Run R-ECA — runRECA • RstoxFDA

Runs eca.estimate and eca.predict. Not to be confused with RunRecaEstimate, which is primarily intended for including in Stox projects.

Usage

runRECA(
  RecaObj,
  nSamples,
  burnin,
  lgamodel = "log-linear",
  fitfile = "fit",
  predictfile = "pred",
  resultdir = NULL,
  thin = 10,
  delta.age = 0.001,
  seed = NULL,
  caa.burnin = 0
)

Arguments

RecaObj: RecaData as returned from prepRECA or PrepareRecaEstimate
nSamples: number of MCMC samples that will be made available for eca.predict. See documentation for eca.estimate,
burnin: number of MCMC samples run and discarded by eca.estimate before any samples are saved. See documentation for eca.estimate.
lgamodel: The length age relationship to use for length-age fits (options: "log-linear", "non-linear": Schnute-Richards model). See documentation for eca.estimate.
fitfile: name of output files in resultdir. See documentation for eca.estimate.
predictfile: name of output files in resultdir. See documentation for eca.predict.
resultdir: a directory where Reca may store temp-files eca.estimate and eca.predict. . If NULL, a temporary directory will be created. See documentation for eca.estimate.
thin: controls how many iterations are run between each samples saved. This may be set to account for autocorrelation introduced by Metropolis-Hastings simulation. see documentation for eca.estimate
delta.age: see documentation for eca.estimate
seed: see documentation for eca.estimate
caa.burnin: see documentation for eca.predict

Value

RecaResult results from Reca run.

Details

eca.estimate performs Markov-chain Monte Carlo (MCMC) simulations to determine maximum likelihood of parameters for the given samples.

eca.predict samples the posterior distributions of parameters estimated in eca.estimate, in order to obtain proportinos of catches and fish parameters. Using these parameters and the given total landings, predictions of distribution of catch-parameter distributions will be calculated.

If resultdir is NULL, a temporary directory will be created for its purpose. This will be attempted removed after execution. If removal is not successful a warning will be issued which includes the path to the temporary directory.

Examples

 data(recaDataExample)

 # run (produce recaPrediction as in data(recaPrediction))
 if (FALSE) recaPrediction <- runRECA(recaDataExample, 500, 5000)$prediction