Soil Stats & Figures
Jonathan Spiess
July 23, 2021
Nutrients
Monthly
Ammonium
TSF best model. ESD and Grazer only models are actually less explanatory than TSF only.
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## NHT 8 1681.20 0.00 0.62 0.62 -832.54
## NHTE 11 1682.92 1.72 0.26 0.88 -830.34
## NHNull 5 1685.60 4.40 0.07 0.95 -837.78
## NHG 6 1687.62 6.42 0.03 0.97 -837.77
## NHE 8 1688.27 7.07 0.02 0.99 -836.07
## NHInt 20 1690.07 8.87 0.01 1.00 -824.66## Data: Soil181920
## Models:
## NHT: log(NH4_ppm + 1) ~ TSF + (1 | Location/Year/Month)
## NHTE: log(NH4_ppm + 1) ~ TSF + ESD + (1 | Location/Year/Month)
## NHInt: log(NH4_ppm + 1) ~ TSF * ESD + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## NHT 8 1681.1 1721.3 -832.54 1665.1
## NHTE 11 1682.7 1738.0 -830.34 1660.7 4.3858 3 0.2227
## NHInt 20 1689.3 1789.9 -824.66 1649.3 11.3728 9 0.2510## Data: Soil181920
## Models:
## NHNull: log(NH4_ppm + 1) ~ 1 + (1 | Location/Year/Month)
## NHT: log(NH4_ppm + 1) ~ TSF + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## NHNull 5 1685.5 1710.7 -837.78 1675.5
## NHT 8 1681.1 1721.3 -832.54 1665.1 10.48 3 0.0149 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: Soil181920
## Models:
## NHNull: log(NH4_ppm + 1) ~ 1 + (1 | Location/Year/Month)
## NHE: log(NH4_ppm + 1) ~ ESD + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## NHNull 5 1685.5 1710.7 -837.78 1675.5
## NHE 8 1688.1 1728.4 -836.07 1672.1 3.4098 3 0.3326## Data: Soil181920
## Models:
## NHNull: log(NH4_ppm + 1) ~ 1 + (1 | Location/Year/Month)
## NHG: log(NH4_ppm + 1) ~ Treatment + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## NHNull 5 1685.5 1710.7 -837.78 1675.5
## NHG 6 1687.5 1717.7 -837.77 1675.5 0.01 1 0.9202##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(NH4_ppm + 1) ~ TSF + ESD + (1 | Location/Year/Month),
## data = Soil181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 -0.073183 0.034285 -2.135 0.1344
## 3 Years Since Fire - Recently Burned == 0 -0.170252 0.058056 -2.933 0.0165
## Not Yet Burned - Recently Burned == 0 0.004507 0.040176 0.112 0.9995
## 3 Years Since Fire - Intermediate == 0 -0.097069 0.054484 -1.782 0.2700
## Not Yet Burned - Intermediate == 0 0.077690 0.037783 2.056 0.1589
## Not Yet Burned - 3 Years Since Fire == 0 0.174758 0.063823 2.738 0.0286
##
## 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 Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(NH4_ppm + 1) ~ TSF + ESD + (1 | Location/Year/Month),
## data = Soil181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 0.074967 0.055261 1.357 0.517
## Saline Lowland - Clayey == 0 -0.042612 0.042907 -0.993 0.746
## Sandy - Clayey == 0 -0.006713 0.039381 -0.170 0.998
## Saline Lowland - Loamy == 0 -0.117580 0.056261 -2.090 0.150
## Sandy - Loamy == 0 -0.081680 0.049833 -1.639 0.347
## Sandy - Saline Lowland == 0 0.035899 0.034613 1.037 0.720
## (Adjusted p values reported -- single-step method)Nitrate
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## NOTE 11 1523.47 0.00 0.67 0.67 -750.61
## NOT 8 1526.49 3.03 0.15 0.82 -755.18
## NOE 8 1526.95 3.49 0.12 0.93 -755.41
## NOInt 20 1528.71 5.24 0.05 0.98 -743.98
## NOG 6 1531.89 8.42 0.01 0.99 -759.91
## NONull 5 1532.45 8.98 0.01 1.00 -761.20## Data: Soil181920
## Models:
## NOT: log(NO3_ppm + 1) ~ TSF + (1 | Location/Year/Month)
## NOTE: log(NO3_ppm + 1) ~ TSF + ESD + (1 | Location/Year/Month)
## NOInt: log(NO3_ppm + 1) ~ TSF * ESD + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## NOT 8 1526.4 1566.6 -755.18 1510.4
## NOTE 11 1523.2 1578.5 -750.61 1501.2 9.1353 3 0.02754 *
## NOInt 20 1528.0 1628.5 -743.98 1488.0 13.2785 9 0.15040
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: Soil181920
## Models:
## NONull: log(NO3_ppm + 1) ~ 1 + (1 | Location/Year/Month)
## NOT: log(NO3_ppm + 1) ~ TSF + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## NONull 5 1532.4 1557.5 -761.20 1522.4
## NOT 8 1526.4 1566.6 -755.18 1510.4 12.029 3 0.007284 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: Soil181920
## Models:
## NONull: log(NO3_ppm + 1) ~ 1 + (1 | Location/Year/Month)
## NOE: log(NO3_ppm + 1) ~ ESD + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## NONull 5 1532.4 1557.5 -761.20 1522.4
## NOE 8 1526.8 1567.0 -755.41 1510.8 11.569 3 0.009017 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(NO3_ppm + 1) ~ TSF + ESD + (1 | Location/Year/Month),
## data = Soil181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 -0.064651 0.033455 -1.932 0.2046
## 3 Years Since Fire - Recently Burned == 