#'
#'@title Generate run commands for a tcsam02 model run
#'
#'@description Function to generate a script to make a tcsam02 model run
#'
#'@param os - 'win', 'mac', 'osx', or 'linux'
#'@param model - admb model name
#'@param path2model - path to model
#'@param configFile - filename (including path) to model configuration file
#'@param pin - flag (T/F) to use a pin file
#'@param pinFile - name of pin file (if different from default)
#'@param mseMode - mse mode for model run (NULL [off: default], "opModMode", "estModMode")
#'@param hess - flag (T/F) to calculate the hessian
#'@param minPhase - start phase (or NULL) for minimization calculations
#'@param maxPhase - last phase (or NULL) for minimization calculations
#'@param mcmc - flag (T/F) to do mcmc calculations
#'@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 - flag (T/F) to use jitter initial values
#'@param iSeed - value for random number seed
#'@param fitSimData - flag (T/F) to fit simulated data
#'@param simDataSeed - random number seed value for simulated data
#'@param calcOFL - flag (T/F) to do 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 (T/F) to do dynamic B0 calculations
#'@param fullClean - flag to clean up almost all files (use when making multiple jitter runs)
#'@param cleanup - flag (T/F) to clean up unnecessary files
#'@param verbose - flag (T/F) to print diagnostic info
#'
#'@details. If \code{cleanup} is TRUE, then .bar, .b0*, .p0*, .r0*, variance,
#'EchoOut.dat, CheckFile.dat, and fimn.log files are deleted.\cr
#'If the path associated with \code{configFile} is a relative one, it should
#'be relative to the path for model output.
#'
#'@export
#'
getRunCommands<-function(os='osx',
model='tcsam02',
path2model='',
configFile='',
pin=FALSE,
pinFile=NULL,
mseMode=NULL,
hess=FALSE,
minPhase=NULL,
maxPhase=NULL,
mcmc=FALSE,
mc.N=1000000,
mc.save=1000,
mc.scale=1000,
jitter=FALSE,
iSeed=NULL,
fitSimData=FALSE,
simDataSeed=NULL,
calcOFL=FALSE,
calcTAC=FALSE,
HCR=1,
calcDynB0=FALSE,
fullClean=TRUE,
cleanup=TRUE,
verbose=FALSE){
nopath<-FALSE;
if ((path2model=='.')||(path2model=='./')||(path2model=='.\\')||(path2model=="")) nopath=TRUE;
echo.on <-"echo on";
echo.off<-"echo off";
cln<-"";
if (cleanup) {
cln<-"del &&model1
del &&model.bar
del &&model.b0*
del &&model.p0*
del &&model.r0*
del *.rept
del variance
del ModelData.Sim.init.dat
del MPI.init.dat
del EchoData.dat
del CheckFile.dat
del fmin.log";
if (fullClean){
fullcln<-"del *.rep
del &&model.ModelFits.?-1.R
del ModelData.Sim*.dat
del MPI*.dat
del ModelParametersInfo*.R";
cln<-paste0(cln,"\n",fullcln);
}
}
rn.mcmc<-'';
cpy<-'';
opts <- paste0(" -rs -nox -configFile &&configFile &&mnPhs &&mxPhs &&mcmc &&nohess ",
"&&calcOFL &&calcTAC &&HCR &&calcDynB0 &&jitter &&iSeed &&fitSimData &&simDataSeed ",
"&&pin !!pinFile &&mseMode");
