fit_cpue_indices: Fit commercial catch per unit effort standardization models

In pbs-assess/gfsynopsis: Data Synopsis Reports for PBS Groundfish

Fit commercial catch per unit effort standardization models

Description

This function helps it fit the CPUE standardization models across multiple areas for a single species.

Usage

fit_cpue_indices(
  dat,
  species = "pacific cod",
  areas = c("3[CD]+|5[ABCDE]+", "5[CDE]+", "5[AB]+", "3[CD]+"),
  center = TRUE,
  cache = here::here("report", "cpue-cache"),
  save_model = FALSE,
  arith_cpue_comparison = TRUE,
  parallel = FALSE,
  year_range = c(1996, lubridate::year(Sys.Date()) - 1)
)

Arguments

dat	A data frame from gfdata::get_cpue_index().
species	The species common name to fit.
areas	A vector of regular expressions representing the statistical areas to fit.
center	Logical for whether or not the index should be centered on its geometric mean.
cache	A folder in which to cache the model output if desired.
save_model	Logical for whether the model should be cached. Defaults to FALSE to save space.
arith_cpue_comparison	Logical: should the unstandardized comparison be an arithmetic 'ratio estimator' CPUE (summed catch for this species divided by summed effort for the entire fleet) (if TRUE) or a GLM / GLMM with only a year predictor.
parallel	Should the various areas be fit in parallel? Make sure you have enough memory. (Disabled for now.)
year_range	Year range.

pbs-assess/gfsynopsis documentation built on March 26, 2024, 7:30 p.m.