extractJitterInfo: Function to extract results from a set of previous jittered...
In wStockhausen/rTCSAM2013: Functions to run and plot output from TCSAM2013 models.

Description Usage Arguments Details Value

This function extracts results from a set of previous jittered TCSAM2013 runs and re-runs the best run to create sd info.

extractJitterInfo(os = "osx", path = ".", model = "tcsam2013alta",
  path2model = "", configFile = "", minPhase = NULL, maxPhase = NULL,
  numRuns = 3, onlyEvalJitter = FALSE, in.csv = "jitterInfo.csv",
  out.csv = "jitterResults.csv", plotResults = 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`	- path to model configuration file
`minPhase`	- min phase to start estimation
`maxPhase`	- max phase for estimation
`numRuns`	- number of jitter runs to make
`in.csv`	- filename for jitter info (seed, obj fun value) from ADMB model run
`out.csv`	- filename for jittered results
`plotResults`	- T/F to plot final results using `plotTCSAM2013I`
`cleanup`	- flag (T/F) to clean up unnecessary files

For each model run, this function reads a set of jittered model runs and determines the seed associated with the 1st model run that yielded the smallest value for the objective function and max gradient. It re-runs the model using this seed to re-create the model run resulting in the minimum objectve function to recreate the model output files. The best model run is done estimating the hessian, so standard deviations for estimated model parameters are available in the .std file.

Uses wtsUtilities::formatZeros().

- list w/ 4 elements: imn - index of (1st) smallest value for the objective function seed - seed resulting in the smallest objective function par - dataframe with par results from run w/ smallest objective function objFuns - table of objective function values, max gradients, and seed values from all model runs parList - list of par dataframes for each model run

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