read_wham_fit: Read WHAM fit
In timjmiller/wham: Woods Hole Assessment Model (WHAM)

read_wham_fit

R Documentation

Read WHAM fit

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)

`mod`	output from `fit_wham`
`alphaCI`	(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