Corrected 99 - trait permutation

01b_MesobromionCluster.R

@@ -110,7 +110,7 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
     corXY.output <- foreach(i=1:length(allcomb.t), .combine=rbind) %myinfix% {
       tt <- unlist(allcomb.t[i])
       corXY.output <- rbind(corXY.output, 
-                            get.corXY.bootstrap(comm=species, trait=traits, 
+                            myfunction(comm=species, trait=traits, 
                                                 trait.sel=tt, bootstrap=nperm))
     }
     save(corXY.output, file = paste(output,"_", chunk.i, "_.RData", sep=""))

99_HIDDEN_functions.R

@@ -89,14 +89,15 @@ get.corXY.bootstrap <- function(comm, traits, trait.sel="all", bootstrap=199){
   for(b in 1:bootstrap){
     #RV.tmp <- RV.rtest(W.beals[index.bootstr[[b]],], as.data.frame(syn.out.tmp)[index.bootstr[[b]],])
     RD.tmp <- dcor(W.beals[index.bootstr[[b]],], as.data.frame(syn.out.tmp)[index.bootstr[[b]],])^2
-    syn.out.perm.tmp <- matrix.x(comm=comm, traits=traits[index.traits[[bootstrap]],ii,drop=F], 
+    syn.out.perm.tmp <- matrix.x(comm=comm, traits=traits[index.traits[[b]],ii,drop=F], 
                                  scale=T)$matrix.X #, asym.bin=binary.traits
     #RV.perm.tmp <- RV.rtest(W.beals[index.bootstr[[b]],], as.data.frame(syn.out.perm.tmp)[index.bootstr[[b]],])
     RD.perm.tmp <- dcor(W.beals[index.bootstr[[b]],], as.data.frame(syn.out.perm.tmp)[index.bootstr[[b]],])^2
     corXY <- rbind(corXY,
                    data.frame(Trait.comb=lab.tmp, bootstr.n=b, Test="RD", 
                               Coef.obs=RD.tmp, Coef.perm=RD.perm.tmp))
-    if(b %in% round(seq(1,bootstrap, length.out=10))){print(paste("trait", paste0(ii, collapse="_"), "perm", b))}
+    if(b %in% round(seq(1,bootstrap, length.out=10))){
+      print(paste("trait", paste0(ii, collapse="_"), "perm", b, paste(colnames(traits[trait.sel]), collapse="+")))}
   }
   return(corXY)
 }