[R-sig-eco] How to get the total variance explained from an envfit object?

[Juan Antonio Balbuena]

Hi,

Unfortunately, I cannot give a direct answer to your question since I am 
not familiar with envfit.

However, I wonder whether you have a specific reason to use 
unconstrained ordination. If you use a constrained method, varpart will 
produce exactly what you want. (See e.g. 
https://www.davidzeleny.net/anadat-r/doku.php/en:varpart_examples).

Best

Juan A. Balbuena

El 07/11/2019 a las 21:02, Couch, Claire Elizabeth escribió:
> I am analyzing some microbiome data by using unconstrained ordination (PCA
> or NMDS) followed by environmental vector fitting with the envfit function
> in the vegan package. The output of envfit includes an r2 value for each
> vector or factor included in the envfit model, but I am interested in the
> total amount of variation explained by all the vectors/factors, rather than
> just stand-alone variables. I presume I cannot simply add up the R2 values
> assigned to each environmental variable, because there may be overlap in
> the microbiome variation that is "explained" by each environmental
> variable. However, there does not seem to be any way of accessing the total
> r2 value for the model.
>
> Using an example dataset, this is what I have tried so far:
>
> library(vegan)
> library(MASS)
>
> data(varespec, varechem)
> library(MASS)
> ord <- metaMDS(varespec)
> fit <- envfit(ord, varechem, perm = 999)
> fit
>
> This shows r2 for each environmental variable, but how do I extract the r2
> value for the entire model?
>
> I have tried running fit$r, attributes(fit)$r, and Rsquare.Adj(fit), but
> these all return NULL.
>
> I would greatly appreciate any suggestions!
>
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>
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-- 

Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
Symbiont Ecology and Evolution Lab
University of Valencia http://www.uv.es/~balbuena 
<http://www.uv.es/%7Ebalbuena>
P.O. Box 22085 http://www.uv.es/cophylpaco
46071 Valencia, Spain
e-mail: j.a.balbuena using uv.es <mailto:j.a.balbuena using uv.es>tel. +34 963 543 
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