getRunCommands: Generate run commands for a tcsam02 model run

Description Usage Arguments Details

View source: R/getRunCommands.R

Description

Function to generate a script to make a tcsam02 model run

Usage

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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,
  jit.seed = 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

jit.seed

- value for random number seed to generate jitter

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 Dec. 7, 2018, 7:58 a.m.