load_extra_mcmc_biomass: Load the biomass outputs from the extra MCMC output

In pacific-hake/hake-assessment: Stock Assessment for Pacific Hake

Load the biomass outputs from the extra MCMC output

Description

Load the biomass outputs from the extra MCMC output

Calculate the biomass-at-age in catch

Load the selectivity outputs from the extra MCMC output

Load the vulnerability outputs from the extra MCMC output

Usage

load_extra_mcmc_biomass(
  reps,
  verbose = TRUE,
  start_yr = NULL,
  end_yr = NULL,
  progress_n,
  ...
)

load_extra_mcmc_catage_biomass(reps, catage, wtatage, verbose)

load_extra_mcmc_sel(
  reps,
  progress_n,
  verbose = TRUE,
  start_yr = NULL,
  end_yr = NULL,
  type = c("fishery", "survey"),
  ...
)

load_extra_mcmc_selwt(reps, verbose = TRUE, head_beg_pat, head_end_pat, ...)

Arguments

reps	A list of vectors representing one element per report file
verbose	Logical. Show messages
start_yr	Filter years earlier than this out of the results. If NULL, no filtering will occur for the start year
end_yr	End year in the model
progress_n	Report every time this many list items are processed. Consider how many posteriors there are, this should be a fairly large proportion of that (around 1/8th) or there will be too much output and it will run really slow
...	Absorbs arguments meant for other functions
catage	A catch-at-age data frame as created by load_extra_mcmc_atage()
wtatage	A weight-at-age data frame

Value

A list of outputs

A data frame with the medians of the biomass-at-age in catch

pacific-hake/hake-assessment documentation built on Nov. 8, 2024, 1:16 p.m.