0 -0.165734 0.056068 -2.956 0.0152
## Not Yet Burned - Recently Burned == 0 -0.056897 0.038907 -1.462 0.4472
## 3 Years Since Fire - Intermediate == 0 -0.101083 0.052669 -1.919 0.2100
## Not Yet Burned - Intermediate == 0 0.007754 0.036371 0.213 0.9964
## Not Yet Burned - 3 Years Since Fire == 0 0.108837 0.060923 1.786 0.2684
##
## 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 Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(NO3_ppm + 1) ~ TSF + ESD + (1 | Location/Year/Month),
## data = Soil181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 0.006175 0.053557 0.115 0.9994
## Saline Lowland - Clayey == 0 0.065528 0.041500 1.579 0.3816
## Sandy - Clayey == 0 -0.035168 0.038274 -0.919 0.7889
## Saline Lowland - Loamy == 0 0.059352 0.053961 1.100 0.6819
## Sandy - Loamy == 0 -0.041343 0.048248 -0.857 0.8219
## Sandy - Saline Lowland == 0 -0.100695 0.033525 -3.004 0.0141 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Soil Moisture
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## MTE 11 41.95 0.00 0.89 0.89 -9.80
## MInt 20 46.05 4.11 0.11 1.00 -2.45
## ME 8 64.32 22.37 0.00 1.00 -24.06
## MT 8 165.99 124.04 0.00 1.00 -74.90
## MNull 5 182.42 140.47 0.00 1.00 -86.17
## MG 6 184.39 142.44 0.00 1.00 -86.14## Data: Soil1920
## Models:
## MT: log(Moisture + 1) ~ TSF + (1 | Location/Year/Month)
## MTE: log(Moisture + 1) ~ TSF + ESD + (1 | Location/Year/Month)
## MInt: log(Moisture + 1) ~ TSF * ESD + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## MT 8 165.799 202.781 -74.899 149.799
## MTE 11 41.591 92.441 -9.795 19.591 130.208 3 < 2e-16 ***
## MInt 20 44.904 137.359 -2.452 4.904 14.687 9 0.09991 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: Soil1920
## Models:
## MNull: log(Moisture + 1) ~ 1 + (1 | Location/Year/Month)
## MT: log(Moisture + 1) ~ TSF + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## MNull 5 182.34 205.45 -86.168 172.34
## MT 8 165.80 202.78 -74.899 149.80 22.537 3 5.044e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: Soil1920
## Models:
## MNull: log(Moisture + 1) ~ 1 + (1 | Location/Year/Month)
## ME: log(Moisture + 1) ~ ESD + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## MNull 5 182.335 205.45 -86.168 172.335
## ME 8 64.127 101.11 -24.064 48.127 124.21 3 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: Soil1920
## Models:
## MNull: log(Moisture + 1) ~ 1 + (1 | Location/Year/Month)
## MInt: log(Moisture + 1) ~ TSF * ESD + (1 | Location/Year/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## MNull 5 182.335 205.45 -86.168 172.335
## MInt 20 44.904 137.36 -2.452 4.904 167.43 15 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(Moisture + 1) ~ TSF + ESD + (1 | Location/Year/Month),
## data = Soil1920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 0.03198 0.01958 1.633 0.34677
## 3 Years Since Fire - Recently Burned == 0 0.05803 0.02905 1.997 0.17996
## Not Yet Burned - Recently Burned == 0 -0.10701 0.02884 -3.710 0.00114
## 3 Years Since Fire - Intermediate == 0 0.02605 0.02693 0.967 0.75852
## Not Yet Burned - Intermediate == 0 -0.13899 0.02672 -5.201 < 0.001
## Not Yet Burned - 3 Years Since Fire == 0 -0.16504 0.03665 -4.503 < 0.001
##
## 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 Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(Moisture + 1) ~ TSF + ESD + (1 | Location/Year/Month),
## data = Soil1920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 0.02191 0.03308 0.662 0.9082
## Saline Lowland - Clayey == 0 0.12123 0.02570 4.718 <0.001 ***
## Sandy - Clayey == 0 -0.11843 0.02352 -5.035 <0.001 ***
## Saline Lowland - Loamy == 0 0.09932 0.03354 2.962 0.0154 *
## Sandy - Loamy == 0 -0.14034 0.02977 -4.715 <0.001 ***
## Sandy - Saline Lowland == 0 -0.23966 0.02066 -11.600 <0.001 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Single
Total C
cowplot::plot_grid( TCplot1,TCplot2, TCplot3, nrow = 3, labels=c("A","B","C") )
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## TCTE 10 -136.53 0.00 0.83 0.83 78.67
## TCE 7 -133.33 3.20 0.17 1.00 73.87
## TCInt 19 -120.35 16.18 0.00 1.00 80.63
## TCT 7 -66.53 70.00 0.00 1.00 40.47
## TCNull 4 -64.10 72.43 0.00 1.00 36.12
## TCG 5 -63.66 72.87 0.00 1.00 36.94## Data: SoilJuly181920
## Models:
## TCE: log(TotalC_percent + 1) ~ ESD + (1 | Location/Year)
## TCTE: log(TotalC_percent + 1) ~ TSF + ESD + (1 | Location/Year)
## TCInt: log(TotalC_percent + 1) ~ TSF * ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## TCE 7 -133.74 -108.246 73.870 -147.74
## TCTE 10 -137.34 -100.924 78.671 -157.34 9.6032 3 0.02226 *
## TCInt 19 -123.25 -54.058 80.627 -161.25 3.9116 9 0.91713
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## TCNull: log(TotalC_percent + 1) ~ 1 + (1 | Location/Year)
