Aligned

01b_MesobromionCluster.R

@@ -82,18 +82,17 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
   traits <- traits %>% 
     rename_all(.funs=~gsub(pattern=".mean$", replacement="", x=.))  %>% 
     mutate_if(~is.character(.), .funs=~as.factor(.)) %>%
+    filter(complete.cases(.)) %>% ## TEMPORARY ! only species without any NA
     column_to_rownames("species0")
-
-#temporary    ### Use only a subset of traits
-    #dplyr::select(LeafArea:Disp.unit.leng)
-  print("TEMPORARY - delete species with any NA in traits")
-  traits <- traits %>%
-     filter(complete.cases(.))
+  print("TEMPORARY - only species without any NA")
   species <- species %>%
-     dplyr::select(rownames(traits))
+    dplyr::select(rownames(traits))
 
-  print("TEMPORARY - revert back species to pa")
+  print("TEMPORARY - revert abundances back to pa")
   species <- (species>0)*1
+
+#temporary    ### Use only a subset of traits
+    #dplyr::select(LeafArea:Disp.unit.leng)
   
   if(combinations=="all") {
     ## create list of indices for each combination of traits up to a max number of interactions
@@ -119,10 +118,10 @@ 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, "_.RData", sep=""))
+    save(corXY.output, file = paste(output,"_", chunk.i, "_.RData", sep=""))
   }
   
   

cli_01b.r

@@ -105,4 +105,4 @@ ncores         <- cli$options$ncores
 # ------------------------------------------------------------------------------
 
 source("01b_MesobromionCluster.R")
-Mesobromion(species.path, traits.path, output, myfunction, combinations, start.round, relax.round, max.inter.t, chunk.n, chunk.i, nperm, ncores)
+Mesobromion(species.path, traits.path, output, myfunction, combinations, start.round, relax.round, max.inter.t, chunkn, chunk.i, nperm, ncores)