On 10 May 2004, at 17:15, Heike Schmitt wrote:
I want to include a vector representing the sites - environmental data
correlation in a PCA.
I currently use prcomp (no scaling) to perform the PCA, and envfit to
retrieve the coordinates of the environmental data vector. However, the
vector length is different from the one obtained in CAnoco when performing
a species - environmental biplot (scaling -2). How can I scale the vector
in order to be in accordance with Canoco, or which other scaling options
are there?
Canoco scaling abs(2) does not scale sites, but the sum of squares of site scores = 1 for all axes. In contrast, prcomp scales site axes by eigenvalue, like does Canoco with scaling abs(1). Therefore you cannot get similar results as in Canoco. A simple solution that *may* (or may not) work is to transpose your data: instead of prcomp(x), try prcomp(t(scale(x, scale=F), center=F). This does the centring to the columns of x (like it should be done), then transposes your data and prcomp's without new centring -- which was already made for columns (I didn't test this, but this way it was done in the olden times). Another alternative is to use the function rda in the same package where you found envfit (vegan), since it is not unlike Canoco in its scaling. However, it won't give you negative scalings of PCA (RDA without constraints), since its author (that's I) thinks that you shouldn't use negative scaling of Canoco in RDA/PCA. The package ships with a pdf document which discusses PCA scaling in prcomp, princomp, rda (of vegan) and Canoco (of Cajo ter Braak), and even hints how to get the minus scalings that the author doesn't approve.
cheers, jari oksanen -- Jari Oksanen, Oulu, Finland
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