making assistant functions for calibMuso

RBBGCMuso/R/assistantFunctions.R

@@ -0,0 +1,62 @@
+#' getLogs
+#'
+#'This function gives us the muso logfiles with their paths
+#'
+#'@param outputLoc This is the location of the output files.
+#'@param outputNames These are the prefixis of the logfiles
+#'@return Logfiles with paths
+#'@keywords internal
+
+
+getLogs <- function(outputLoc, outputNames, type = "spinup"){
+    switch(type,
+           "spinup" = return(grep(paste0(outputNames[1], ".log"), list.files(outputLoc), value = TRUE)),
+           "normal" = return(grep(paste0(outputNames[2], ".log"), list.files(outputLoc), value = TRUE)),
+           "both" = return(grep(paste0(outputNames[2], ".log"), list.files(outputLoc), value = TRUE)))
+}
+
+
+#' readErrors
+#'
+#'This function reads the spinup and the normal logfiles and gives back the last line which indicates weather there are any errors.
+#'
+#'@param outputLoc This is the location of the output files.
+#'@param logfiles These are the names of the logfiles
+#'@return vector with 0 and 1 values, 1, if succed, 0 if not. The first is the spinup run, the second is the normal.
+#'@keywords internal
+
+
+readErrors <- function(outputLoc, logfiles){
+    return(as.numeric(as.vector(lapply(paste(outputLoc,logfiles,sep = "/"),function(x) tail(readLines(x,-1),1)))) )
+}
+
+#' getOutFiles
+#'
+#'This function gives us the muso output files with their paths
+#'
+#'@param outputLoc This is the location of the output files.
+#'@param outputNames These are the prefixis of the logfiles
+#'@return Output files with their paths
+#'@keywords internal
+
+
+getOutFiles <- function(outputLoc, outputNames){
+
+    return(grep("out$", grep(paste(paste0(outputNames, "*"), collapse = "|"), list.files(outputLoc), value=TRUE), value = TRUE))
+}
+
+#' getOutFiles
+#'
+#'This function gives us the muso output files with their paths
+#'
+#'@param outputLoc This is the location of the output files.
+#'@param outputNames These are the prefixis of the logfiles
+#'@return Output files with their paths
+#'@keywords internal
+
+stampAndCopyDir <- function(outputLoc,names,stampDir, stampnum=NULL){
+     if(!is.null(stampnum)){file.copy(file.path(outputLoc,names)
+                                    ,file.path(stampDir,paste0((stampnum+1),"-",possibleNames)))
+     } else{file.copy(file.path(outputLoc,names)
+                                    ,file.path(stampDir,paste0((stamp(stampDir)+1),"-",possibleNames)))}
+}

RBBGCMuso/R/calibMuso.R

@@ -70,14 +70,6 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
         }
     }   
 
-##########################################################################
-###########################Defining Functions########################
-########################################################################
-
-    
-
-    
-    
 #############################################################
 ############################spinup run############################
    ########################################################## 
@@ -125,8 +117,8 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     }
 
     
-    
-    logspinup <- grep(paste0(outputNames[1],".log"), list.files(outputLoc),value = TRUE)
+    logspinup <- getLogs(outputLoc,outputNames,type="spinup")
+    ## logspinup <- grep(paste0(outputNames[1],".log"), list.files(outputLoc),value = TRUE)
     ## logspinup <- list.files(outputLoc)[grep("log$",list.files(outputLoc))]#load the logfiles
     
     if(length(logspinup)==0){
@@ -186,16 +178,14 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
                )
         
         if(keepBinary){
-            possibleNames <- grep("out$",grep(paste(paste0(outputNames,"*"), collapse = "|") ,list.files(outputLoc),value=TRUE),value = TRUE)
-            
-            print(stamp(binaryPlace))
+            possibleNames <- getOutFiles(outputLoc = outputLoc,outputNames = outputNames)
             file.copy(file.path(outputLoc,possibleNames)
                      ,file.path(binaryPlace,paste0((stamp(binaryPlace)+1),"-",possibleNames)))
         }
     }
 
