmeans(EukFull, pairwise ~ TSF | ESD)GNB
ESD only: sandy lower than saline lowland, clayey, and loamy by p value, but not by confidence interval
anova(GNBFull)## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.30016 0.10005 3 162.677 1.4316 0.2355
## ESD 1.83616 0.61205 3 163.640 8.7574 2.023e-05 ***
## Treatment 0.01039 0.01039 1 9.745 0.1487 0.7081
## TSF:ESD 0.73888 0.08210 9 162.482 1.1747 0.3145
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1car::Anova(GNBFull)## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(GNB_bio + 1)
## Chisq Df Pr(>Chisq)
## TSF 7.4387 3 0.05916 .
## ESD 41.3039 3 5.637e-09 ***
## Treatment 0.1487 1 0.69979
## TSF:ESD 10.5720 9 0.30619
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1emmeans(GNBFull, pairwise ~ ESD)## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 3.85 0.0918 7.94 3.64 4.06
## Loamy 3.93 0.1129 16.82 3.69 4.17
## Saline Lowland 3.94 0.0888 6.88 3.73 4.15
## Sandy 3.68 0.0818 5.03 3.47 3.89
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.0772 0.1016 164 -0.760 0.8723
## Clayey - Saline Lowland -0.0906 0.0740 164 -1.225 0.6117
## Clayey - Sandy 0.1756 0.0645 162 2.721 0.0360
## Loamy - Saline Lowland -0.0135 0.1027 165 -0.131 0.9992
## Loamy - Sandy 0.2528 0.0906 164 2.790 0.0298
## Saline Lowland - Sandy 0.2662 0.0600 164 4.433 0.0001
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(GNBFull, pairwise ~ ESD))## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 3.85 0.0918 7.94 3.64 4.06
## Loamy 3.93 0.1129 16.82 3.69 4.17
## Saline Lowland 3.94 0.0888 6.88 3.73 4.15
## Sandy 3.68 0.0818 5.03 3.47 3.89
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy -0.0772 0.1016 164 -0.34079 0.186
## Clayey - Saline Lowland -0.0906 0.0740 164 -0.28263 0.101
## Clayey - Sandy 0.1756 0.0645 162 0.00807 0.343
## Loamy - Saline Lowland -0.0135 0.1027 165 -0.28008 0.253
## Loamy - Sandy 0.2528 0.0906 164 0.01762 0.488
## Saline Lowland - Sandy 0.2662 0.0600 164 0.11034 0.422
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesGPB
ESD only: sandy lower than saline lowland and clayey by p value, but not by confidence interval
anova(GPBFull)## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.22071 0.07357 3 162.820 1.1976 0.31247
## ESD 1.50367 0.50122 3 163.862 8.1594 4.273e-05 ***
## Treatment 0.00691 0.00691 1 9.735 0.1124 0.74449
## TSF:ESD 0.95103 0.10567 9 162.625 1.7202 0.08816 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1car::Anova(GPBFull)## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(GPB_bio + 1)
## Chisq Df Pr(>Chisq)
## TSF 4.3522 3 0.22586
## ESD 40.7158 3 7.513e-09 ***
## Treatment 0.1124 1 0.73738
## TSF:ESD 15.4817 9 0.07853 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1emmeans(GPBFull, pairwise ~ ESD)## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 3.85 0.0835 8.36 3.66 4.04
## Loamy 3.83 0.1037 18.27 3.61 4.04
## Saline Lowland 3.88 0.0805 7.17 3.69 4.07
## Sandy 3.65 0.0737 5.14 3.46 3.83
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy 0.0223 0.0952 164 0.234 0.9955
## Clayey - Saline Lowland -0.0336 0.0693 164 -0.485 0.9624
## Clayey - Sandy 0.2033 0.0605 162 3.361 0.0053
## Loamy - Saline Lowland -0.0559 0.0963 165 -0.580 0.9379
## Loamy - Sandy 0.1811 0.0849 164 2.132 0.1473
## Saline Lowland - Sandy 0.2370 0.0563 164 4.209 0.0002
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(GPBFull, pairwise ~ ESD))## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 3.85 0.0835 8.36 3.66 4.04
## Loamy 3.83 0.1037 18.27 3.61 4.04
## Saline Lowland 3.88 0.0805 7.17 3.69 4.07
## Sandy 3.65 0.0737 5.14 3.46 3.83
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy 0.0223 0.0952 164 -0.2249 0.269
