[R-sig-eco] "partial" ordination

[Gavin Simpson]

That will work, as long as env is a matrix, not a data frame. An alternative is:

    ppca <- rda(X = spe, Z = env)

G

On 24 January 2014 09:56, Duarte Viana <viana.sptd at gmail.com> wrote:
> Hello all,
>
> I'm interested in applying an ordination method (e.g. PCA or NMDS) to
> a species matrix. However, I want to remove the potential effect of
> the environment, which I'm not interested in modelling, from the
> ordination (i.e. partialling out the environmental effect).
>
> I've thought in the following approach (with the vegan package):
>
> # spe: species matrix
> # env: environment matrix
> partial.pca<-rda(spe~1+Condition(env))
> plot(partial.pca)
>
> Is this a reasonable approach?
>
> Some feedback would be great.
> Thanks,
>
> Duarte
>
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-- 
Gavin Simpson, PhD