RunRecaEstimate: Run Reca.
In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

RunRecaEstimate

R Documentation

Run Reca.

Description

This function is deprecated and are being kept for testing purposes. It is replaced by ParameterizeRecaModels and RunRecaModels

Usage

RunRecaEstimate(
  RecaData,
  Nsamples = integer(),
  Burnin = integer(),
  Thin = integer(),
  Lgamodel = c("log-linear", "non-linear"),
  Resultdir = character(),
  Delta.age = numeric(),
  Seed = numeric(),
  Caa.burnin = numeric()
)

Arguments

`RecaData`	`RecaData` as returned from `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`.
`Thin`	controls how many iterations are run between each samples saved. Defaults to 0. This may be set to account for autocorrelation introduced by Metropolis-Hastings simulation. 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`.
`Resultdir`	a directory where Reca may store temp-files `eca.estimate` and `eca.predict`. . If not given a temporary directory will be created. See documentation for `eca.estimate`.
`Delta.age`	see documentation for `eca.estimate`. Defaults to 0.001.
`Seed`	see documentation for `eca.estimate`. Defaults to random seed.
`Caa.burnin`	see documentation for `eca.predict`. Defaults to 0.

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 proportions 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.