runRECA: Run R-ECA
In edvinf/prepRECA: Prepares data for running R-ECA

Description Usage Arguments Details Value Examples

Runs eca.estimate and eca.predict.

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

`RecaObj`	as returned from `prepRECA`
`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`

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, atemporary 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.

list() with elements:

fit: as returned by eca.estimate
prediction: as returned by eca.predict
covariateMaps: list() mapping from Reca covariate encoding to values fed to prepRECA. As on parameter 'RecaObj'