## Clayey - Saline Lowland -0.0336 0.0693 164 -0.2136 0.146
## Clayey - Sandy 0.2033 0.0605 162 0.0463 0.360
## Loamy - Saline Lowland -0.0559 0.0963 165 -0.3058 0.194
## Loamy - Sandy 0.1811 0.0849 164 -0.0394 0.401
## Saline Lowland - Sandy 0.2370 0.0563 164 0.0908 0.383
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates#emmeans(GPBFull, pairwise ~ TSF | ESD)Actino
TSF and ES only: sandy lower than saline lowland by p value, but not by confidence interval
anova(ActinoFull)## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.22675 0.075585 3 162.320 1.5295 0.2088605
## ESD 0.94165 0.313883 3 163.075 6.3516 0.0004243 ***
## Treatment 0.00449 0.004486 1 9.799 0.0908 0.7694763
## TSF:ESD 0.69793 0.077548 9 162.139 1.5692 0.1284931
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1car::Anova(ActinoFull)## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: log(Actino_bio + 1)
## Chisq Df Pr(>Chisq)
## TSF 8.3571 3 0.03918 *
## ESD 42.8205 3 2.687e-09 ***
## Treatment 0.0908 1 0.76318
## TSF:ESD 14.1231 9 0.11801
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1emmeans(ActinoFull, pairwise ~ ESD)## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 2.92 0.0852 6.90 2.71 3.12
## Loamy 2.91 0.1016 13.29 2.69 3.12
## Saline Lowland 3.03 0.0829 6.15 2.83 3.23
## Sandy 2.81 0.0777 4.78 2.61 3.02
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy 0.0113 0.0854 163 0.132 0.9992
## Clayey - Saline Lowland -0.1133 0.0622 163 -1.821 0.2674
## Clayey - Sandy 0.1020 0.0543 162 1.880 0.2407
## Loamy - Saline Lowland -0.1245 0.0864 165 -1.441 0.4755
## Loamy - Sandy 0.0907 0.0762 164 1.191 0.6333
## Saline Lowland - Sandy 0.2153 0.0505 163 4.263 0.0002
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(ActinoFull, pairwise ~ ESD))## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 2.92 0.0852 6.90 2.71 3.12
## Loamy 2.91 0.1016 13.29 2.69 3.12
## Saline Lowland 3.03 0.0829 6.15 2.83 3.23
## Sandy 2.81 0.0777 4.78 2.61 3.02
##
## Results are averaged over the levels of: TSF, Treatment
## 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
## Clayey - Loamy 0.0113 0.0854 163 -0.2104 0.2330
## Clayey - Saline Lowland -0.1133 0.0622 163 -0.2747 0.0482
## Clayey - Sandy 0.1020 0.0543 162 -0.0388 0.2429
## Loamy - Saline Lowland -0.1245 0.0864 165 -0.3488 0.0997
## Loamy - Sandy 0.0907 0.0762 164 -0.1070 0.2885
## Saline Lowland - Sandy 0.2153 0.0505 163 0.0842 0.3463
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Results are given on the log (not the response) scale.
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates#emmeans(ActinoFull, pairwise ~ TSF | ESD)FBR
TSF and ESD significant, not interaction.
Fungal:bacteria ratio higher in 3yr than RB and NYB Loamy and sandy higher than saline lowland
anova(FBRFull)## Type III Analysis of Variance Table with Satterthwaite's method
## Sum Sq Mean Sq NumDF DenDF F value Pr(>F)
## TSF 0.0096491 0.0032164 3 163.592 7.1547 0.0001522 ***
## ESD 0.0094057 0.0031352 3 165.384 6.9742 0.0001903 ***
## Treatment 0.0000049 0.0000049 1 9.803 0.0110 0.9186475
## TSF:ESD 0.0064301 0.0007145 9 163.800 1.5893 0.1222325
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1car::Anova(FBRFull)## Analysis of Deviance Table (Type II Wald chisquare tests)
##
## Response: FBR
## Chisq Df Pr(>Chisq)
## TSF 24.778 3 1.718e-05 ***
## ESD 19.892 3 0.0001788 ***
## Treatment 0.011 1 0.9165344
## TSF:ESD 14.304 9 0.1119270
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1emmeans(FBRFull, pairwise ~ TSF)## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 0.118 0.00510 12.28 0.107 0.129
