Veg Structure Stats and Graphs
Jonathan Spiess
April 1, 2021
Overview
Mostly showing graphs and yearly Tukey’s for now
Consistent patch contrast across variables except for 2019
No differences between grazer treatments
VOR Graphs
VOR Stats
VORt17a <- lmer(log(VOR_Mean+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2017"), REML = FALSE)
Mult_VOR17a <- glht(VORt17a, linfct=mcp(TSF = "Tukey"))
summary(Mult_VOR17a) #Unburned higher than RB##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(VOR_Mean + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2017"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Unburned - RB == 0 0.32499 0.05217 6.229 4.68e-10 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)VORt18a <- lmer(log(VOR_Mean+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2018"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluesMult_VOR18a <- glht(VORt18a, linfct=mcp(TSF = "Tukey"))
summary(Mult_VOR18a) #unburned higher than RB and 1-2##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(VOR_Mean + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2018"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 0.16341 0.08616 1.897 0.1387
## Unburned - RB == 0 0.34437 0.07465 4.613 <0.001 ***
## Unburned - 1yr2yr == 0 0.18096 0.07463 2.425 0.0403 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)VORt19a <- lmer(log(VOR_Mean+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2019"), REML = FALSE)
Mult_VOR19a <- glht(VORt19a, linfct=mcp(TSF = "Tukey"))
summary(Mult_VOR19a) #no differences##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(VOR_Mean + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2019"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 0.012110 0.092315 0.131 0.999
## 2yr3yr - RB == 0 0.149552 0.093014 1.608 0.374
## Unburned - RB == 0 0.153959 0.094077 1.637 0.358
## 2yr3yr - 1yr2yr == 0 0.137443 0.088975 1.545 0.411
## Unburned - 1yr2yr == 0 0.141850 0.092308 1.537 0.415
## Unburned - 2yr3yr == 0 0.004407 0.093007 0.047 1.000
## (Adjusted p values reported -- single-step method)VORt20a <- lmer(log(VOR_Mean+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2020"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient
## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluesMult_VOR20a <- glht(VORt20a, linfct=mcp(TSF = "Tukey"))
summary(Mult_VOR20a) #RB lower than everyone##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(VOR_Mean + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2020"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 0.61590 0.08051 7.650 <0.001 ***
## 2yr3yr - RB == 0 0.56275 0.08050 6.990 <0.001 ***
## 3yr4yr - RB == 0 0.72058 0.08052 8.949 <0.001 ***
## 2yr3yr - 1yr2yr == 0 -0.05315 0.08050 -0.660 0.912
## 3yr4yr - 1yr2yr == 0 0.10468 0.08052 1.300 0.563
## 3yr4yr - 2yr3yr == 0 0.15784 0.08052 1.960 0.203
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Max Live Height Graphs
Max Live Height Stats
#2017
MLt17a <- lmer(MaxLive ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2017"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluesMult_ML17a <- glht(MLt17a, linfct=mcp(TSF = "Tukey"))
summary(Mult_ML17a) #Unburned > RB##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = MaxLive ~ TSF + (1 | Transect/Pasture), data = subset(HRECVeg,
## Year == "2017"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Unburned - RB == 0 0.7381 0.2642 2.793 0.00522 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)#2018
MLt18a <- lmer(MaxLive ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2018"), REML = FALSE)
Mult_ML18a <- glht(MLt18a, linfct=mcp(TSF = "Tukey"))
summary(Mult_ML18a) #RB lower than other two patches##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = MaxLive ~ TSF + (1 | Transect/Pasture), data = subset(HRECVeg,
## Year == "2018"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 0.8906 0.3573 2.493 0.0335 *
## Unburned - RB == 0 1.4396 0.3095 4.651 <0.001 ***
## Unburned - 1yr2yr == 0 0.5491 0.3095 1.774 0.1771
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)#2019
MLt19a <- lmer(MaxLive ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2019"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.198794 (tol = 0.002, component 1)Mult_ML19a <- glht(MLt19a, linfct=mcp(TSF = "Tukey"))
summary(Mult_ML19a) #no difference##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = MaxLive ~ TSF + (1 | Transect/Pasture), data = subset(HRECVeg,
## Year == "2019"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 -0.578542 0.533300 -1.085 0.699
## 2yr3yr - RB == 0 -0.045671 0.537248 -0.085 1.000
## Unburned - RB == 0 -0.039172 0.543552 -0.072 1.000
## 2yr3yr - 1yr2yr == 0 0.532871 0.512006 1.041 0.725
## Unburned - 1yr2yr == 0 0.539370 0.533260 1.011 0.743
## Unburned - 2yr3yr == 0 0.006499 0.537208 0.012 1.000
## (Adjusted p values reported -- single-step method)#2020
MLt20a <- lmer(MaxLive ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2020"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00623886 (tol = 0.002, component 1)Mult_ML20a <- glht(MLt20a, linfct=mcp(TSF = "Tukey"))
summary(Mult_ML20a) #RB lower than other patches##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = MaxLive ~ TSF + (1 | Transect/Pasture), data = subset(HRECVeg,
## Year == "2020"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 2.70805 0.36941 7.331 <1e-04 ***
## 2yr3yr - RB == 0 2.09720 0.36939 5.678 <1e-04 ***
## 3yr4yr - RB == 0 2.65104 0.36951 7.174 <1e-04 ***
## 2yr3yr - 1yr2yr == 0 -0.61084 0.36939 -1.654 0.349
## 3yr4yr - 1yr2yr == 0 -0.05701 0.36951 -0.154 0.999
## 3yr4yr - 2yr3yr == 0 0.55384 0.36950 1.499 0.438
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Max Dead Height Graphs
Max Dead Height Stats
#2017
MDt17a <- lmer(log(MaxDead+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2017"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluesMult_MDt17a <- glht(MDt17a, linfct=mcp(TSF = "Tukey"))
