##Supplementary file 11_GLMM on Treatment effect on tree species richness, Evergreen tree cover and palatable tree cover(Table 1)

## R packages

library(glmmTMB)
library(emmeans)


##Treatment effect on tree species richness
## load data from "Tree species richness data" file (Supplementary file 9)

Tree.sp<-glmmTMB(Treespecies~Treatment+(1|location/plot),data = Tree_species_richness_data, family = poisson(link = "log"))
summary(Tree.sp)

##Posthoc test
emmeans(Tree.sp, pairwise~Treatment, adjust="tukey", type="response")


## load data from "Vegetation_cover_data" file (Supplementary file 10)
## Vegetation cover cover exceeding 100% adjusted to 99.9%

##Treatment effect on evergreen tree cover
Tree.evergreen<-glmmTMB(evergreentree~Treatment+(1|location/plot),data = Vegetation_cover_data, family = beta_family(link = "logit"))
summary(Tree.evergreen)

##Posthoc test
emmeans(Tree.evergreen,pairwise~Treatment, adjust="tukey")


##Treatment effect on palatable tree cover
Tree.pala<-glmmTMB(palatabletree~Treatment+(1|location/plot),data = Vegetation_cover_data, family = beta_family(link = "logit"))
summary(Tree.pala)

##Posthoc test
emmeans(Tree.pala,pairwise~Treatment, adjust="tukey")