## TCT: log(TotalC_percent + 1) ~ TSF + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## TCNull 4 -64.244 -49.676 36.122 -72.244
## TCT 7 -66.939 -41.445 40.469 -80.939 8.6948 3 0.03364 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## TCNull: log(TotalC_percent + 1) ~ 1 + (1 | Location/Year)
## TCE: log(TotalC_percent + 1) ~ ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## TCNull 4 -64.244 -49.676 36.122 -72.244
## TCE 7 -133.740 -108.246 73.870 -147.740 75.496 3 2.837e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(TotalC_percent + 1) ~ TSF + ESD + (1 | Location/Year),
## data = SoilJuly181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 -0.007195 0.026704 -0.269 0.9929
## 3 Years Since Fire - Recently Burned == 0 -0.021071 0.043213 -0.488 0.9604
## Not Yet Burned - Recently Burned == 0 -0.083794 0.030216 -2.773 0.0266
## 3 Years Since Fire - Intermediate == 0 -0.013876 0.040774 -0.340 0.9859
## Not Yet Burned - Intermediate == 0 -0.076598 0.027582 -2.777 0.0266
## Not Yet Burned - 3 Years Since Fire == 0 -0.062722 0.044759 -1.401 0.4880
##
## 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 Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(TotalC_percent + 1) ~ TSF + ESD + (1 | Location/Year),
## data = SoilJuly181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 0.07673 0.04303 1.783 0.27330
## Saline Lowland - Clayey == 0 0.12410 0.03330 3.726 0.00107 **
## Sandy - Clayey == 0 -0.11222 0.03073 -3.651 0.00141 **
## Saline Lowland - Loamy == 0 0.04737 0.04352 1.088 0.68894
## Sandy - Loamy == 0 -0.18895 0.03882 -4.868 < 0.001 ***
## Sandy - Saline Lowland == 0 -0.23631 0.02695 -8.767 < 0.001 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Total N
cowplot::plot_grid( TNplot1,TNplot2, TNplot3, nrow = 3, labels=c("A","B","C") )
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## TNTE 10 -900.36 0.00 0.62 0.62 460.59
## TNE 7 -899.35 1.01 0.38 1.00 456.88
## TNInt 19 -883.67 16.70 0.00 1.00 462.28
## TNT 7 -838.40 61.96 0.00 1.00 426.41
## TNNull 4 -837.76 62.61 0.00 1.00 422.95
## TNG 5 -836.58 63.79 0.00 1.00 423.40## Data: SoilJuly181920
## Models:
## TNE: TotalN_percent ~ ESD + (1 | Location/Year)
## TNTE: TotalN_percent ~ TSF + ESD + (1 | Location/Year)
## TNInt: TotalN_percent ~ TSF * ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## TNE 7 -899.76 -874.27 456.88 -913.76
## TNTE 10 -901.18 -864.76 460.59 -921.18 7.4117 3 0.05987 .
## TNInt 19 -886.57 -817.37 462.28 -924.57 3.3926 9 0.94668
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## TNNull: TotalN_percent ~ 1 + (1 | Location/Year)
## TNE: TotalN_percent ~ ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## TNNull 4 -837.90 -823.33 422.95 -845.90
## TNE 7 -899.76 -874.27 456.88 -913.76 67.863 3 1.224e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## TNNull: TotalN_percent ~ 1 + (1 | Location/Year)
## TNT: TotalN_percent ~ TSF + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## TNNull 4 -837.90 -823.33 422.95 -845.90
## TNT 7 -838.81 -813.32 426.41 -852.81 6.9111 3 0.07479 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = TotalN_percent ~ TSF + ESD + (1 | Location/Year),
## data = SoilJuly181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 -0.003176 0.006814 -0.466 0.9649
## 3 Years Since Fire - Recently Burned == 0 -0.001587 0.011265 -0.141 0.9990
## Not Yet Burned - Recently Burned == 0 -0.020344 0.007834 -2.597 0.0438
## 3 Years Since Fire - Intermediate == 0 0.001588 0.010614 0.150 0.9987
## Not Yet Burned - Intermediate == 0 -0.017168 0.007251 -2.368 0.0792
## Not Yet Burned - 3 Years Since Fire == 0 -0.018757 0.012002 -1.563 0.3883
##
## 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 Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = TotalN_percent ~ ESD + (1 | Location/Year), data = SoilJuly181920,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 0.005811 0.011032 0.527 0.9509
## Saline Lowland - Clayey == 0 0.022011 0.008501 2.589 0.0456 *
## Sandy - Clayey == 0 -0.035128 0.007893 -4.451 <0.001 ***
## Saline Lowland - Loamy == 0 0.016200 0.011134 1.455 0.4556
## Sandy - Loamy == 0 -0.040939 0.009949 -4.115 <0.001 ***
## Sandy - Saline Lowland == 0 -0.057139 0.006872 -8.315 <0.001 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)P
cowplot::plot_grid( P_ppmplot1,P_ppmplot2, P_ppmplot3, nrow = 3, labels=c("A","B","C") )
