Updated 01b to save intermediate steps

01b_MesobromionCluster.R

@@ -72,9 +72,9 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
   species <- read_delim(species.path, delim="\t") %>%
 		as.data.frame()
   traits <- read_delim(traits.path, delim="\t") %>%
-		as.data.frame()# %>% 
+		as.data.frame() %>% 
 ### TEMPORARY FOR TESTING!
-#    dplyr::select(1:11)
+    dplyr::select(1:11)
   
   
   traits <- traits %>% 
@@ -115,8 +115,9 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
   
   
   if(combinations=="sequential"){
-    corXY.output <- NULL
+    corXY.ci <- NULL
     for(nround in 1:max.inter.t){
+      corXY.output <- NULL
       ## select combination of traits based on best
       if(nround==1) {
         allcomb.t <- lapply(1:ncol(traits), function(x){return(x)})
@@ -167,7 +168,8 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
       #save(corXY.output, file = paste(output, "_", nround, ".RData", sep=""))
       
       print(paste("Summarize after round", nround, "and find best, significant trait combos"))
-      corXY.ci <- get.ci(corXY.output)
+      corXY.ci <- corXY.ci %>% 
+        bind_rows(get.ci(corXY.output))
       ##get best or new best
       if(nround==1) {
         traits.sign.alone <- corXY.ci %>% 
@@ -208,9 +210,9 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
           print(paste("new best at round=", nround, "is trait combination", best))
         } else {print(paste("no new best at round=", nround))}
       }
-    }
-    save(corXY.output, file = paste(output, ".RData", sep=""))
-    
+    print(paste("save intermediate results at round", nround))
+    save(corXY.output, file = paste(output, "_round_",nround, ".RData", sep=""))
+    }    
   }
   if(ncores>1){stopCluster(cl)} 
 }

session.R

 
 species.path <- "_data/Mesobromion/species.out.10perc.txt"
 traits.path  <- "_data/Mesobromion/traits.out.10perc.txt"
-output  <- "test"
+output  <- "test99"
 myfunction <- "get.corXY.bootstrap"
-max.inter.t <- 4
-chunkn <- 1
+max.inter.t <- 3
 chunk.i <- NA
-nperm <- 25
+nperm <- 20
 ncores <- 10
+chunkn <- 3*ncores
 combinations <- "sequential"
 
 source("01b_MesobromionCluster.R")