RecaParameterData: Reca Parameter Data (RecaParameterData)
In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

RecaParameterData

R Documentation

Reca Parameter Data (RecaParameterData)

Description

Data and some data parameters prepared for running various report functions that invoke eca.predict.

model fit

For inspection or analysis of model fit, the lists 'FitProportionAtAge', 'FitLengthGivenAge' and 'FitWeightGivenLength' is of interest. For stock-splitting analysis, the lists FitLengthGivenAgeCC and FitWeightGivenLengthCC will be added as well, corresponding to one of the stocks. These lists correspond to the three Reca-models and contain:

LogLikeliehood: A data.table tabulating the logarithm of the likeliehood of the parameter set for each iteration
...: A data.table for each of the model effects (e.g. covariates).

In addition to configurable covariates, the models always contain a constant effect (named 'constant'), a catch or haul effect (named 'catchSample') and effects for fish measurements (named 'fish'). Where relevant the following parameters may be tabulated for each effect:

Age: Identifying the age the effect applies to
Level: Identifying the value or level of the covariate the effect applies to
Iteration: Identifying the iteration the fit is provided for
AgeIndex: Age identifier used internally in Reca
LevelIndex: Level identifier used internally in Reca
Slope: The value of the regression slope
tau_Slope: The value of tau parameter for the regression slope
ar_Slope: The value of regression slope of a the autoregressive coefficient associated with the effect
Intercept: The value of the regression intercept
tau_Intercept: The value of tau parameter for the regression intercept
ar_Intercept: The value of the regression intercept of a autoregressive coefficient associated with the effect

Consult Hirst et.al. 2005 for description of the parameters

@section other data: The lists 'AgeLength', 'WeightLength', 'Landings', 'GlobalParameters' and 'CovariateMaps' may be passed to eca.predict in functions consuming output from this function. All in all the following lists can be accessed on RecaParameterData objects:

FitProportionAtAge: list of data tables with parameters for for the Proportion-at-age model
FitLengthGivenAge: list of data tables with parameters for for the Length-given-age model
FitWeightGivenLength: list of data tables with parameters for for the Weight-given-length model
AgeLength: input needed for eca.estimate and eca.predict
WeightLength: input needed for eca.estimate and eca.predict
Landings: input needed for eca.estimate and eca.predict
GlobalParameters: input needed for eca.estimate and eca.predict. see details
CovariateMaps: Mapping of values for each covariate in landings and samples (including non-configurable catchId) to integer value used in R-ECA.