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## PE 7 280.75 0.00 0.73 0.73 -133.17
## PTE 10 282.70 1.95 0.27 1.00 -130.95
## PInt 19 295.80 15.05 0.00 1.00 -127.45
## PNull 4 352.12 71.37 0.00 1.00 -171.99
## PT 7 353.82 73.07 0.00 1.00 -169.71
## PG 5 354.13 73.38 0.00 1.00 -171.96## Data: SoilJuly181920
## Models:
## PE: log(P_ppm + 1) ~ ESD + (1 | Location/Year)
## PTE: log(P_ppm + 1) ~ TSF + ESD + (1 | Location/Year)
## PInt: log(P_ppm + 1) ~ TSF * ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## PE 7 280.34 305.84 -133.17 266.34
## PTE 10 281.89 318.31 -130.95 261.89 4.4524 3 0.2166
## PInt 19 292.90 362.10 -127.45 254.90 6.9905 9 0.6381## Data: SoilJuly181920
## Models:
## PNull: log(P_ppm + 1) ~ 1 + (1 | Location/Year)
## PE: log(P_ppm + 1) ~ ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## PNull 4 351.97 366.54 -171.99 343.97
## PE 7 280.34 305.84 -133.17 266.34 77.63 3 < 2.2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## PNull: log(P_ppm + 1) ~ 1 + (1 | Location/Year)
## PT: log(P_ppm + 1) ~ TSF + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## PNull 4 351.97 366.54 -171.99 343.97
## PT 7 353.41 378.90 -169.71 339.41 4.5641 3 0.2066##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(P_ppm + 1) ~ TSF + ESD + (1 | Location/Year),
## data = SoilJuly181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 0.04547 0.05528 0.823 0.837
## 3 Years Since Fire - Recently Burned == 0 -0.08417 0.09191 -0.916 0.789
## Not Yet Burned - Recently Burned == 0 -0.05481 0.06383 -0.859 0.819
## 3 Years Since Fire - Intermediate == 0 -0.12964 0.08656 -1.498 0.426
## Not Yet Burned - Intermediate == 0 -0.10027 0.05929 -1.691 0.317
## Not Yet Burned - 3 Years Since Fire == 0 0.02936 0.09863 0.298 0.990
## (Adjusted p values reported -- single-step method)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(P_ppm + 1) ~ ESD + (1 | Location/Year), data = SoilJuly181920,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 -0.10584 0.08956 -1.182 0.630
## Saline Lowland - Clayey == 0 -0.02947 0.06901 -0.427 0.973
## Sandy - Clayey == 0 -0.46569 0.06408 -7.267 <1e-04 ***
## Saline Lowland - Loamy == 0 0.07637 0.09034 0.845 0.828
## Sandy - Loamy == 0 -0.35985 0.08076 -4.456 <1e-04 ***
## Sandy - Saline Lowland == 0 -0.43623 0.05579 -7.820 <1e-04 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)K
cowplot::plot_grid( K_ppmplot1,K_ppmplot2, K_ppmplot3, nrow = 3, labels=c("A","B","C") )
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## KTE 10 135.74 0.00 0.98 0.98 -57.46
## KE 7 143.49 7.75 0.02 1.00 -64.54
## KInt 19 152.24 16.50 0.00 1.00 -55.67
## KT 7 197.07 61.33 0.00 1.00 -91.33
## KNull 4 203.07 67.33 0.00 1.00 -97.46
## KG 5 203.58 67.85 0.00 1.00 -96.68## Data: SoilJuly181920
## Models:
## KE: log(K_ppm + 1) ~ ESD + (1 | Location/Year)
## KTE: log(K_ppm + 1) ~ TSF + ESD + (1 | Location/Year)
## KInt: log(K_ppm + 1) ~ TSF * ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## KE 7 143.08 168.57 -64.540 129.08
## KTE 10 134.92 171.34 -57.462 114.92 14.1562 3 0.0027 **
## KInt 19 149.34 218.53 -55.669 111.34 3.5853 9 0.9365
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## KNull: log(K_ppm + 1) ~ 1 + (1 | Location/Year)
## KE: log(K_ppm + 1) ~ ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## KNull 4 202.93 217.49 -97.463 194.93
## KE 7 143.08 168.57 -64.540 129.08 65.846 3 3.307e-14 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## KNull: log(K_ppm + 1) ~ 1 + (1 | Location/Year)
## KT: log(K_ppm + 1) ~ TSF + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## KNull 4 202.93 217.49 -97.463 194.93
## KT 7 196.66 222.15 -91.330 182.66 12.266 3 0.006526 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(K_ppm + 1) ~ TSF + ESD + (1 | Location/Year),
## data = SoilJuly181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 -0.01049 0.04356 -0.241 0.99485
## 3 Years Since Fire - Recently Burned == 0 0.04657 0.07178 0.649 0.91248
## Not Yet Burned - Recently Burned == 0 -0.17196 0.04997 -3.441 0.00278
## 3 Years Since Fire - Intermediate == 0 0.05707 0.06765 0.844 0.82738
## Not Yet Burned - Intermediate == 0 -0.16146 0.04616 -3.498 0.00239
## Not Yet Burned - 3 Years Since Fire == 0 -0.21853 0.07619 -2.868 0.02013
##
## 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 Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(K_ppm + 1) ~ TSF + ESD + (1 | Location/Year),
## data = SoilJuly181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 0.045077 0.068650 0.657 0.911
## Saline Lowland - Clayey == 0 0.051672 0.052922 0.976 0.757
## Sandy - Clayey == 0 -0.274207 0.049384 -5.553 <1e-04 ***
## Saline Lowland - Loamy == 0 0.006596 0.067583 0.098 1.000
## Sandy - Loamy == 0 -0.319283 0.061815 -5.165 <1e-04 ***
## Sandy - Saline Lowland == 0 -0.325879 0.043011 -7.577 <1e-04 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Ca
cowplot::plot_grid( Ca_ppmplot1,Ca_ppmplot2, Ca_ppmplot3, nrow = 3, labels=c("A","B","C") )
