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 (resulting in 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(), method bray (FL.dist)

The assumption of homogeneity of dispersion among groups was tested and fulfilled. To perform the permanova I used the following code:

FL.div