if (tolower(os)=='win'){
model1<-paste(model,'exe',sep='.');
if (!nopath) cpy<-"copy &&path2model &&model1";
rn.mdl<-paste("&&model",opts);
if (mcmc) rn.mcmc<-"&&model -configFile &&configFile -mceval &&calcOFL &&calcDynB0";
##cln is correct for 'win', so do nothing
run.cmds<-paste(echo.on,cpy,rn.mdl,rn.mcmc,cln,sep="\n");
path2model<-gsub("/","\\",file.path(path2model,model1),fixed=TRUE);
} else if (tolower(os) %in% c('mac','osx','linux')){
model1<-model;
if (!nopath) cpy<-"cp &&path2model ./&&model";
rn.mdl<-paste("./&&model",opts);
if (mcmc) rn.mcmc<-"./&&model -configFile &&configFile -mceval &&calcOFL &&calcDynB0";
if (cleanup) cln<-gsub("del ","rm ",cln,fixed=TRUE);
cdr<-paste('DIR="$( cd "$( dirname "$0" )" && pwd )"','cd ${DIR}',sep='\n');
run.cmds<-paste("#!/bin/sh",echo.on,cdr,cpy,rn.mdl,rn.mcmc,cln,sep="\n");
path2model<-file.path(path2model,model1);
}
if (!nopath) run.cmds<-gsub("&&path2model", path2model, run.cmds,fixed=TRUE);
run.cmds<-gsub("&&model1", model1, run.cmds,fixed=TRUE);
run.cmds<-gsub("&&model", model, run.cmds,fixed=TRUE);
run.cmds<-gsub("&&configFile", configFile, run.cmds,fixed=TRUE);
str<-''; if (pin) str<-"-pin";
run.cmds<-gsub("&&pin",str,run.cmds,fixed=TRUE);
str<-''; if (!is.null(pinFile)) str<-pinFile;
run.cmds<-gsub("!!pinFile",str,run.cmds,fixed=TRUE);
str<-''; if (!is.null(mseMode)) str<-paste0("-mseMode ",mseMode);
run.cmds<-gsub("&&mseMode",str,run.cmds,fixed=TRUE);
str<-''; if (!hess) str<-"-nohess";
run.cmds<-gsub("&&nohess",str,run.cmds,fixed=TRUE);
str<-''; if (calcOFL) str<-"-calcOFL";
run.cmds<-gsub("&&calcOFL",str,run.cmds,fixed=TRUE);
str<-''; if (calcTAC) str<-"-calcTAC";
run.cmds<-gsub("&&calcTAC",str,run.cmds,fixed=TRUE);
str<-''; if (calcTAC) str<-paste0(HCR);
run.cmds<-gsub("&&HCR",str,run.cmds,fixed=TRUE);
str<-''; if (calcDynB0) str<-"-calcDynB0";
run.cmds<-gsub("&&calcDynB0",str,run.cmds,fixed=TRUE);
str<-''; if (jitter) str<-"-jitter";
run.cmds<-gsub("&&jitter",str,run.cmds,fixed=TRUE);
str<-''; if (is.numeric(iSeed)) str<-paste("-iSeed",iSeed);
run.cmds<-gsub("&&iSeed",str,run.cmds,fixed=TRUE);
str<-''; if (fitSimData) str<-"-fitSimData";
run.cmds<-gsub("&&fitSimData",str,run.cmds,fixed=TRUE);
str<-''; if (is.numeric(simDataSeed)) str<-paste("-iSimDataSeed",simDataSeed);
run.cmds<-gsub("&&simDataSeed",str,run.cmds,fixed=TRUE);
str<-''; if (mcmc) str<-paste("-mcmc",mc.N,"-mcsave",mc.save,"-mcscale",mc.scale);
run.cmds<-gsub("&&mcmc",str,run.cmds,fixed=TRUE);
str<-''; if (!is.null(minPhase)) str<-paste0("-phase ",minPhase);
run.cmds<-gsub("&&mnPhs",str,run.cmds,fixed=TRUE);
str<-''; if (!is.null(maxPhase)) str<-paste0("-maxph ",maxPhase);
run.cmds<-gsub("&&mxPhs",str,run.cmds,fixed=TRUE);
if (verbose) cat("Run commands:\n",run.cmds,"\n\n");
return(run.cmds);
}
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