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## CaE 7 410.19 0.00 0.76 0.76 -197.89
## CaTE 10 412.91 2.72 0.19 0.95 -196.05
## CaNull 4 416.87 6.68 0.03 0.98 -204.36
## CaG 5 418.55 8.36 0.01 0.99 -204.17
## CaT 7 419.44 9.25 0.01 1.00 -202.51
## CaInt 19 424.48 14.30 0.00 1.00 -191.79## Data: SoilJuly181920
## Models:
## CaE: log(Ca_ppm + 1) ~ ESD + (1 | Location/Year)
## CaTE: log(Ca_ppm + 1) ~ TSF + ESD + (1 | Location/Year)
## CaInt: log(Ca_ppm + 1) ~ TSF * ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## CaE 7 409.78 435.27 -197.89 395.78
## CaTE 10 412.10 448.52 -196.05 392.10 3.6788 3 0.2983
## CaInt 19 421.58 490.78 -191.79 383.58 8.5166 9 0.4830## Data: SoilJuly181920
## Models:
## CaNull: log(Ca_ppm + 1) ~ 1 + (1 | Location/Year)
## CaE: log(Ca_ppm + 1) ~ ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## CaNull 4 416.72 431.29 -204.36 408.72
## CaE 7 409.78 435.27 -197.89 395.78 12.946 3 0.004755 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## CaNull: log(Ca_ppm + 1) ~ 1 + (1 | Location/Year)
## CaT: log(Ca_ppm + 1) ~ TSF + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## CaNull 4 416.72 431.29 -204.36 408.72
## CaT 7 419.03 444.52 -202.51 405.03 3.6936 3 0.2965##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(Ca_ppm + 1) ~ TSF + ESD + (1 | Location/Year),
## data = SoilJuly181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 0.007168 0.070252 0.102 1.000
## 3 Years Since Fire - Recently Burned == 0 -0.029141 0.114862 -0.254 0.994
## Not Yet Burned - Recently Burned == 0 -0.127341 0.080096 -1.590 0.373
## 3 Years Since Fire - Intermediate == 0 -0.036308 0.108305 -0.335 0.986
## Not Yet Burned - Intermediate == 0 -0.134508 0.073616 -1.827 0.251
## Not Yet Burned - 3 Years Since Fire == 0 -0.098200 0.120625 -0.814 0.842
## (Adjusted p values reported -- single-step method)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(Ca_ppm + 1) ~ ESD + (1 | Location/Year), data = SoilJuly181920,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 0.35196 0.11407 3.086 0.01055 *
## Saline Lowland - Clayey == 0 0.22347 0.08792 2.542 0.05137 .
## Sandy - Clayey == 0 0.25552 0.08156 3.133 0.00877 **
## Saline Lowland - Loamy == 0 -0.12849 0.11534 -1.114 0.67285
## Sandy - Loamy == 0 -0.09644 0.10289 -0.937 0.77852
## Sandy - Saline Lowland == 0 0.03205 0.07106 0.451 0.96830
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Mg
cowplot::plot_grid( Mg_ppmplot1,Mg_ppmplot2, Mg_ppmplot3, nrow = 3, labels=c("A","B","C") )
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## MgE 7 221.40 0.00 0.74 0.74 -103.50
## MgTE 10 223.85 2.45 0.22 0.96 -101.52
## MgInt 19 227.41 6.01 0.04 0.99 -93.25
## MgNull 4 232.14 10.74 0.00 1.00 -112.00
## MgG 5 234.21 12.81 0.00 1.00 -112.00
## MgT 7 234.23 12.83 0.00 1.00 -109.91## Data: SoilJuly181920
## Models:
## MgE: log(Mg_ppm + 1) ~ ESD + (1 | Location/Year)
## MgTE: log(Mg_ppm + 1) ~ TSF + ESD + (1 | Location/Year)
## MgInt: log(Mg_ppm + 1) ~ TSF * ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## MgE 7 220.99 246.48 -103.495 206.99
## MgTE 10 223.04 259.46 -101.519 203.04 3.9524 3 0.26665
## MgInt 19 224.51 293.70 -93.253 186.51 16.5315 9 0.05658 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## MgNull: log(Mg_ppm + 1) ~ 1 + (1 | Location/Year)
## MgE: log(Mg_ppm + 1) ~ ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## MgNull 4 232.00 246.56 -112.0 224.00
## MgE 7 220.99 246.48 -103.5 206.99 17.006 3 0.0007048 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilJuly181920
## Models:
## MgNull: log(Mg_ppm + 1) ~ 1 + (1 | Location/Year)
## MgT: log(Mg_ppm + 1) ~ TSF + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## MgNull 4 232.00 246.56 -112.00 224.00
## MgT 7 233.82 259.31 -109.91 219.82 4.1801 3 0.2427##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(Mg_ppm + 1) ~ TSF + ESD + (1 | Location/Year),
## data = SoilJuly181920, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 0.02488 0.05038 0.494 0.959
## 3 Years Since Fire - Recently Burned == 0 -0.03942 0.08334 -0.473 