As far as I know, the only software that allows you to make a CPO is CANOCO. I was wondering if there is a R package to make the same analysis or an equivalent. Thank you!
EDIT: In case new people has the same question, I found a way using the classic cca function in the vegan package. To perform a CPO you need your community matrix, with species in roes and sites in columns, and environmental matrix, with species in rows and environmental variables in columns, and third, constrain matrix, which in this case will be a matrix with species in rows and ancestors in columns, being the ancestors the nodes in a phylogenetic tree. Species under the same ancestor receive a 1 in the matrix, otherwise it will be a 0.
So, the formula would be something like
cpo1
To Mr. Pelegrin
You can read more about Phylogenetic canonical correlation analysis using R on this page: http://blog.phytools.org/2011/09/phylogenetic-canonical-correlation.html
The code in R is:
> source("http://faculty.umb.edu/liam.revell/phytools/phyl.cca/v0.1/phyl.cca.R")
> result
To Mr. Pelegrin
You can read more about Phylogenetic canonical correlation analysis using R on this page: http://blog.phytools.org/2011/09/phylogenetic-canonical-correlation.html
The code in R is:
> source("http://faculty.umb.edu/liam.revell/phytools/phyl.cca/v0.1/phyl.cca.R")
> result
Thank you very much Halldis. I found not only the PCC but the entire Phytools package very useful.
Cheers,
Hi Nicolas,
If you are interested in comparative methods you can find an overview of many methods in this book (http://www.mpcm-evolution.org/). The book also includes online practical materials.
Cheers,
Danny
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