### nMDS analysis require(vegan) nmds<-metaMDS(fi_specallsp1983, distance = "bray") nmds ### betadisper analysis require(vegan) dis1 <- vegdist(fi_specallsp1983) groups <- factor(c(rep(1,16), rep(2,16), rep(3,16)), labels = c("9","10","11")) mod <- betadisper(dis1, groups) mod anova(mod) ### PERMANOVA analysis require(vegan) permanova<-adonis(fi_specallsp1975 ~ site, data = fi_env, method="bray",perm=999) #test for diff in comp between groups permanova ### SIMPER analysis require(vegan) (sim <- with(fi_env, simper(fi_specallsp2017, site))) # contribution of each sp lapply(sim, FUN=function(x){x$overall}) # % diff of sp bet each comm. summary(sim) ### pairwiseAdonis require(pairwiseAdonis) ?pairwise.adonis pairwise.adonis(fi_specallsp1983,fi_env$site)