0.963
## Not Yet Burned - Recently Burned == 0 -0.07686 0.05795 -1.326 0.534
## 3 Years Since Fire - Intermediate == 0 -0.06429 0.07852 -0.819 0.840
## Not Yet Burned - Intermediate == 0 -0.10174 0.05366 -1.896 0.220
## Not Yet Burned - 3 Years Since Fire == 0 -0.03745 0.08886 -0.421 0.974
## (Adjusted p values reported -- single-step method)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(Mg_ppm + 1) ~ ESD + (1 | Location/Year), data = SoilJuly181920,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 -0.006025 0.080743 -0.075 1.000
## Saline Lowland - Clayey == 0 0.083349 0.062134 1.341 0.528
## Sandy - Clayey == 0 -0.122521 0.057901 -2.116 0.143
## Saline Lowland - Loamy == 0 0.089374 0.080785 1.106 0.678
## Sandy - Loamy == 0 -0.116496 0.072763 -1.601 0.369
## Sandy - Saline Lowland == 0 -0.205870 0.050292 -4.093 <0.001 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Litter Bags
cowplot::plot_grid( Decompplot1,Decompplot2, Decompplot3, nrow = 3, labels=c("A","B","C") )
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## DecTE 9 1937.50 0.00 0.85 0.85 -959.36
## DecT 6 1941.34 3.83 0.12 0.97 -964.49
## DecInt 17 1945.05 7.55 0.02 0.99 -954.14
## DecE 6 1947.04 9.54 0.01 1.00 -967.34
## DecNull 3 1950.81 13.31 0.00 1.00 -972.35
## DecG 4 1952.72 15.22 0.00 1.00 -972.28## Data: LitBag
## Models:
## DecE: Decomp ~ ESD + (1 | Year)
## DecTE: Decomp ~ TSF + ESD + (1 | Year)
## DecInt: Decomp ~ TSF * ESD + (1 | Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## DecE 6 1946.7 1967.6 -967.34 1934.7
## DecTE 9 1936.7 1968.0 -959.36 1918.7 15.959 3 0.001156 **
## DecInt 17 1942.3 2001.5 -954.14 1908.3 10.429 8 0.236206
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: LitBag
## Models:
## DecNull: Decomp ~ 1 + (1 | Year)
## DecE: Decomp ~ ESD + (1 | Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## DecNull 3 1950.7 1961.2 -972.35 1944.7
## DecE 6 1946.7 1967.6 -967.34 1934.7 10.031 3 0.0183 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: LitBag
## Models:
## DecNull: Decomp ~ 1 + (1 | Year)
## DecT: Decomp ~ TSF + (1 | Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## DecNull 3 1950.7 1961.2 -972.35 1944.7
## DecT 6 1941.0 1961.9 -964.49 1929.0 15.733 3 0.001286 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = Decomp ~ TSF + (1 | Year), data = LitBag, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 6.253 2.071 3.019 0.0125
## 3 Years Since Fire - Recently Burned == 0 2.525 3.122 0.809 0.8438
## Not Yet Burned - Recently Burned == 0 -2.877 2.972 -0.968 0.7585
## 3 Years Since Fire - Intermediate == 0 -3.727 3.039 -1.226 0.5978
## Not Yet Burned - Intermediate == 0 -9.130 2.722 -3.354 0.0041
## Not Yet Burned - 3 Years Since Fire == 0 -5.403 3.887 -1.390 0.4927
##
## 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 Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = Decomp ~ TSF + ESD + (1 | Year), data = LitBag,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 8.6745 3.1846 2.724 0.0319 *
## Saline Lowland - Clayey == 0 3.3459 2.7326 1.224 0.6057
## Sandy - Clayey == 0 0.7216 2.5629 0.282 0.9920
## Saline Lowland - Loamy == 0 -5.3286 2.7889 -1.911 0.2189
## Sandy - Loamy == 0 -7.9528 2.6635 -2.986 0.0145 *
## Sandy - Saline Lowland == 0 -2.6242 2.0605 -1.274 0.5741
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)pH & EC
pH 2020
print(aictab(cand.set = pH.mods, modnames = pH.mod.names))##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## pHInt 15 642.02 0.00 1 1 -305.34
## pHTE 9 653.84 11.82 0 1 -317.67
## pHT 6 666.92 24.90 0 1 -327.35
## pHE 7 670.92 28.90 0 1 -328.31
## pHNull 4 684.95 42.93 0 1 -338.42
## pHG 5 686.97 44.96 0 1 -338.41anova(pHE, pHTE, pHInt)## Data: Soil20
## Models:
## pHE: pH ~ ESD + (1 | Location/Month)
## pHTE: pH ~ TSF + ESD + (1 | Location/Month)
## pHInt: pH ~ TSF * ESD + (1 | Location/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## pHE 7 670.61 698.12 -328.31 656.61
## pHTE 9 653.35 688.71 -317.67 635.35 21.266 2 2.411e-05 ***
## pHInt 15 640.69 699.63 -305.34 610.69 24.660 6 0.0003946 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1anova(pHE, pHNull)## Data: Soil20
## Models:
## pHNull: pH ~ 1 + (1 | Location/Month)
## pHE: pH ~ ESD + (1 | Location/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## pHNull 4 684.85 700.56 -338.42 676.85
## pHE 7 670.61 698.12 -328.31 656.61 20.234 3 0.0001518 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1anova(pHT, pHNull)## Data: Soil20
## Models:
## pHNull: pH ~ 1 + (1 | Location/Month)
## pHT: pH ~ TSF + (1 | Location/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## pHNull 4 684.85 700.56 -338.42 676.85
## pHT 6 666.69 690.27 -327.35 654.69 22.154 2 1.547e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1summary(Mult_pHT) #additive model##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = pH ~ TSF + ESD + (1 | Location/Month), data = Soil20,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 0.32038 0.07008 4.572 < 0.001
## 3 Years Since Fire - Recently Burned == 0 0.27315 0.08063 3.388 0.00205
## 3 Years Since Fire - Intermediate == 0 -0.04723 0.07126 -0.663 0.78414
##
## Intermediate - Recently Burned == 0 ***
## 3 Years Since Fire - Recently Burned == 0 **
## 3 Years Since Fire - Intermediate == 0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)summary(Mult_pHE) #additive##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = pH ~ TSF + ESD + (1 | Location/Month), data = Soil20,
## REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 0.42043 0.11735 3.583 0.00171 **
## Saline Lowland - Clayey == 0 0.34239 0.09162 3.737 0.00104 **
## Sandy - Clayey == 0 0.29319 0.08365 3.505 0.00254 **
## Saline Lowland - Loamy == 0 -0.07804 0.11807 -0.661 0.90887
## Sandy - Loamy == 0 -0.12724 0.10571 -1.204 0.61621
## Sandy - Saline Lowland == 0 -0.04921 0.07421 -0.663 0.90810
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)EC 2020
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## ECTE 9 815.92 0.00 0.67 0.67 -398.71
## ECInt 15 817.37 1.45 0.32 1.00 -393.02
## ECE 7 826.58 10.66 0.00 1.00 -406.14
## ECT 6 828.80 12.88 0.00 1.00 -408.29
## ECNull 4 843.32 27.40 0.00 1.00 -417.61
## ECG 5 845.36 29.44 0.00 1.00 -417.60## Data: Soil20
## Models:
## ECE: log(EC + 1) ~ ESD + (1 | Location/Month)
## ECTE: log(EC + 1) ~ TSF + ESD + (1 | Location/Month)
## ECInt: log(EC + 1) ~ TSF * ESD + (1 | Location/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## ECE 7 826.28 853.78 -406.14 812.28
## ECTE 9 815.43 850.80 -398.71 797.43 14.847 2 0.0005969 ***
## ECInt 15 816.04 874.98 -393.02 786.04 11.392 6 0.0769866 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: Soil20
## Models:
## ECNull: log(EC + 1) ~ 1 + (1 | Location/Month)
## ECE: log(EC + 1) ~ ESD + (1 | Location/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## ECNull 4 843.21 858.93 -417.61 835.21
## ECE 7 826.28 853.78 -406.14 812.28 22.933 3 4.17e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: Soil20
## Models:
## ECNull: log(EC + 1) ~ 1 + (1 | Location/Month)
## ECT: log(EC + 1) ~ TSF + (1 | Location/Month)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## ECNull 4 843.21 858.93 -417.61 835.21
## ECT 6 828.57 852.15 -408.29 816.57 18.639 2 8.966e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(EC + 1) ~ TSF + ESD + (1 | Location/Month),
## data = Soil20, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Intermediate - Recently Burned == 0 0.33623 0.08735 3.849 0.00034
## 3 Years Since Fire - Recently Burned == 0 0.16909 0.10051 1.682 0.21077
## 3 Years Since Fire - Intermediate == 0 -0.16714 0.08879 -1.882 0.14288
##
## Intermediate - Recently Burned == 0 ***
## 3 Years Since Fire - Recently Burned == 0
## 3 Years Since Fire - Intermediate == 0
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(EC + 1) ~ TSF + ESD + (1 | Location/Month),
## data = Soil20, REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 0.34241 0.14542 2.355 0.08275 .
## Saline Lowland - Clayey == 0 0.40187 0.11333 3.546 0.00220 **
## Sandy - Clayey == 0 0.07856 0.10385 0.756 0.87023
## Saline Lowland - Loamy == 0 0.05946 0.14511 0.410 0.97599
## Sandy - Loamy == 0 -0.26386 0.13092 -2.015 0.17623
## Sandy - Saline Lowland == 0 -0.32332 0.09192 -3.517 0.00245 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Microbes
Total Abundance
cowplot::plot_grid( Total_Biomassplot1,Total_Biomassplot2, Total_Biomassplot3, nrow = 3, labels=c("A","B","C") )
##
## Model selection based on AICc:
##
## K AICc Delta_AICc AICcWt Cum.Wt LL
## BioTE 10 1867.03 0.00 0.63 0.63 -922.89
## BioE 7 1868.17 1.13 0.36 0.98 -926.77
## BioInt 19 1874.34 7.31 0.02 1.00 -915.91
## BioT 7 1888.08 21.05 0.00 1.00 -936.73
## BioNull 4 1890.83 23.80 0.00 1.00 -941.31
## BioG 5 1892.91 25.88 0.00 1.00 -941.29## Data: SoilM
## Models:
## BioE: Total_Biomass + 0.001 ~ ESD + (1 | Location/Year)
## BioTE: Total_Biomass + 0.001 ~ TSF + ESD + (1 | Location/Year)
## BioInt: Total_Biomass + 0.001 ~ TSF * ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## BioE 7 1867.5 1890.2 -926.77 1853.5
