convertRecaData: Convert RecaData
In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

convertRecaData

R Documentation

Convert RecaData

Description

Converts RecaData prepared for StoX-Reca to the input format accepted by eca.estimate. This facilitates preparing input data with a StoX-project for more cusomized programs directly interfacing Reca.

Usage

convertRecaData(
  RecaData,
  nSamples = as.integer(NA),
  burnin = as.integer(NA),
  thin = as.integer(NA),
  resultdir = as.character(NA),
  lgamodel = as.character(NA),
  delta.age = as.numeric(NA),
  seed = as.numeric(NA),
  fitfile = as.character(NA),
  predictfile = as.character(NA)
)

Arguments

`RecaData`	`RecaData`, as prepared by `PrepareRecaEstimate`.
`nSamples`	nSamples as specified in `eca.estimate`
`burnin`	burnin as specified in `eca.estimate`
`thin`	thin as specified in `eca.estimate`
`resultdir`	resultdir as specified in `eca.estimate`
`lgamodel`	lgamodel as specified in `eca.estimate`
`delta.age`	delta.age as specified in `eca.estimate`
`seed`	seed as specified in `eca.estimate`
`fitfile`	fitfile as specified in `eca.estimate`
`predictfile`	predictfile as specified in `eca.estimate`

Details

The StoX-function interfacing Reca-parameterisation (RunRecaModels) accepts a data format RecaData that is not exactly compatible with the format accepted by eca.estimate. This inconvenience is introduced to make sure that output from PrepareRecaEstimate adheres to restrictions in the StoX-user interface, so that the results are inspectable there.

Reca-input include model parameters and options, but PrepareRecaEstimate only sets parameters that have implications for data formatting, other parameters are subsequently set in for instance RunRecaModels. The optional arguments to this function can be used to set those parameters that is handled by RunRecaModels in the StoX-workflow.

Reca requires categorical variables to be encoded as consecutive integers, starting with 1. In order to keep track of how this correspond to other representations, this function provides the mapping in the list 'CovariateMaps'. CovariateMaps is not an input to Reca, but only provided to assist book-keeping.

Value

list with 5 members:

AgeLength: Data prepared for the argument AgeLength to eca.estimate
WeightLength: Data prepared for the argument WeightLength to eca.estimate
Landings: Data prepared for the argument Landings to eca.estimate
GlobalParameters: Data prepared for the argument GlobalParameters to eca.estimate, Completeness of this data structure depend on whether optional parameters where provided.
CovariateMaps: Not input to Reca. Nested list, providing mapping between integer encoding and character encoding of the levels of categorical variables.