[R-sig-eco] How to obtain P value from Monte Carlo sampling for adonis (permanova)?

[Eduard Szöcs]

Dear Ellen,

You can create a Permutation matrix holding ALL possible permutations
for a given permutation design using permute::allPerms() [Checkout the
help therein].

This matrix can be passed to adonis/adonis2 via the permutations= argument.

Hope this helps,

Eduard

On 18.11.2016 09:39, Ellen Pape wrote:
> Dear all,
> 
> I have recently decided to switch from Permanova/Primer to R, because the
> latter is freeware (and I don't know for how long I will still have a
> license). However, if I cannot seem to resolve my problem (see below), I
> might have to go back to using Primer/Permanova.
> 
> If I run pairwise permanova/adonis tests on my data, the number of unique
> permutations is small (I have two groups, each group has 3 observations)
> and the minimum P value I can get is larger than the alpha value I (and
> most people) that I use to determine statistical significance (i.e. 0.05).
> In the manual of the PERMANOVA+ add-on in Primer by Anderson et al. (2008)
>  it is mentioned (page 28 and onwards) that when the number of unique
> permutations is small (<100) than one should preferably interpret the
> Monte-Carlo p value.
> 
> Does anyone know how to do this in R?
> 
> 
> In my internet search I stumbled upon this page:
> http://r.789695.n4.nabble.com/monte-carlo-simulations-in-permanova-in-vegan-package-td4714034.html.
> "JAri Oksanen answered here: 2. If you want to do so, you can generate your
> resampling matrices by hand and use that matrix as the argument of
> permutations=. See the documentations (?adonis) which tells how to do so.
> ", but I don't understand how to this..
> 
> Thank you very much!
> 
> Ellen
> 
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> 
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-- 
Eduard Szöcs

Quantitative Landscape Ecology
Institute for Environmental Sciences
University Koblenz-Landau
Tel: +49 6341 280 31552
Office: Building I, Room 2.27
http://www.uni-koblenz-landau.de/en/campus-landau/faculty7/environmental-sciences/landscape-ecology/Staff/eduardszoecs