Hello everyone,

I am working with forest restoration and I want to test the effect of 3 treatments in the species composition.

To summarize my data: I have presence/absence and abundance data for 34 vascular plants species in 18 sites ("ID"). In these sites, 3 different treatments were applied (in result I have 6 sites within each "Treatment") and the data was collected before, right after and 8 years after ("Timeline") the treatments were applied, therefore I am also working with repeated measures.

Before performing the permanova test with adonis2, I applied a square root transformation to my data and then created a distance matrix using vegdist function, method "bray" ("FL.dist")

The assumption of homogeneity of dispersion among groups was tested and fulfilled.

To perform the permanova analyses I used the following script

FL.div