## BioTE 10 1865.8 1898.2 -922.89 1845.8 7.7544 3 0.05137 .
## BioInt 19 1869.8 1931.3 -915.91 1831.8 13.9689 9 0.12344
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilM
## Models:
## BioNull: Total_Biomass + 0.001 ~ 1 + (1 | Location/Year)
## BioE: Total_Biomass + 0.001 ~ ESD + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## BioNull 4 1890.6 1903.6 -941.31 1882.6
## BioE 7 1867.5 1890.2 -926.77 1853.5 29.068 3 2.167e-06 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1## Data: SoilM
## Models:
## BioNull: Total_Biomass + 0.001 ~ 1 + (1 | Location/Year)
## BioT: Total_Biomass + 0.001 ~ TSF + (1 | Location/Year)
## npar AIC BIC logLik deviance Chisq Df Pr(>Chisq)
## BioNull 4 1890.6 1903.6 -941.31 1882.6
## BioT 7 1887.5 1910.1 -936.73 1873.5 9.149 3 0.02737 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: glmer(formula = Total_Biomass + 0.001 ~ TSF + ESD + (1 | Location/Year),
## data = SoilM, family = Gamma)
##
## Linear Hypotheses:
## Estimate Std. Error z value
## Intermediate - Recently Burned == 0 -3.057e-04 3.278e-04 -0.933
## 3 Years Since Fire - Recently Burned == 0 4.927e-05 4.519e-04 0.109
## Not Yet Burned - Recently Burned == 0 1.362e-03 6.649e-04 2.049
## 3 Years Since Fire - Intermediate == 0 3.550e-04 4.067e-04 0.873
## Not Yet Burned - Intermediate == 0 1.668e-03 6.375e-04 2.617
## Not Yet Burned - 3 Years Since Fire == 0 1.313e-03 7.415e-04 1.771
## Pr(>|z|)
## Intermediate - Recently Burned == 0 0.7745
## 3 Years Since Fire - Recently Burned == 0 0.9995
## Not Yet Burned - Recently Burned == 0 0.1578
## 3 Years Since Fire - Intermediate == 0 0.8075
## Not Yet Burned - Intermediate == 0 0.0399 *
## Not Yet Burned - 3 Years Since Fire == 0 0.2703
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: glmer(formula = Total_Biomass + 0.001 ~ TSF + ESD + (1 | Location/Year),
## data = SoilM, family = Gamma)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Loamy - Clayey == 0 -0.0002728 0.0005079 -0.537 0.9490
## Saline Lowland - Clayey == 0 -0.0010025 0.0004197 -2.388 0.0775 .
## Sandy - Clayey == 0 0.0009116 0.0004063 2.243 0.1094
## Saline Lowland - Loamy == 0 -0.0007297 0.0005143 -1.419 0.4822
## Sandy - Loamy == 0 0.0011844 0.0004618 2.564 0.0495 *
## Sandy - Saline Lowland == 0 0.0019141 0.0003651 5.243 <0.001 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)TSF Comp %
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: 0.03597419
## 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 0.826
## NO3_ppm -0.79825 -0.54047 0.26589 0.0543 0.054 .
## Moisture -0.62822 -0.11260 -0.76985 0.0571 0.012 *
## P_ppm -0.60529 -0.79437 -0.05093 0.0562 0.032 *
## 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 0.092 .
## TotalN_percent -0.27291 -0.73625 -0.61924 0.0300 0.436
## 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 0.006 **
## 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$TSF
## 999 permutations
##
## Recently Burned Intermediate 3 Years Since Fire
## Intermediate 0.950 - -
## 3 Years Since Fire 0.003 0.003 -
## Not Yet Burned 0.077 0.077 0.008
##
## P value adjustment method: fdr##
## Pairwise comparisons using factor fitting to an ordination
##
## data: Mic.cape2 by MicEnv1920_3$ESD
## 999 permutations
##
## Clayey Loamy Saline Lowland
## Loamy 0.975 - -
## Saline Lowland 0.069 0.134 -
## Sandy 0.975 0.975 0.069
##
## P value adjustment method: fdr
Ordi Patches
##
## Call:
## metaMDS(comm = MicBiomassPatches, distance = "euclidean", k = 3, trymax = 50)
##
## global Multidimensional Scaling using monoMDS
##
## Data: wisconsin(sqrt(MicBiomassPatches))
## Distance: euclidean
##
## Dimensions: 3
## Stress: 0.03007112
## Stress type 1, weak ties
## Two convergent solutions found after 20 tries
## Scaling: centring, PC rotation
## Species: expanded scores based on 'wisconsin(sqrt(MicBiomassPatches))'## importance.MDS1 importance.MDS2 importance.MDS3
## Eigenvalue 0.07 0.05 0.02
## Proportion Explained 0.47 0.34 0.13
## Cumulative Proportion 0.47 0.81 0.94
## importance.MDS4 importance.MDS5
## Eigenvalue 0.01 0.00
## Proportion Explained 0.04 0.02
## Cumulative Proportion 0.98 1.00##
## ***VECTORS
##
## MDS1 MDS2 MDS3 r2 Pr(>r)
## NH4_ppm -0.95464 -0.03853 -0.29525 0.0498 0.480
## NO3_ppm -0.78352 -0.61354 0.09830 0.1293 0.012 *
## Moisture -0.80715 -0.14347 0.57265 0.0797 0.022 *
## P_ppm -0.50055 -0.83128 0.24171 0.0467 0.300
## K_ppm 0.38507 -0.77470 0.50156 0.0649 0.270
## Ca_ppm -0.64769 0.53494 0.54253 0.2132 0.002 **
## Mg_ppm -0.93318 0.35743 -0.03762 0.0230 0.336
## TotalN_percent 0.05687 -0.94496 0.32220 0.0385 0.552
## TotalC_percent -0.49572 -0.67075 0.55168 0.0641 0.046 *
## TCNR -0.85835 0.13420 0.49520 0.1723 0.012 *
## ---
## 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 0.0334 0.0189 -0.0231
## ESDLoamy 0.0414 0.0450 0.0692
## ESDSaline Lowland -0.0739 -0.0661 -0.0345
## ESDSandy 0.0264 0.0265 0.0172
## TSFRecently Burned -0.0352 -0.0053 -0.0061
## TSFIntermediate -0.0198 -0.0116 0.0623
## TSF3 Years Since Fire 0.1953 -0.0100 -0.0989
## TSFNot Yet Burned -0.0457 0.0672 -0.1382
## TreatmentCattle -0.0256 0.0346 0.0201
## TreatmentSheep 0.0279 -0.0376 -0.0218
##
## Goodness of fit:
## r2 Pr(>r)
## ESD 0.0434 0.176
## TSF 0.0984 0.012 *
## Treatment 0.0205 1.000
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Blocks: strata
## Permutation: free
## Number of permutations: 499