     
-    logfiles <- grep(paste(paste0(outputNames,".log"), collapse = "|"), list.files(outputLoc),value = TRUE)
+    logfiles <- getLogs(outputLoc,outputNames,type="both")
     ## list.files(outputLoc)[grep("log$",list.files(outputLoc))]#creating a vector for logfilenames
 
 ###############################################    
@@ -204,7 +194,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
 
 
     
-    perror<-as.numeric(as.vector(lapply(paste(outputLoc,logfiles,sep="/"),function(x) tail(readLines(x,-1),1))))                                      #vector of spinup and normalrun error
+    perror <- readErrors(outputLoc=outputLoc,logfiles=logfiles)                                    #vector of spinup and normalrun error
     
   
     ##if errorsign is 1 there is error, if it is 0 everything ok
@@ -226,7 +216,7 @@ calibMuso <- function(settings,parameters=NULL, timee="d", debugging=FALSE, logf
     if(keepEpc){#if keepepc option turned on
 
         if(length(unique(dirname(epc)))>1){
-            print("Why are you playing with my nervs? Seriously? You hold your epc-s in different folders?")
+            stop("Why are you playing with my nervs? Seriously? You hold your epc-s in different folders?")
         } else {
 
             ## epcfiles <- list.files(epcdir)[grep("epc$",list.files(

RBBGCMuso/R/setupMuso.R

@@ -214,7 +214,7 @@ setupMuso <- function(executable=NULL,
     
     inputFiles<-c(iniInput,epcInput,metInput)
     numData<-rep(NA,3)
-    numYears <-  as.numeric(unlist(strsplit(grep("simulation years",iniFiles[[2]],value=TRUE),"[\ \t]"))[1])gfrurgc dhxv
+    numYears <-  as.numeric(unlist(strsplit(grep("simulation years",iniFiles[[2]],value=TRUE),"[\ \t]"))[1])
     ##    numYears<-unlist(read.table(iniInput[2],skip = 14,nrows = 1)[1])
     numValues <-  as.numeric(unlist(strsplit(grep("number of daily output variables",iniFiles[[2]],value=TRUE),"[\ \t]"))[1])
     ## numValues will be replaced to numVar

RBBGCMuso/man/getLogs.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/assistantFunctions.R
+\name{getLogs}
+\alias{getLogs}
+\title{getLogs}
+\usage{
+getLogs(outputLoc, outputNames, type = "spinup")
+}
+\arguments{
+\item{outputLoc}{This is the location of the output files.}
+
+\item{outputNames}{These are the prefixis of the logfiles}
+}
+\value{
+Logfiles with paths
+}
+\description{
+This function gives us the muso logfiles with their paths
+}
+\keyword{internal}

RBBGCMuso/man/getOutFiles.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/assistantFunctions.R
+\name{getOutFiles}
+\alias{getOutFiles}
+\title{getOutFiles}
+\usage{
+getOutFiles(outputLoc, outputNames)
+}
+\arguments{
+\item{outputLoc}{This is the location of the output files.}
+
+\item{outputNames}{These are the prefixis of the logfiles}
+}
+\value{
+Output files with their paths
+}
+\description{
+This function gives us the muso output files with their paths
+}
+\keyword{internal}

RBBGCMuso/man/readErrors.Rd

@@ -0,0 +1,20 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/assistantFunctions.R
+\name{readErrors}
+\alias{readErrors}
+\title{readErrors}
+\usage{
+readErrors(outputLoc, logfiles)
+}
+\arguments{
+\item{outputLoc}{This is the location of the output files.}
+
+\item{logfiles}{These are the names of the logfiles}
+}
+\value{
+vector with 0 and 1 values, 1, if succed, 0 if not. The first is the spinup run, the second is the normal.
+}
+\description{
+This function reads the spinup and the normal logfiles and gives back the last line which indicates weather there are any errors.
+}
+\keyword{internal}