Read ASAP3 fit

Source: R/read_asap3_fit.R

Gets output from a fit ASAP3 model for plotting with WHAM models.

read_asap3_fit(wd, asap.name, pSPR = 40)

Arguments

wd

character, directory where ASAP3 output files are located (ex: 'C:/MY/file/directories/model/'). 5 files are needed: .rdat, .dat, .std, .cor, and .par.

asap.name

character, base name of original .dat file (i.e. without the .dat extension)

pSPR

scalar, user-specified percent SPR to use for reference points, expressed as 100*SSBPR(Fspr)/SSBPR(F=0). Default = 40.

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. For ASAP this will be the same as $years.

$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, n_years x n_fleets, indices of selAA used by each fleet in each year

$selblock_pointer_indices

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

$MAA

matrix, n_years x n_ages, natural mortality

$log_SSB

matrix, n_years x 2, log-scale spawning stock biomass. 1st col = MLE, 2nd col = SE (from .std file in ADMB).

$log_F

matrix, n_years x 2, log-scale fully-selected F. 1st col = MLE, 2nd col = SE (from .std file in ADMB).

$log_NAA

matrix, n_years x n_ages, numbers at age

$NAA_CV

matrix, n_years x n_ages, CV of numbers at age

$percentSPR

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

$log_Y_FXSPR

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

$log_FXSPR

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

$log_SSB_FXSPR

matrix, n_years x 2, log-scale SSB at FXSPR, i.e. annual numerator of SPR(FXSPR) * Recruits. 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

Examples

if (FALSE) {
base <- read_asap3_fit(wd=file.path(getwd(),'asap_results'), asap.name='BASE_5C.DAT', pSPR=40)
m1 <- fit_wham(input1)
m2 <- fit_wham(input2)
mods <- list(base=base, m1=m1, m2=m2)
res <- compare_wham_models(mods)
}