[R-sig-eco] Principal Response Curves- Calculating treatment effects

irantzu.primicia at unavarra.es irantzu.primicia at unavarra.es
Thu Feb 16 11:27:03 CET 2012

Dear all,

I am very interested in carrying out a principal response curves analysis
(PRC) on my data using the vegan package in R. To fully understand the
analysis, I started by simulating the example of Van den Brink & Ter Braak
(1999), data pyrifos in vegan, and I carried out the analyses in Canoco
and R. I think that the R script should be:


And then use the “lc” site scores: site.scr<- scores(PRCpyrifos,
scaling=1, display="lc")

However, the site and species scores calculated in Canoco and R are
different, as I think they are multiplied by a constant in both software.
I’ve read the “decision-vegan.pdf” documentation, but I don’t fully
understand it. What could I do it to compare them? Besides, I would like
to calculate the treatment effect on a determined species in a specific
moment as Van den Brink & Ter Braak (1999) do in their paper, but as the
scores obtained in R are different from those with Canoco, I don’t know
how to do it in R. I also would like to calculate the second PRC axis, so
I'd need these data for it as well.

I would really appreciate any help,

Thank you in advance,

Irantzu Primicia

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