fixed bug

01_Mesobromion.R

@@ -293,9 +293,9 @@ ggplot(data=mydata) +
 
 
 traits.sign <- traits %>% 
+  rownames_to_column("species0") %>% 
   dplyr::select(traits.sign.alone)
-write_csv(traits.sign, "_data/Mesobromion/traits.out.10perc.sign.txt")
-
+write_delim(traits.sign, path="_data/Mesobromion/traits.out.10perc.sign.txt", delim="\t")
 
 break()
 

01b_MesobromionCluster.R

@@ -59,15 +59,13 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
 #  cor.perm <- matrix(NA, nrow=length(allcomb.t), ncol=nperm, 
 #                     dimnames = list(paste("t", names.t, sep=""), paste("p",1:nperm, sep="")))
                                                                              
-  speciesb <- species
-  traitsb <- traits
   corXY.output <- NULL
   for(i in 1:length(allcomb.t)) {
     tt <- unlist(allcomb.t[i])
     #bootstrap species matrix 
 #    set.seed(1984)
     corXY.output <- rbind(corXY.output, 
-                          get.corXY.bootstrap(comm=speciesb, trait=traitsb.perm, trait.sel=tt, stat="RV", bootstrap=nperm))
+                          get.corXY.bootstrap(comm=species, trait=traits, trait.sel=tt, stat="RV", bootstrap=nperm))
     save(corXY.output, file = paste(output, "_", chunk.i, ".RData", sep=""))
   }
 }