runRECA: Run R-ECA
In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

runRECA

R Documentation

Run R-ECA

Description

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`

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.

Value

RecaResult results from Reca run.

Examples

 data(recaDataExample)

 # run (produce recaPrediction as in data(recaPrediction))
 ## Not run: recaPrediction <- runRECA(recaDataExample, 500, 5000)$prediction

StoXProject/RstoxFDA documentation built on Dec. 17, 2024, 10:58 a.m.