runTCSAM2013: Function to run TCSAM2013.
In wStockhausen/rTCSAM2013: Functions to run and plot output from TCSAM2013 models.

Description Usage Arguments Details Value

This functions runs a TCSAM2013 model once.

runTCSAM2013(os = "osx", path = ".", model = "tcsam2013alta",
  path2model = "", configFile = "", pin = FALSE, hess = FALSE,
  mcmc = FALSE, minPhase = NULL, maxPhase = NULL, jitter = FALSE,
  seed = NULL, plotResults = hess, rmEXE = FALSE, cleanup = TRUE)

`os`	- 'win' or 'mac' or 'osx'
`path`	- path for model output
`model`	- TCSAM2013 model executable name
`path2model`	- path to model executable
`configFile`	- filename (including path) to model configuration file
`pin`	- flag (T/F) to use/not use a default pin file, or an ascii filename to use a non-default one
`hess`	- T/F to compute hessian (and .std file)
`mcmc`	- T/F to run mcmc
`minPhase`	- min phase to start estimation
`maxPhase`	- max phase for estimation
`jitter`	- T/F to jitter parameters
`seed`	- seed for random number generator (or NULL)
`plotResults`	- T/F to plot results using `plotTCSAM2013I.GG`
`rmEXE`	- flag to remove model executable from run folder
`cleanup`	- flag (T/F) to clean up unnecessary files

This function creates a shell script ('./tmp.sh') in the working directory and uses it to run a version of the TCSAM2013 model.
Initial model parameters can be jittered based on the system clock time as a seed to the random number generator. The seed and final objective function value are saved for each model run in a csv file (the value of out.csv).

If the path associated with configFile is a relative one, it should be relative to the path variable.

- dataframe with 2 columns (name, value) with jitter seed (if jittered) and par file info, or NULL if par file does not exist

wStockhausen/rTCSAM2013 documentation built on May 3, 2019, 7:13 p.m.