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.tabletabulating the logarithm of the likeliehood of the parameter set for each iteration- ...
A
data.tablefor 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 measurments (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.estimateandeca.predict- WeightLength
input needed for
eca.estimateandeca.predict- Landings
input needed for
eca.estimateandeca.predict- GlobalParameters
input needed for
eca.estimateandeca.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.