Conditional CCA and Monte Carlo - Help!
Hi All, I am using canonical correspondence analysis to compare a community composition matrix to a matrix of sample spatial relationships and environmental variables. In order to parse out how much variance is explained purely by space (S/E) or the environment (E/S) I am using a conditional (partial) CCA. I want to test significance via Monte Carlo but I can not find a way to do this with a conditional CCA. I have been using vegan for the CCA and attempting to use ade4 to run a Monte Carlo. However, these two packages conflict when it comes to CCA. If I use vegan I can run a conditional CCA, and if I use ade4 I can do a Monte Carlo - but I can't figure out how to do a conditional CCA with ade4 OR a Monte Carlo with vegan. If anyone has experience with this I would be truly grateful for your help! I am fairly new to R, and I have quickly found myself in a place where "Google-ing" has no longer proven useful. Below are my scripts and error messages. Using Vegan:
vare.cca <- cca(InvertR.csv ~ Space1 + Space2... + Condition(Env1) + Condition(Env2)..., HabitatSpaceR.csv) randtest(vare.cca, nrepet = 1000)
Error in randtest.cca(vare.cca, nrepet = 1000) : Object of class dudi expected Using ade4:
vare.cca <- cca(InvertR.csv ~ Space1 + Space2... + Condition(Env1) + Condition(Env2)..., HabitatSpaceR.csv)
Error in cca(InvertR.csv ~ Space1 + Space2... + Condition(Env1) + Condition(Env2)... + : data.frame expected -- View this message in context: http://r.789695.n4.nabble.com/Conditional-CCA-and-Monte-Carlo-Help-tp4662572.html Sent from the R help mailing list archive at Nabble.com.