runJitter: Function to run TCSAM2013 multiple times using jittered...
In wStockhausen/rTCSAM2013: Functions to run and plot output from TCSAM2013 models.

Description Usage Arguments Details Value

This function runs a TCSAM2013 model multiple times, jittering the initial starting values to assess model convergence.

runJitter(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
`onlyEvalJitter`	- flag (T/F) to only evaluate a (previous) set of jitter runs, not make new runs
`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 creates a shell script ('./tmp.sh') in the working directory and uses it to run the ADMB version of the TCSAM2013 model. Initial model parameters are 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).

When all the models requested have been run, the function determines the seed associated with the 1st model run that yielded the smallest value for the objective function and re-runs the modelusing this seed to re-create the model run resulting in the minimum objectve function to recreate the model output files. The final 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.