## Intermediate 0.123 0.00423 5.92 0.113 0.133
## 3 Years Since Fire 0.149 0.00678 34.53 0.135 0.163
## Not Yet Burned 0.124 0.00657 30.66 0.110 0.137
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Recently Burned - Intermediate -0.004556 0.00446 161 -1.022 0.7371
## Recently Burned - 3 Years Since Fire -0.030838 0.00689 164 -4.473 0.0001
## Recently Burned - Not Yet Burned -0.005322 0.00674 165 -0.790 0.8590
## Intermediate - 3 Years Since Fire -0.026282 0.00634 165 -4.148 0.0003
## Intermediate - Not Yet Burned -0.000766 0.00607 165 -0.126 0.9993
## 3 Years Since Fire - Not Yet Burned 0.025516 0.00845 166 3.021 0.0153
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(FBRFull, pairwise ~ TSF))## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## TSF emmean SE df lower.CL upper.CL
## Recently Burned 0.118 0.00510 12.28 0.107 0.129
## Intermediate 0.123 0.00423 5.92 0.113 0.133
## 3 Years Since Fire 0.149 0.00678 34.53 0.135 0.163
## Not Yet Burned 0.124 0.00657 30.66 0.110 0.137
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Recently Burned - Intermediate -0.004556 0.00446 161 -0.0161 0.00702
## Recently Burned - 3 Years Since Fire -0.030838 0.00689 164 -0.0487 -0.01294
## Recently Burned - Not Yet Burned -0.005322 0.00674 165 -0.0228 0.01217
## Intermediate - 3 Years Since Fire -0.026282 0.00634 165 -0.0427 -0.00984
## Intermediate - Not Yet Burned -0.000766 0.00607 165 -0.0165 0.01499
## 3 Years Since Fire - Not Yet Burned 0.025516 0.00845 166 0.0036 0.04743
##
## Results are averaged over the levels of: ESD, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimatesemmeans(FBRFull, pairwise ~ ESD)## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 0.125 0.00553 16.51 0.113 0.136
## Loamy 0.144 0.00763 41.23 0.128 0.159
## Saline Lowland 0.113 0.00542 14.58 0.101 0.124
## Sandy 0.133 0.00439 6.93 0.122 0.143
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df t.ratio p.value
## Clayey - Loamy -0.0192 0.00814 165 -2.359 0.0893
## Clayey - Saline Lowland 0.0117 0.00611 165 1.918 0.2245
## Clayey - Sandy -0.0083 0.00518 162 -1.603 0.3796
## Loamy - Saline Lowland 0.0309 0.00836 159 3.695 0.0017
## Loamy - Sandy 0.0109 0.00726 164 1.502 0.4389
## Saline Lowland - Sandy -0.0200 0.00506 164 -3.955 0.0007
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## P value adjustment: tukey method for comparing a family of 4 estimatesconfint(emmeans(FBRFull, pairwise ~ ESD))## NOTE: Results may be misleading due to involvement in interactions## $emmeans
## ESD emmean SE df lower.CL upper.CL
## Clayey 0.125 0.00553 16.51 0.113 0.136
## Loamy 0.144 0.00763 41.23 0.128 0.159
## Saline Lowland 0.113 0.00542 14.58 0.101 0.124
## Sandy 0.133 0.00439 6.93 0.122 0.143
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
##
## $contrasts
## contrast estimate SE df lower.CL upper.CL
## Clayey - Loamy -0.0192 0.00814 165 -0.04032 0.00193
## Clayey - Saline Lowland 0.0117 0.00611 165 -0.00414 0.02756
## Clayey - Sandy -0.0083 0.00518 162 -0.02173 0.00514
## Loamy - Saline Lowland 0.0309 0.00836 159 0.00919 0.05263
## Loamy - Sandy 0.0109 0.00726 164 -0.00794 0.02974
## Saline Lowland - Sandy -0.0200 0.00506 164 -0.03314 -0.00688
##
## Results are averaged over the levels of: TSF, Treatment
## Degrees-of-freedom method: kenward-roger
## Confidence level used: 0.95
## Conf-level adjustment: tukey method for comparing a family of 4 estimates
Ordi Setup
