[R-sig-eco] ANOSIM in vegan

[Jari Oksanen]

On 12/11/10 02:23 AM, "Soumi Ray" <soumiray74 at gmail.com> wrote:

> Hi,
> 
> I have a dataset consisting of species collected from the same location
> during 2 time periods - i want to see if the community composition is
> similar during the two time periods. My entire dataset is presence/absence
> (0/1) data. There are around 23 species and 400 samples (during each time
> period, so a total of 800 samples). Will ANOSIM from the vegan package be an
> right test to apply? I was going through some papers online where they have
> used methods like db-RDA in similar situations. Would it be right to use it
> for qualitative data? Any suggestion would be of great help.

Soumi,

I only comment the db-RDA/anosim choice: if you can use one, you can use the
other. They are very similar and have the same limitation and "assumptions".
Both are based on dissimilarity measures, and you can use the same
dissimilarities in both methods. They also handle the dissimilarities very
similarly. Overall tests for db-RDA by terms (as implemented in anova(...,
by = "term") for vegan::capscale) and adonis tests give very similar
results. However, they are not identical. The difference is that for
non-Euclidean dissimilarities you will have some negative eigenvalues. These
are ignored in db-RDA (capscale), but they are taken into account in adonis.
Which method to use depends on your questions, and what else you want to do
with your data than get the test statistics.

Cheers, Jari Oksanen