summary(Mult_MDt17a) #different##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(MaxDead + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2017"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Unburned - RB == 0 0.59683 0.04403 13.55 <2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)#2018
MDt18a <- lmer(log(MaxDead+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2018"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient
## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluesMult_MDt18a <- glht(MDt18a, linfct=mcp(TSF = "Tukey"))
summary(Mult_MDt18a) #Unburned > 1-2 > RB ##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(MaxDead + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2018"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 0.22277 0.05079 4.386 3.26e-05 ***
## Unburned - RB == 0 0.44043 0.04404 10.000 < 1e-05 ***
## Unburned - 1yr2yr == 0 0.21766 0.04401 4.946 < 1e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)#2019
MDt19a <- lmer(log(MaxDead+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2019"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00799883 (tol = 0.002, component 1)Mult_MDt19a <- glht(MDt19a, linfct=mcp(TSF = "Tukey"))
summary(Mult_MDt19a) #RB lower than everybody, others equal##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(MaxDead + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2019"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 0.29476 0.06879 4.285 0.000113 ***
## 2yr3yr - RB == 0 0.39428 0.06914 5.703 < 1e-04 ***
## Unburned - RB == 0 0.33128 0.06943 4.771 < 1e-04 ***
## 2yr3yr - 1yr2yr == 0 0.09952 0.06780 1.468 0.457059
## Unburned - 1yr2yr == 0 0.03652 0.06878 0.531 0.951557
## Unburned - 2yr3yr == 0 -0.06300 0.06912 -0.911 0.798747
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)#2020
MDt20a <- lmer(log(MaxDead+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2020"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.18257 (tol = 0.002, component 1)Mult_MDt20a <- glht(MDt20a, linfct=mcp(TSF = "Tukey"))
summary(Mult_MDt20a) #RB lower than everybody, others equal##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(MaxDead + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2020"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 1.01550 0.10025 10.130 <1e-04 ***
## 2yr3yr - RB == 0 1.12683 0.10024 11.241 <1e-04 ***
## 3yr4yr - RB == 0 1.20602 0.10028 12.027 <1e-04 ***
## 2yr3yr - 1yr2yr == 0 0.11133 0.10024 1.111 0.683
## 3yr4yr - 1yr2yr == 0 0.19052 0.10028 1.900 0.228
## 3yr4yr - 2yr3yr == 0 0.07919 0.10028 0.790 0.859
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Mean Litter Depth Graphs
Mean Litter Depth Stats
#2017
LMt17a <- lmer(log(LitMean+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2017"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0117383 (tol = 0.002, component 1)Mult_LMt17a <- glht(LMt17a, linfct=mcp(TSF = "Tukey"))
summary(Mult_LMt17a)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(LitMean + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2017"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## Unburned - RB == 0 0.18805 0.04495 4.184 2.87e-05 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)#2018
LMt18a <- lmer(log(LitMean+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2018"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluesMult_LMt18a <- glht(LMt18a, linfct=mcp(TSF = "Tukey"))
summary(Mult_LMt18a)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(LitMean + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2018"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 0.05945 0.05932 1.002 0.574
## Unburned - RB == 0 0.42198 0.05141 8.209 <1e-04 ***
## Unburned - 1yr2yr == 0 0.36253 0.05139 7.055 <1e-04 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)#2019
LMt19a <- lmer(log(LitMean+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2019"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## unable to evaluate scaled gradient
## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge: degenerate Hessian with 1 negative eigenvaluesMult_LMt19a <- glht(LMt19a, linfct=mcp(TSF = "Tukey"))
summary(Mult_LMt19a)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(LitMean + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2019"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 0.15448 0.06087 2.538 0.05395 .
## 2yr3yr - RB == 0 0.18467 0.06125 3.015 0.01362 *
## Unburned - RB == 0 0.37744 0.06168 6.119 < 0.001 ***
## 2yr3yr - 1yr2yr == 0 0.03019 0.05949 0.508 0.95732
## Unburned - 1yr2yr == 0 0.22296 0.06086 3.664 0.00139 **
## Unburned - 2yr3yr == 0 0.19277 0.06124 3.148 0.00866 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)#2020
LMt20a <- lmer(log(LitMean+1) ~ TSF + (1|Transect/Pasture), data=subset(HRECVeg, Year=="2020"), REML = FALSE)## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.0563234 (tol = 0.002, component 1)Mult_LMt20a <- glht(LMt20a, linfct=mcp(TSF = "Tukey"))
summary(Mult_LMt20a)##
## Simultaneous Tests for General Linear Hypotheses
##
## Multiple Comparisons of Means: Tukey Contrasts
##
##
## Fit: lmer(formula = log(LitMean + 1) ~ TSF + (1 | Transect/Pasture),
## data = subset(HRECVeg, Year == "2020"), REML = FALSE)
##
## Linear Hypotheses:
## Estimate Std. Error z value Pr(>|z|)
## 1yr2yr - RB == 0 0.76204 0.10735 7.099 <1e-04 ***
## 2yr3yr - RB == 0 0.91733 0.10735 8.545 <1e-04 ***
## 3yr4yr - RB == 0 0.88177 0.10737 8.212 <1e-04 ***
## 2yr3yr - 1yr2yr == 0 0.15528 0.10735 1.447 0.470
## 3yr4yr - 1yr2yr == 0 0.11972 0.10737 1.115 0.680
## 3yr4yr - 2yr3yr == 0 -0.03556 0.10737 -0.331 0.987
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## (Adjusted p values reported -- single-step method)Bare Ground Cover Graphs
Ground Litter Cover Graphs
Vertical Litter Cover Graphs
