"partial" ordination
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