#'
#'@title Function to run TCSAM02.
#'
#'@description This function runs a TCSAM02 model once.
#'
#'@details
#'This function creates a shell script ('./tmp.sh') in the
#'working directory and uses it to run a version of the TCSAM02 model.\cr
#'Initial model parameters can be jittered based on the system clock time or using iSeed
#'to set the random number generator. The iSeed and final objective function value are
#'saved for each model run in a csv file (the value of out.csv).
#'
#'@param os - 'win', 'mac', 'osx', or 'linux'
#'@param path - path for model output
#'@param model - TCSAM02 model executable name
#'@param path2model - path to model executable
#'@param configFile - filename (including path) to model configuration file
#'@param pin - T/F to use a pin file
#'@param pinFile - name of pin file to use (if pin=TRUE)
#'@param mseMode - flag to run model in MSE mode (see \code{getRunComands})
#'@param minPhase - phase to start minimization (or NULL)
#'@param maxPhase - final minimization phase (or NULL)
#'@param calcOFL - flag (T/F) to perform OFL calculations
#'@param calcTAC - flag (T/F) to calculate the TAC for the next fishing year
#'@param HCR - integer indicating the Harvest Control Rule used to calculate the TAC
#'@param calcDynB0 - flag to calculate dynamic B0
#'@param hess - T/F to compute hessian (and .std file)
#'@param mcmc - T/F to run mcmc
#'@param mc.N - number of mcmc iterations to do
#'@param mc.save - number of iterations to skip when saving mcmc calculations
#'@param mc.scale - number of iterations to adjust scale for mcmc calculations
#'@param jitter - T/F to jitter parameters
#'@param iSeed - seed for random number generator (or NULL)
#'@param fitSimData - flag (T/F) to fit simulated data
#'@param simDataSeed - random number seed value for simulated data
#'@param saveResults - T/F to save results to ModelResults.RData as a tcsam02.resLst object using \code{getResLst(...)}
#'@param test - flag (T/F) to run function in "test" mode
#'@param cleanup - flag (T/F) to clean up some output files
#'@param verbose - flag to print debugging info
#'
#'@return - dataframe of class 'tcam02.par', with 2 columns (name, value) with jitter iSeed (if jittered)
#'and par file info, or NULL if par file does not exist.
#'
#'@details If the path associated with \code{configFile} is a relative one, it should
#'be relative to the \code{path} variable. If saveResults=TRUE, getResLst() is used to read in
#'the report file, prs file, and std files and the resulting tcsam02.resLst object is
#' saved to 'ModelResults.RData'. If jitter=TRUE, hess=FALSE, and cleanup=TRUE, then most output files
#' (including the .rep files) are deleted after the model run to save disk space.
#'
#'@export
#'
runTCSAM02<-function(os='osx',
path='.',
model='tcsam02',
path2model='',
configFile='',
pin=FALSE,
pinFile=NULL,
mseMode=NULL,
minPhase=1,
maxPhase=NULL,
calcOFL=FALSE,
calcTAC=FALSE,
HCR=1,
calcDynB0=FALSE,
hess=FALSE,
mcmc=FALSE,
mc.N=1000000,
mc.save=1000,
mc.scale=1000,
jitter=FALSE,
iSeed=NULL,
fitSimData=FALSE,
simDataSeed=NULL,
saveResults=hess,
test=FALSE,
cleanup=TRUE,
verbose=FALSE){
#start timing
stm<-Sys.time();
#switch to run folder (create if necessary)
currdir<-getwd();
on.exit(setwd(currdir));
if (!file.exists(path)) dir.create(path,recursive=TRUE)
setwd(path);
cat("Running tcsam02 model at '",path,"'.\n");
#set up copy commands
fn.par<-file.path(getwd(),"&&model.par");
fn.par<-gsub('&&model',tolower(model),fn.par)
run.cmds<-getRunCommands(os=os,
model=model,
path2model=path2model,
configFile=configFile,
pin=pin,
pinFile=pinFile,
mseMode=mseMode,
minPhase=minPhase,
maxPhase=maxPhase,
hess=hess,
mcmc=mcmc,
mc.N=mc.N,
mc.save=mc.save,
mc.scale=mc.scale,
jitter=jitter,
iSeed=iSeed,
fitSimData=fitSimData,
simDataSeed=simDataSeed,
calcOFL=calcOFL,
calcTAC=calcTAC,
HCR=HCR,
calcDynB0=calcDynB0,
fullClean=jitter&(!hess)&cleanup,
cleanup=cleanup)
if (tolower(os)=='win'){
cat(run.cmds,file="tmp.bat")
Sys.chmod("tmp.bat",mode='7777')
if (!test) system("tmp.bat",wait=TRUE);
} else {
cat(run.cmds,file="./tmp.sh")
Sys.chmod("./tmp.sh",mode='7777')
if (!test) system("./tmp.sh",wait=TRUE);
}
#print timing-related info
etm<-Sys.time();
elt<-etm-stm;
cat("start time: ")
print(stm);
cat("end time: ")
print(etm);
cat("elapsed time: ")
print(elt);
#parse par file into dataframe
par<-paste(model,'.par',sep='')
dfr<-NULL;
if (!test) dfr<-rTCSAM02::readParFile(par);
#get jitter or simulation info
if (!test){
if ((jitter||fitSimData)&(!is.null(dfr))) {
if (jitter)
tbl<-utils::read.csv('jitterInfo.csv',header=TRUE);
if (fitSimData)
tbl<-utils::read.csv('simInfo.csv',header=TRUE);
if ("B0" %in% colnames(tbl)){
dfr<-rbind(data.frame(name='seed',value=tbl$seed[1]),
data.frame(name='MMB', value=tbl$MMB[1]),
data.frame(name='B0', value=tbl$B0[1]),
data.frame(name='Bmsy',value=tbl$Bmsy[1]),
data.frame(name='Fmsy',value=tbl$Fmsy[1]),
data.frame(name='OFL', value=tbl$OFL[1]),
data.frame(name='curB',value=tbl$curB[1]),
dfr);
} else {
dfr<-rbind(data.frame(name='seed',value=tbl$seed[1]),
data.frame(name='MMB', value=tbl$MMB[1]),
dfr);
}
dfr$value[dfr$name=='objective function']<-tbl$objfun[1];
dfr$value[dfr$name=='max gradient']<-tbl$maxGrad[1];
}
}#!test
if (!test & saveResults){
resLst<-rTCSAM02::getResLst(inp.dir="./",rep=paste0(model,".rep"),model=model,prsType='all')
save(resLst,file="ModelResults.RData")
}
#return dataframe (and return to original folder as working directory)
if (!is.null(dfr)) class(dfr)<-c('tcsam02.par',class(dfr));
return(dfr);
}
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