Nothing
SSgetoutput <-
function(keyvec=NULL,dirvec=NULL,getcovar=TRUE,getcomp=TRUE,forecast=FALSE,
verbose=TRUE,ncols=210,listlists=TRUE,underscore=FALSE)
{
# a function to run the function SS_output to create a list in the R workspace
# for a Stock Synthesis model with output filenames ending with the same "key"
if(!is.null(keyvec)) cat('length(keyvec) as input to SSgetoutput:',length(keyvec),'\n')
if(!is.null(dirvec)) cat('length(dirvec) as input to SSgetoutput:',length(dirvec),'\n')
# change inputs so that keyvec and dirvec have matching lengths or keyvec=NULL
if(listlists) biglist <- list()
n1 <- length(keyvec)
n2 <- length(dirvec)
if(n1>1 & n2>1 & n1!=n2){
cat("inputs 'keyvec' and 'dirvec' have unmatched lengths > 1\n")
}else{
n <- max(1, n1, n2) # n=1 or n=length of either optional input vector
}
if(n1==1) keyvec <- rep(keyvec,n)
objectnames <- paste("replist",keyvec,sep="")
if(n1==0) objectnames <- paste("replist",1:n,sep="")
if(n2==0) dirvec <- getwd()
if(length(dirvec)==1) dirvec <- rep(dirvec,n)
dirvec <- paste(dirvec,"/",sep="")
# loop over directories or key strings
for(i in 1:n)
{
key <- keyvec[i]
mydir <- dirvec[i]
if(is.null(key)){
key2 <- NULL
}else{
key2 <- ifelse(underscore,paste("_",key,sep=""),key)
}
newobject <- objectnames[i]
if(verbose & !is.null(key)) cat("getting files with key =",key,"\n")
repfilename <- paste("Report",key2,".sso",sep="")
covarname <- paste("covar",key2,".sso",sep="")
if(getcomp){
compfilename <- paste("CompReport",key2,".sso",sep="")
NoCompOK <- FALSE
}else{
compfilename <- "nothing"
NoCompOK <- TRUE
}
if(file.exists(paste(mydir,covarname,sep="")) & getcovar) mycovar=TRUE else mycovar=FALSE
fullfile <- paste(mydir,repfilename,sep="")
if(verbose) cat("reading output from",fullfile,"\n")
repfilesize <- file.info(fullfile)$size
if(!is.na(repfilesize) && repfilesize>0){ # if there's a non-empty file
output <- SS_output(dir=mydir, repfile=repfilename, covarfile=covarname,
compfile=compfilename, NoCompOK=NoCompOK, printstats=FALSE,
covar=mycovar, forecast=forecast, verbose=FALSE, ncols=ncols)
if(is.null(output)){
# for some reason covarfile exists, but is old so SS_output rejects
cat("output==NULL so trying again with covar=FALSE\n")
output <- SS_output(dir=mydir, repfile=repfilename, covarfile=covarname,
compfile=compfilename, NoCompOK=NoCompOK, printstats=FALSE,
covar=FALSE, forecast=forecast, verbose=FALSE, ncols=ncols)
}
output$key <- as.character(key)
}else{
cat("!repfile doesn't exists or is empty\n")
}
cat("added element '", newobject, "' to list\n",sep="")
if(listlists) biglist[[newobject]] <- output
## if(global)
## {
## if(exists(newobject) && !is.null(get(newobject)) & !replace)
## {
## cat("exists and not replacing:",newobject,"\n")
## }else{
## assign(newobject,output,pos=1)
## cat("created new object:",newobject,"\n")
## }
## }
}
return(invisible(biglist))
}
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