runJitter: Function to run TCSAM2013 multiple times using jittered...

Description Usage Arguments Details Value

Description

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

Usage

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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)

Arguments

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

Details

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().

Value

- 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.