Hi, I am using the analyses; Canonical analysis of principal coordinates (CAP) and Similarity Percentages - species contributions (SIMPER) in the stats program, PRIMER. However, I prefer to use R and was wondering what the equivalent functions were? I believe the vegan package is where one goes for permutational analyses but am not sure which functions to use. Any help would be appreciated. Cheers
Hi Jessica,
Yes vegan has the simper() function.
For CAP analysis you need to use the rda() function. You will need to transform your data into euclidean space though (Hellinger transformation). If you are using bray-curtis dissimilarities, you should use db-RDA using the capscale() function.
http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/capscale.html
Vegan is a great substitute for the PRIMER software.
Good luck!
Chris
Hi Jessica,
vegan has a simper function:
library(vegan)
?simper
Best wishes
Malcolm
Hi Jessica,
Yes vegan has the simper() function.
For CAP analysis you need to use the rda() function. You will need to transform your data into euclidean space though (Hellinger transformation). If you are using bray-curtis dissimilarities, you should use db-RDA using the capscale() function.
http://cc.oulu.fi/~jarioksa/softhelp/vegan/html/capscale.html
Vegan is a great substitute for the PRIMER software.
Good luck!
Chris
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