My recent study is on plant species abundance in two different habitats - along trail and along stream. I would like to know:

(1) if the species diversity is different between the two habitats,

(2) if there is any difference in species composition within the habitats, e.g. between the four transects in the stream habitats.

I am looking at using ANOSIM and NMDS to conduct my analysis. However, I am not sure how to:

(1) interpret the results of ANOSIM and NMDS

(2) prepare my data before I run the tests, (Rows=samples / Columns=Response variables?)

(3) can presence/absence data be used?

I sincerely hope I can get some of your expert insights on this. I deeply appreciate all the help rendered.