[R-sig-eco] Specifying contrasts for an interaction in mvabund/manyglm

[Juan Antonio Balbuena]

Hi

You may also wish to try package rrpp (Collyer & Adams 2018, 
https://doi.org/10.1111/2041-210X.13029). The abstract reads: "a 
pairwise function provides statistical tests for comparisons of 
least‐squares means or slopes, among designated groups".

Perhaps it works for you.

All the best

Juan A. Balbuena

El 23/09/2020 a las 02:42, Kyle Tyler escribió:
> Hi Diogo,
>
>  From my joining of factors it appears that way, but this is just to identify which season and site combo the sample comes from for the post-hoc test to run on for the interaction. Season is otherwise orthogonal with Site.
>
> I will look at gllvm again, but I am not sure it can perform hypothesis testing, or if it uses likelihood ratios so that I can then also determine taxa contributions to model deviance; my other reasons for using mvabund.
>
> Cheers,
> Kyle
>
> Get Outlook for Android<https://aka.ms/ghei36>
>
> ________________________________
> From: Diogo B. Provete <dbprovete using gmail.com>
> Sent: Wednesday, September 23, 2020 1:38:38 AM
> To: r-sig-ecology <r-sig-ecology using r-project.org>; Kyle Tyler <kyle.tyler using cdu.edu.au>
> Subject: Specifying contrasts for an interaction in mvabund/manyglm
>
> Hi Kyle,
> from the bottom of your message it seems that what you have is a nested design, with Season nested within Site. If you specify your model with just the additive effect and the interaction it doesn't take that into account.
> I'm not sure if mvabund allows that kind of planned comparisons you want to conduct. I'd try the newer package gllvm that is much more flexible and can handle random factors.
>
> All the best
> Diogo
>
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