getRunCommands: Generate run commands for a tcsam02 model run

In wStockhausen/rTCSAM02: A set of tools to set up input for, and interact with output from, TCSAM02 model runs

Generate run commands for a tcsam02 model run

Description

Function to generate a script to make a tcsam02 model run

Usage

getRunCommands(
  os = "osx",
  model = "tcsam02",
  path2model = "",
  configFile = "",
  pin = FALSE,
  pinFile = NULL,
  mseMode = NULL,
  hess = FALSE,
  minPhase = NULL,
  maxPhase = NULL,
  mcmc = FALSE,
  mc.N = 1e+06,
  mc.save = 1000,
  mc.scale = 1000,
  jitter = FALSE,
  iSeed = NULL,
  calcOFL = FALSE,
  calcTAC = FALSE,
  HCR = 1,
  calcDynB0 = FALSE,
  fullClean = TRUE,
  cleanup = TRUE,
  verbose = FALSE
)

Arguments

os	'win', 'mac', 'osx', or 'linux'
model	admb model name
path2model	path to model
configFile	filename (including path) to model configuration file
pin	flag (T/F) to use a pin file
pinFile	name of pin file (if different from default)
mseMode	mse mode for model run (NULL off: default, "opModMode", "estModMode")
hess	flag (T/F) to calculate the hessian
minPhase	start phase (or NULL) for minimization calculations
maxPhase	last phase (or NULL) for minimization calculations
mcmc	flag (T/F) to do mcmc calculations
mc.N	number of mcmc iterations to do
mc.save	number of iterations to skip when saving mcmc calculations
mc.scale	number of iterations to adjust scale for mcmc calculations
jitter	flag (T/F) to use jitter initial values
iSeed	value for random number seed
calcOFL	flag (T/F) to do OFL calculations
calcTAC	flag (T/F) to calculate the TAC for the next fishing year
HCR	integer indicating the Harvest Control Rule used to calculate the TAC
calcDynB0	flag (T/F) to do dynamic B0 calculations
fullClean	flag to clean up almost all files (use when making multiple jitter runs)
cleanup	flag (T/F) to clean up unnecessary files
verbose	flag (T/F) to print diagnostic info

Details

. If cleanup is TRUE, then .bar, .b0*, .p0*, .r0*, variance, EchoOut.dat, CheckFile.dat, and fimn.log files are deleted.
If the path associated with configFile is a relative one, it should be relative to the path for model output.

wStockhausen/rTCSAM02 documentation built on April 16, 2024, 6:25 a.m.