getRunCommands: Generate run commands for a tcsam2015 model run

In wStockhausen/rTCSAM2015: A set of tools to set up input for, and interact with output from, a TCSAM2015 model run, as well as to compare TCSAM2015 and rsimTCSAM runs.

Description

Function to generate a script to make a tcsam2015 model run

Usage

getRunCommands(os = "osx", model = "tcsam2015", path2model = "",
  configFile = "", pin = FALSE, 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,
  cleanup = TRUE)

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
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
cleanup	- flag (T/F) to clean up unnecessary files

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/rTCSAM2015 documentation built on May 3, 2019, 7:14 p.m.