Read WHAM fit

Source: R/read_wham_fit.R

Gets output from a fit WHAM model for plotting with other models. Internal function, called within compare_wham_models.

read_wham_fit(mod, alphaCI = 0.05)

Arguments

mod

output from fit_wham

alphaCI

(1-alpha)% confidence intervals will be calculated. Default = 0.05 for 95% CI.

Value

a named list with the following elements:

$years

numeric vector, model years only, e.g. 1972:2020

$years_full

numeric vector, model + proj years, e.g. 1972:2022

$selAA

list of length(n_selblocks), first the fleet blocks then indices, i.e. if 4 fleet blocks and 3 indices, selAA[[5]] is for index 1. Each element is a matrix, years (rows) x ages (cols), selectivity at age

$selblock_pointer_fleets

matrix, years x fleets, indices of selAA used by each fleet in each year

$selblock_pointer_indices

matrix, years x indices, indices of selAA used by each index in each year

$MAA

array, stocks x regions x years x ages, natural mortality

$log_SSB

matrix, years x 2, log-scale spawning stock biomass. 1st col = MLE, 2nd col = SE.

$log_F

matrix, years x 2, log-scale fully-selected F. 1st col = MLE, 2nd col = SE.

$log_NAA_rep

array, stocks x regions x years x ages, numbers at age

$NAA_CV

array, stocks x regions x years x ages, CV of numbers at age

$percentSPR

scalar, X% SPR used to calculate reference points, default = 40

$log_Y_FXSPR

matrix, years x 2, log-scale yield at FXSPR. 1st col = MLE, 2nd col = SE.

$log_FXSPR

matrix, years x 2, log-scale FXSPR. 1st col = MLE, 2nd col = SE.

$log_SSB_FXSPR

matrix, years x 2, log-scale SSB at FXSPR. 1st col = MLE, 2nd col = SE.

$log_rel_ssb_F_cov

list, length n_years, each element is a 2x2 covariance matrix with SSB/SSB_FXSPR first and F/F_FXSPR second