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Run Reca Models

Source: R/StoxAnalysisFunctions.R
RunRecaModels.Rd

Runs prediction (catch-at-age estimate) for parameterized Reca models.

Usage

RunRecaModels(
  RecaParameterData,
  StoxLandingData,
  GroupingVariables = character(),
  TemporalResolution = c("Quarter", "Month"),
  Caa.burnin = numeric(),
  CollapseLength = TRUE
)

Arguments

RecaParameterData

Parameters for Reca models.

StoxLandingData

Landings data (StoxLandingData).

GroupingVariables

character vector identifying columns in 'StoxLandingData' that results should be provided for.

TemporalResolution

Code for temporal resolution in landings: "Month" or "Quarter". Defaults to Quarter. Regulates temporal resolution for calculating fractional ages of fish. Not to be confused with any temporal covariate.

Caa.burnin

see documentation for eca.predict. Defaults to 0.

CollapseLength

indicates whether length groups should be collapsed in result. Defaults to TRUE. See details.

Value

RecaCatchAtAge

Details

Parameters may be obtained with ParameterizeRecaModels. If the function-parameter 'GroupingVariables' is provided, predictions will be provided for corresponding partitions of landings. The parameter 'StoxLandingData' may differ from the landings used in parameterisation (passed to ParameterizeRecaModels), as long as all not additional values / levels for the model covariates / effects are introduced.

If The models are configured for stock-splitting analysis. The variable 'Stock' will be added to 'GroupingVariables' in the return value (RecaCatchAtAge)

If the 'GroupingVariables' specify a very large number of partitions of the landings, this function may exhaust available computer memory.

CollapseLength

By default length groups are collapsed into one length group in the result. This does not facilitate reporting length resolved data, such as length distributions. The full age-length prediction may be extracted by setting the parameter 'CollapseLength' to FALSE. If this is used in combination with several grouping variables, there is some risk of exhausting available computer memory.

See also

ParameterizeRecaModels for model parameterisation, ReportRecaCatchAtAge, ReportRecaLengthAtAge, ReportRecaWeightAtAge for compiling reports of predictions / estimates.