addNage {DATRAS}R Documentation

Add numbers-at-age to a DATRASraw object.

Description

Add numbers-at-age to a DATRASraw object. Numbers are estimated using a continuation-ratio logit model. This is just a short-cut for calling 'fitALK' to fit the model followed by 'predict.ALKmodel' and adding numbers-at-age per haul to the DATRASraw object in a variable called 'Nage'.

Usage

  addNage(x, ages, mc.cores = 1,
    model = c(paste("cra~LngtCm"), paste("cra~poly(LngtCm,2)"), paste("cra~LngtCm+s(lon,lat,bs='ts')"))[method],
    method = 1, autoChooseK = FALSE, useBIC = FALSE,
    varCof = FALSE, maxK = 100, gamma = 1.4,
    verbose = FALSE, ...)

Arguments

x

a DATRASraw object.

ages

Vector with consecutive ages to consider, last age is plus group.

mc.cores

The number of cores to use, i.e. how many processes will be spawned (at most)

model

Model formula(string) for ALK, or a vector of strings specifying the formula for each logit (i.e. number of age groups minus one).

method

Use default formula: 1=Normal distributed age-at-length (1st order), 2=Second order polynomial, 3=Spatial ALK, first order length-effect.

autoChooseK

Automatic choice of the max. dimension for the basis used to represent the smooth term for spatial ALK. See ?s in the mgcv-package.

useBIC

Use Bayesian Information Criterion for smoothness selection instead of AIC.

varCof

Use varying coefficients model for spatial effect.

maxK

Maximum k to use. Only applies if autoChooseK is TRUE.

gamma

Multiplier for AIC score (see ?gam)

verbose

Print details about the fitting process.

...

Optional extra arguments to gam()

Value

A DATRASraw object.


[Package DATRAS version 1.0 Index]