#Supplementary file 12_Treatment effect on vegetation cover (Figure 1)


## R packages
library(glmmTMB)
library(emmeans)

##Load data file from "vegetation cover data"(Supplementary file 10)

## Vegetation cover cover exceeding 100% adjusted to 99.9%
##Treatment effect on tree cover using adjusted tree cover values

test1<-glmmTMB(Treecover.adj~Treatment+(1|location/plot),data = Vegetation_cover_data, family = beta_family(link = "logit"))
summary(test1)

##Posthoc test 

emmeans(test1,pairwise~Treatment, adjust="tukey")


##Treatment effect on non-tree cover

test2<-glmmTMB(groundvegetation~Treatment+(1|location/plot),data = Vegetation_cover_data, family = beta_family(link = "logit"))
summary(test2)

##Posthoc test

emmeans(test2, pairwise~Treatment, adjust="tukey")