musoMonte function(2)

RBBGCMuso/R/#musoMonte.R#

@@ -1,121 +0,0 @@
-musoMonte <- function(settings=NULL,
-                     parameters,
-                      inputDir = "./",
-                      outLoc = "./calib",
-                      iterations = 10,
-                      preTag = "mont-",
-                      inputName = paste0(pretag,"epcs.csv"),
-                      outputType = "moreCsv",
-                      fun=mean,
-                      varIndex=8,
-                      doSensitivity=FALSE,
-                      onDisk=FALSE,
-                      ...){
-
-  currDir <- getwd()
-  tmp <- file.path(outLoc,"tmp/")
-
-    if(!dir.exists(outLoc)){
-    dir.create(outLoc)
-    warning(paste(outLoc," is not exists, so it was created"))
-  }
-
-  if(dir.exists(tmp){
-    stop("There is a tmp directory inside the output location, please replace it. tmp is an important temporary directory for the function")
-    }
-  dir.create(tmp)
-  inputFiles <- file.path(inputDir,grep(basename(outLoc),list.files(inputDir),invert = TRUE,value = TRUE)) 
-
-  
-  for(i in inputFiles){
-    file.copy(i,tmp)
-  }
-  setwd(tmp)
-  
-  if(is.null(settings)){
-    settings <- setupMuso()
-  }
-  
-  parameterNames <- parameters[,1]
-  parReal <- parameters[,-1]
-  Otable <- OtableMaker(parReal)
-  A <- as.matrix(Otable[[1]][,c(2,4,5,6)])
-  B <- as.matrix(Otable[[2]])
-  settings$calibrationPar <- A[,1] 
-  pretag <- file.path(outLoc,preTag)
-  
-  ##reading the original epc file at the specified
-  ## row numbers
-  
-  origEpcFile <- readLines(settings$epcInput[2])
-  
-  origEpc <- unlist(lapply(settings$calibrationPar, function (x) {
-    as.numeric(unlist(strsplit(origEpcFile[x],split="[\t ]"))[1])
-  }))
-  
-  ## Prepare the preservedEpc matrix for the faster
-  ##  run.
-  preservedEpc <- matrix(nrow = (iterations +1 ), ncol = length(settings$calibrationPar))
-  preservedEpc[1,] <- origEpc
-  colnames(preservedEpc) <- Otable[[1]][,1]
-  
-  ## Save the backupEpc, while change the settings
-  ## variable and set the output.
-  file.copy(settings$epc[2],"savedEpc",overwrite = TRUE) # do I need this? 
-  pretag <- file.path(outLoc,preTag)
-  
-  ## Creating function for generating separate
-  ## csv files for each run
-  a<-1:100000
-  moreCsv <- function(){
-    for(i in 1:iterations){
-      parVar <- musoRandomizer(A,B)[,2]
-      #preservedEpc[(i+1),] <- parVar
-      exportName <- paste0(preTag,i,".csv")
-      tryCatch (calibMuso(settings,debugging = "stamplog",
-                parameters = parVar,export = exportName,
-                keepEpc = TRUE),error=function(e) NA )
-    }
-    return(preservedEpc)
-  }
-  
-  ## Creating function for generating one
-  ## csv files for each run
-  
-  oneCsv <- function () {
-    numDays <- settings$numdata[1]
-    if(!onDisk){
-      for(i in 1:iterations){
-      
-        parVar <- apply(parameters,1,function (x) {
-          runif(1, as.numeric(x[3]), as.numeric(x[4]))})
-        preservedEpc[(i+1),] <- parVar
-        exportName <- paste0(preTag,".csv")
-        write.csv(parvar,"preservedEpc.csv",append=TRUE)
-        calibMuso(settings,debugging = "stamplog",
-                  parameters = parVar,keepEpc = TRUE) %>%
-                  {mutate(.,iD = i)} %>%
-                  {write.csv(.,file=exportName,append=TRUE)}
-      }
-      
-    return(preservedEpc)
-      } else {
-      
-    }
-  }
-  
-  netCDF <- function () {
-    stop("This function is not inplemented yet")
-  }
-  
-  ## Call one function according to the outputType
-  switch(outputType,
-         "oneCsv" = (preservedEpc <- oneCsv()),
-         "moreCsv" = (preservedEpc <- moreCsv()),
-         "netCDF" = (preservedEpc <- netCDF()))
-  
-  ## Change back the epc file to the original
-  
-  file.copy(savedEpc,settings$epc[2],overwrite = TRUE)
-  write.csv(preservedEpc,"preservedEpc.csv")
-}

RBBGCMuso/R/musoMonte.R

@@ -10,7 +10,8 @@ musoMonte <- function(settings=NULL,
                       varIndex=8,
                       doSensitivity=FALSE,
                       onDisk=FALSE,
-                      ...){
+                     ...)
+{
 
   currDir <- getwd()
   tmp <- file.path(outLoc,"tmp/")
@@ -58,7 +59,7 @@ musoMonte <- function(settings=NULL,
   preservedEpc <- matrix(nrow = (iterations +1 ), ncol = length(settings$calibrationPar))
   preservedEpc[1,] <- origEpc
   colnames(preservedEpc) <- Otable[[1]][,1]
-  
+  write.csv(preservedEpc,"preservedEpc.csv")
   ## Save the backupEpc, while change the settings
   ## variable and set the output.
   file.copy(settings$epc[2],"savedEpc",overwrite = TRUE) # do I need this? 
@@ -66,17 +67,21 @@ musoMonte <- function(settings=NULL,
   
   ## Creating function for generating separate
   ## csv files for each run
-  a<-1:100000
   moreCsv <- function(){
+      a <- list()
       for(i in 1:iterations){
           parVar <- musoRandomizer(A,B)[,2]
                                         #preservedEpc[(i+1),] <- parVar
+          write.csv(x=parVar,file="preservedEpc.csv", append=TRUE)
           exportName <- paste0(preTag,i,".csv")
-      tryCatch (calibMuso(settings,debugging = "stamplog",
+          tempData <- calibMuso(settings,debugging = "stamplog",
-                parameters = parVar,export = exportName,
+                               parameters = parVar,
-                keepEpc = TRUE),error=function(e) NA )
+                               keepEpc = TRUE)
+          write.csv(x=tempData,file=exportName)
+          a[[i]]<-fun(tempData[,varIndex])
+      
       }
-    return(preservedEpc)
+      return(a)
   }
   
   ## Creating function for generating one
@@ -89,6 +94,7 @@ musoMonte <- function(settings=NULL,
       
         parVar <- apply(parameters,1,function (x) {
             runif(1, as.numeric(x[3]), as.numeric(x[4]))})
+          
         preservedEpc[(i+1),] <- parVar
         exportName <- paste0(preTag,".csv")
         write.csv(parvar,"preservedEpc.csv",append=TRUE)
@@ -110,12 +116,13 @@ musoMonte <- function(settings=NULL,
   
   ## Call one function according to the outputType
   switch(outputType,
-         "oneCsv" = (preservedEpc <- oneCsv()),
+         "oneCsv" = (a <- oneCsv()),
-         "moreCsv" = (preservedEpc <- moreCsv()),
+         "moreCsv" = (a <- moreCsv()),
-         "netCDF" = (preservedEpc <- netCDF()))
+         "netCDF" = (a <- netCDF()))
   
   ## Change back the epc file to the original
   
   file.copy(savedEpc,settings$epc[2],overwrite = TRUE)
-  write.csv(preservedEpc,"preservedEpc.csv")
+  return(do.call("c",a))
+
 }