##' Change SS files
##' @param main.dir main directory
##' @param sppname.in species name
##' @param file.make vector that controls whether or not files are copied. Expected vector is c(par file, forecast file, data file, control file, ss executable). Value can be 1 = copy file. or 0 = do not copy
##' @param starter.par Y/N switch to use the par file
##' @author Jason Cope
##' @export
Change.SSfiles<-function(main.dir,sppname.in,file.make=c(1,1,1,1,1),starter.par="N")
{
for(i in 1:length(sppname.in))
{
if(file.make[1]==1)
{
if(starter.par=="N"){file.copy(from=paste(main.dir,"/baseSSfiles/starterfiles/",sppname.in[i],"_starter.ss",sep=""),to=paste(main.dir,"/",sppname.in[i],"/starter.SS",sep=""),overwrite=TRUE)}
if(starter.par=="Y"){file.copy(from=paste(main.dir,"/baseSSfiles/starterfilespar/",sppname.in[i],"_starter.ss",sep=""),to=paste(main.dir,"/",sppname.in[i],"/starter.SS",sep=""),overwrite=TRUE)}
}
if(file.make[2]==1){file.copy(from=paste(main.dir,"/baseSSfiles/forecastfiles/",sppname.in[i],"_forecast.ss",sep=""),to=paste(main.dir,"/",sppname.in[i],"/forecast.SS",sep=""),overwrite=TRUE)}
if(file.make[3]==1){file.copy(from=paste(main.dir,"/baseSSfiles/datfiles/",sppname.in[i],".dat",sep=""),to=paste(main.dir,"/",sppname.in[i],"/",sppname.in[i],".dat",sep=""),overwrite=TRUE)}
if(file.make[4]==1){file.copy(from=paste(main.dir,"/baseSSfiles/ctlfiles/",sppname.in[i],".ctl",sep=""),to=paste(main.dir,"/",sppname.in[i],"/",sppname.in[i],".ctl",sep=""),overwrite=TRUE)}
if(file.make[5]==1){file.copy(from=paste(main.dir,"/baseSSfiles/ss.exe",sep=""),to=paste(main.dir,"/",sppname.in[i],"/ss.exe",sep=""),overwrite=TRUE)}
}
}
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