Predict catch-at-age

This function runs the C prediction program and writes results to binary files.

eca.predict(AgeLength, WeightLength, Landings, GlobalParameters)

Arguments

AgeLength

A list with elements connected to the age-length model, see eca.estimate.

WeightLength

A list with elements connected to the weight-length model, see eca.estimate.

Landings

A list with elements connected to landings, see Details

GlobalParameters

A list with input parameters that are given by the user, see Details

Value

A list with elements

TotalCount

array of the total catch (in numbers) with dimensions #length intervals x #age categories x #samples

MeanLength

matrix of the mean length in the different age categories with dimensions #age categories x #samples

MeanWeight

matrix of the mean weight in the different age categories with dimensions #age categories x #samples

AgeCategories

vector with age categories

LengthIntervalsLog

vector with length intervals, on log scale

If a multiple stocks (coastal cod/Atlantic cod) analysis is run, the function returns the same list, but where the dimension of age categories in all the elements is 2 times the number of age categories in the model (ncat). The first ncat valuels correspond to Atlantic cod while the last ncat values correspond to coastal cod.

Details

Landings

  • LiveWeightKG - Catch data given in kilograms for each cell.

  • AgeLengthCov - Covariate matrix for age-length model specifying which level of the different covariates the corresponding cell in LiveWeightKG has, e.g. constant, season, gearfactor, spatial. It also contains a column midseason which is the fraction of the year where the catch is taken.

  • WeightLengthCov - Covariate matrix for weight-length model specifying which level of the different covariates the corresponding cell in LiveWeightKG has, e.g. constant, season, gearfactor, spatial. It also contains a column midseason which is the fraction of the year where the catch is taken.

GlobalParameters

  • minage - minimum age category

  • maxage - maximum age category

  • CC - TRUE if coastal cod is included in the model, FALSE otherwise

  • resultdir - directory path where the results are stored. Two directories cfiles and resfiles are in this folder (created if they don't exist). In cfiles the temporary binary input files to the c-program are stored, and in resfiles the binary output files are stored.

  • fitfile - name of the output files from estimating the model. The files are given the extensions .mcmc1 and .mcmc2 for the age and length-given-age model and for the weight-given-length model, respectively.

  • predictfile - name of the output file from prediction. The file is given the extension .pred.

  • caa.burnin - number of MCMC samples discarded before running the prediction

  • seed - random seed value

See also

eca.estimate for estimating the catch-at-age model.