##
## Call:
## metaMDS(comm = MicBiomass1920_2, distance = "euclidean", k = 3, trymax = 50)
##
## global Multidimensional Scaling using monoMDS
##
## Data: wisconsin(sqrt(MicBiomass1920_2))
## Distance: euclidean
##
## Dimensions: 3
## Stress: 0.03597431
## Stress type 1, weak ties
## Two convergent solutions found after 20 tries
## Scaling: centring, PC rotation
## Species: expanded scores based on 'wisconsin(sqrt(MicBiomass1920_2))'## importance.MDS1 importance.MDS2 importance.MDS3
## Eigenvalue 0.19 0.11 0.04
## Proportion Explained 0.51 0.29 0.11
## Cumulative Proportion 0.51 0.81 0.92
## importance.MDS4 importance.MDS5
## Eigenvalue 0.02 0.01
## Proportion Explained 0.06 0.02
## Cumulative Proportion 0.98 1.00##
## ***VECTORS
##
## MDS1 MDS2 MDS3 r2 Pr(>r)
## NH4_ppm -0.89188 -0.07672 0.44571 0.0149 0.858
## NO3_ppm -0.79825 -0.54047 0.26589 0.0543 0.040 *
## Moisture -0.62822 -0.11260 -0.76985 0.0571 0.008 **
## P_ppm -0.60529 -0.79437 -0.05093 0.0562 0.024 *
## K_ppm 0.36828 -0.58320 -0.72405 0.0739 0.016 *
## Ca_ppm -0.60721 0.50630 -0.61234 0.1495 0.002 **
## Mg_ppm -0.68564 0.72674 0.04177 0.0353 0.120
## TotalN_percent -0.27291 -0.73625 -0.61924 0.0300 0.452
## TotalC_percent -0.62612 -0.30759 -0.71650 0.0773 0.004 **
## TCNR -0.78968 0.18822 -0.58393 0.1292 0.002 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499
##
## ***FACTORS:
##
## Centroids:
## MDS1 MDS2 MDS3
## ESDClayey 0.0383 0.0138 0.0127
## ESDLoamy 0.0449 0.0216 -0.1065
## ESDSaline Lowland -0.0657 -0.0430 0.0474
## ESDSandy 0.0204 0.0204 -0.0132
## TSFRecently Burned -0.0311 -0.0142 0.0122
## TSFIntermediate -0.0261 -0.0243 -0.0311
## TSF3 Years Since Fire 0.2042 0.0370 -0.0112
## TSFNot Yet Burned -0.0334 0.0861 0.1054
## TreatmentCattle -0.0208 0.0231 -0.0278
## TreatmentSheep 0.0219 -0.0243 0.0293
##
## Goodness of fit:
## r2 Pr(>r)
## ESD 0.0364 0.026 *
## TSF 0.0705 0.004 **
## Treatment 0.0139 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499##
## Pairwise comparisons using factor fitting to an ordination
##
## data: Mic.cape2 by MicEnv1920_3$TSF
## 999 permutations
##
## Recently Burned Intermediate 3 Years Since Fire
## Intermediate 0.957 - -
## 3 Years Since Fire 0.002 0.002 -
## Not Yet Burned 0.086 0.074 0.002
##
## P value adjustment method: fdr##
## Pairwise comparisons using factor fitting to an ordination
##
## data: Mic.cape2 by MicEnv1920_3$ESD
## 999 permutations
##
## Clayey Loamy Saline Lowland
## Loamy 0.976 - -
## Saline Lowland 0.066 0.142 -
## Sandy 0.976 0.976 0.066
##
## P value adjustment method: fdrGraphs
Nutrients
Ammonium
cowplot::plot_grid( AmmTSF,AmmES, nrow = 2)
Nitrate
cowplot::plot_grid( NitTSF,NitES, nrow = 2)
Moisture
cowplot::plot_grid( WaterTSF,WaterES, nrow = 2)
###Total Carbon
cowplot::plot_grid( TCplot1,TCplot2, nrow = 2)
Total Nitrogen
cowplot::plot_grid( TNplot1,TNplot2, nrow = 2)
Ca Mg P ES
cowplot::plot_grid( Caplot1,Mgplot1, APplot1, nrow = 3)
Ca Mg P TSF
cowplot::plot_grid( Caplot2,Mgplot2, APplot2, nrow = 3)
Potassium
cowplot::plot_grid( K_ppmplot1,K_ppmplot2, nrow = 2 )
pH
EC
cowplot::plot_grid( K_ppmplot1,K_ppmplot2, nrow = 2 )
Microbes
TSF Comp %
Stack + FBR
cowplot::plot_grid( CompStack,FBRplot1,FBRplot2, nrow = 3 )
FBR stack only
cowplot::plot_grid(FBRplot1,FBRplot2, nrow = 2 )
Total Abundance
cowplot::plot_grid(TAplot1,TAplot2, nrow = 2 )
GNB tsf and es
cowplot::plot_grid(GNBplot1,GNBplot2, nrow = 2 )
GPB tsf and es
cowplot::plot_grid(GPBplot1,GPBplot2, nrow = 2 )
GN GP ES stacl
cowplot::plot_grid(GNBplot2,GPBplot2, nrow = 2 )
AMF
cowplot::plot_grid(AMFplot1,AMFplot2, nrow = 2 )
Fungi
cowplot::plot_grid(Fungiplot1,Fungiplot2, nrow = 2 )
Am Fungi&Fungi int stack
cowplot::plot_grid(AMInt,FungiInt, nrow = 2 )
Euk
cowplot::plot_grid(Eukplot1,Eukplot2, nrow = 2 )
Actino
cowplot::plot_grid(Actinoplot1,Actinoplot2, nrow = 2 )
Euk act es stack
cowplot::plot_grid(Eukplot2,Actinoplot2, nrow = 2 )
TSFOrdi
TSF ES Ordi
