######TWEAKING FOR WINDOWS
##SM: THIS IS WAHL-AMMNA BASE CASE ONLY
#SM: downloaded from http://www.cgd.ucar.edu/ccr/ammann/millennium/codes/mann_masterfile.r
  #SM: There are undoubtedly other ways of tweaking for Windows, but these worked for me

#SM: create a directory to host results

#SM: Function to Create a directory and subdirectories if they do not exist.
remove(list=ls())           #clean up this case before starting

createsubdirs<-function(dirpath1) {
	if( ! file.exists(dirpath1) ) {
		if( ! file.exists(dirname(dirpath1)) ) {
			# If parent directory is missing, request its creation.
			createsubdirs( dirname(dirpath1) )
		}
		# the parent directory exists but not this dir
		dir.create( dirpath1 )
	}
	}

  master.directory<-"c:/climate/data/wahl" #SM added
  param.file<-"http://www.climateaudit.org/data/wa.2005/control_WA_original.tweaked.txt" #SM: tweaks are to directories to make Windows compatible
	#there may be a simpler way to do this other than just changing directory names but this worked and there were only a few to do
  createsubdirs(master.directory) #SM: make the subdirectory	
	
  #temp.directory<-"c:/climate/data/wahl/case" #SM:  this is where I located the case files. This can be user-determined
  #case.directory<-"c:/climate/data/wahl/base" #SM: this is where I located the scripts and masters
  #createsubdirs(temp.directory) #SM: make the subdirectory	

  source(file.path("http://www.cgd.ucar.edu/ccr/ammann/millennium/codes","mann_Rfunctions.r")) #SM: tweaked a little from WA 

param.input<-read.control(param.file) #SM:file.path added in 
param.input$caselabel<-file.path(master.directory,"WA.basecase") #SM: this implements the WA comment 

#the following two commands will work under unix only; if under windows,
#make a folder called as the caselabel and skip them 
###system(paste("rm -r",param.input$caselabel))  #delete any directory that happens to be there called as the caselabel
####system(paste("mkdir",param.input$caselabel))  #make a new directory called as the caselabel

 createsubdirs(param.input$caselabel) #SM: this implements WA comment	

###logfile<-paste(param.input$caselabel,"/logfile.",param.input$caselabel,sep="") #SM: commented out. This creates weird directory when I tried it
  logfile<-file.path(param.input$caselabel,"logfile.txt") #SM: this works much better

write("log:",file=logfile)



#loop over reconstruction networks:

for(i in 1:param.input$proxy.periods){
  print(i)
  write(paste("*******************************************************"),file=logfile,append=TRUE)
  write(paste("Proxy period number",i),file=logfile,append=TRUE)
  write(paste("----------------------",""),file=logfile,append=TRUE)

  data.objects<-format.datamatrices(param.input,i)
	#controldata<-param.input	

  svdproduct<-get.svd(param.input,i,data.objects,logfile)

  proxyfit<-mann.fit(param.input,data.objects,svdproduct,logfile)

  writeout.res(param.input,data.objects,svdproduct,proxyfit,logfile)
  
}


#the following command will work under unix only, skip it if under windows...
#then zip everything in the folder called as the caselabel up if you like
##system(paste("tar cvf ",param.input$caselabel,".tar ","mann* ",param.input$caselabel,"/",sep=""))  #tar up everyting