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)
output from fit_wham
(1-alpha)% confidence intervals will be calculated. Default = 0.05 for 95% CI.
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
matrix, 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
matrix, years x ages, numbers at age
$NAA_CV
matrix, 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