Added new argument start.round

01b_MesobromionCluster.R

@@ -55,7 +55,8 @@ get.best <- function(x, N){
 
 
 Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY.bootstrap", 
-                        combinations=c("all", "sequential"), max.inter.t, chunkn, chunk.i, nperm=199, ncores){
+                        combinations=c("all", "sequential"), start.round=NA, max.inter.t, 
+                        chunkn, chunk.i, nperm=199, ncores){
   
   if(ncores>1){
     require(parallel)
@@ -72,9 +73,9 @@ 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 +116,11 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
   
   
   if(combinations=="sequential"){
-    corXY.ci <- NULL
-    for(nround in 1:max.inter.t){
+    if(!is.na(start.round)){
+      print(paste("Load data from previous round=", start.round-1))
+      load(file = paste(output, "_round_", start.round-1, ".RData", sep=""))
+      } else {corXY.ci <- NULL}
+    for(nround in start.round:max.inter.t){
       corXY.output <- NULL
       ## select combination of traits based on best
       if(nround==1) {
@@ -211,8 +215,9 @@ Mesobromion <- function(species.path, traits.path, output, myfunction="get.corXY
         } else {print(paste("no new best at round=", nround))}
       }
     print(paste("save intermediate results at round", nround))
-    save(corXY.output, file = paste(output, "_round_",nround, ".RData", sep=""))
+    save(corXY.output, best, traits.sign.alone, corXY.ci, file = paste(output, "_round_",nround, ".RData", sep=""))
     }    
   }
   if(ncores>1){stopCluster(cl)} 
 }
+

cli_01b.r

@@ -65,7 +65,7 @@ parser <- OptionParser(
        epilogue    = "use with caution, the awesomeness might slap you in the face!"
 )
 
-cli <- parse_args(parser, positional_arguments = 5)
+cli <- parse_args(parser, positional_arguments = 6)
 
 # ------------------------------------------------------------------------------
 # assign a few shortcuts
@@ -76,6 +76,7 @@ traits.path  	 <- cli$args[2]
 output  	     <- cli$args[3]
 myfunction   	 <- cli$args[4]
 combinations   <- cli$args[5]
+start.round    <- cli$args[6]
 max.inter.t    <- cli$options$max.inter.t
 chunkn         <- cli$options$chunkn
 chunk.i        <- cli$options$chunk.i

session.R

@@ -6,11 +6,12 @@ myfunction <- "get.corXY.bootstrap"
 max.inter.t <- 3
 chunk.i <- NA
 nperm <- 20
-ncores <- 10
+ncores <- 1
 chunkn <- 3*ncores
 combinations <- "sequential"
+start.round <- 4
 
 source("01b_MesobromionCluster.R")
 #Mesobromion(species.path, traits.path, output, myfunction, max.inter.t, chunkn, chunk.i, nperm)
-Mesobromion(species.path, traits.path, output, myfunction, combinations, max.inter.t, 
+Mesobromion(species.path, traits.path, output, myfunction, combinations, start.round, max.inter.t, 
             chunkn, chunk.i, nperm, ncores)

submit_01b.sh

@@ -29,4 +29,5 @@ Rscript \
     /data/splot/HIDDEN/traits.out.10perc.txt \
     "$output" \
     "get.corXY.bootstrap" \
-    "sequential"
+    "sequential" \
+    4