split_catch_maturity: Split catch densities by mass ratio of maturity classes

In seananderson/pbs-synopsis: Data Extraction and Plotting for DFO PBS Groundfish Stocks

Split catch densities by mass ratio of maturity classes

Description

Split catch densities by mass ratio of maturity classes

Usage

split_catch_maturity(
  survey_sets,
  fish,
  split_dens_type = "density_kgpm2",
  survey = c("SYN HS", "SYN QCS", "SYN WCVI", "SYN WCHG"),
  years = NULL,
  cutoff_quantile = 0.9995,
  p_threshold = 0.5,
  use_median_ratio = TRUE,
  sample_id_re = TRUE,
  year_re = FALSE,
  plot = FALSE
)

Arguments

survey_sets	Data from gfdata::get_survey_sets().
fish	Data from gfdata::get_survey_samples().
split_dens_type	Which density type will be split and saved as a column providing units for adult_density and imm_density columns.
survey	List of survey abbreviations.
years	List of years. Default 'NULL' includes all years.
cutoff_quantile	Set max cutoff quantile for mass modeled from lengths.
p_threshold	Probability of maturity to split at. Default = 0.5. Alternatives are 0.05 or 0.95.
use_median_ratio	If TRUE, uses median proportion mature (if FALSE uses mean proportion mature) when catch too small to have biological samples collected.
sample_id_re	If TRUE then the model will include random intercepts for sample ID.
year_re	Option to have lengths at maturity vary by year, but this requires the gfvelocities package.
plot	Logical for whether to produce plots (length-weight and length-at-maturity relationships).

Examples

## Not run: 
d_survey_sets <- gfdata::get_survey_sets("pacific cod")
d_survey_samples <- gfdata::get_survey_samples("pacific cod")

d_by_maturity <- split_catch_maturity(
  d_survey_sets, d_survey_samples,
  survey = c("SYN HS", "SYN QCS"),
  years = NULL,
  plot = TRUE
)

## End(Not run)

seananderson/pbs-synopsis documentation built on April 4, 2024, 1:36 p.m.