[R-sig-eco] PCA with vegan

[amelie_can]

Hello all, 

I am doing a pca using the vegan library with the function rda on two
dataset: 
1) species abundances (where I have my sites on the lines and the species
names on the columns, they were previously transformed with Hellinger) 
2) on a community mean weight analysis (where I have my sites on the lines
and my traits in columns). That second matrix was calculated by multiplying
two matrix (the first one was species abundances which were the relative
contribution of each species to its community (pi) was calculated and the
second one was quantitative traits associated to each species). 

The first time I did the pca on each dataset, I wrote SCALE = FALSE, which
means that my data are centered by column but not reduced. From what I
understood, as we have the same kind of data within my matrix, we do not
need to reduce it, otherwise it would be a "double standardization". My
supervisor was not sure about that method as I got a result where my first
axis explained 84% of the variation of my response variable. They thought it
was too high to be right.  

If I do a  SCALE = TRUE, it reduces my percent explained by my first axis. R
says that it  "Scale species to unit variance (like correlations)".

Can anybody advice me ? 

Thank you, 

Amelie



>From what I understand, I should write SCALE = FALSE but I just want to make
sure I am right. 

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