changes for summarising UK land use script

scripts/summariseUKlanduse.R

@@ -23,7 +23,7 @@ cropIntensitySummary = function (luDt, cropType) {
                            area = sum(area))]
 }
 
-summariseLandUseOutput = function(simDir, writeFile=TRUE) {
+summariseLandUseOutput = function(simDir) {
   
   countryCells = data.table(read.table("/exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/data/halfdeg/ukCells.txt", header=TRUE))
   years = list.files(simDir, pattern="[0-9]+")
@@ -57,20 +57,16 @@ summariseLandUseOutput = function(simDir, writeFile=TRUE) {
     } else {
       print(paste("Can't find file, so skipping:", fileName))
     }
-    
-    
+     
   }
-  
-  
-  if (writeFile) write.table(resDt, file.path(simDir, "ukLC.csv"), sep=",", row.names=FALSE, quote=FALSE)
+ 
+  write.table(resDt, file.path(simDir, "ukLC.csv"), sep=",", row.names=FALSE, quote=FALSE)
   resDt
 }
 
 baseOutputDir="/exports/csce/eddie/geos/groups/LURG/models/PLUM/output" 
 
-ensemble = commandArgs(trailingOnly = TRUE)[1]
-
-for (directory in list.dirs(path = file.path(baseOutputDir,ensemble), full.names = TRUE, recursive = FALSE)){
+for (directory in list.dirs(full.names = TRUE, recursive = FALSE)){
   for (scenario in basename(list.dirs(path = directory, full.names = TRUE, recursive = FALSE))){
     ensDir=file.path(directory,scenario)
     if (dir.exists(ensDir)) {

scripts/summariseUKlanduse.sh

@@ -8,9 +8,10 @@ if [ "$#" -ne 1  ]; then
    exit
 fi
 
+cd $1
 source /etc/profile
 module load R
-R < /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/summariseUKlanduse.R  --no-save $1
+R < /exports/csce/eddie/geos/groups/LURG/models/PLUM/plumv2/scripts/summariseUKlanduse.R  --no-save
 
 concatUKLCFile=ukLC_concat.txt
 echo "Scenario,Year,IrrigCrops,FertCrops,Cropland,Pasture,ManForest,UnmanForest,Natural,AbPasture" > $concatUKLCFile