Resample data and compute length and age population expansion

Following Fig. 1 in Hulson and Williams 2024 this function resamples cpue, length frequency, and age specimen data, adds ageing error and growth variability, and expands these data to population at length and age.

srvy_comps(
  lfreq_data,
  specimen_data,
  cpue_data,
  strata_data,
  r_t,
  yrs = NULL,
  bin = 1,
  boot_hauls = FALSE,
  boot_lengths = FALSE,
  boot_ages = FALSE,
  al_var = FALSE,
  al_var_ann = FALSE,
  age_err = FALSE,
  len_samples = NULL,
  age_samples = NULL,
  plus_len = NULL,
  plus_age = NULL,
  by_strata = FALSE,
  global = FALSE
)

Arguments

lfreq_data: length frequency input dataframe
specimen_data: age-length specimen input dataframe
cpue_data: catch-per-unit effort input dataframe
strata_data: strata id and area size input dataframe
r_t: age reader-tester input dataframe, included in surveyISS package data
yrs: any year filter >= (default = NULL)
bin: bin size (default = 1 cm), also can use custom length bins following ss3 bin convention
boot_hauls: Boolean. Resample hauls w/replacement? (default = FALSE)
boot_lengths: Boolean. Resample length frequency w/replacement? (default = FALSE)
boot_ages: Boolean. Resample ages w/replacement? (default = FALSE)
al_var: Boolean. Include age-length variability in resampled age data? (default = FALSE)
al_var_ann: Boolean. Resample age-length variability annually or pooled across years? (default = FALSE)
age_err: Boolean. Include ageing error in resampled age data? (default = FALSE)
len_samples: If set at a value, tests reductions in haul-level length sampling. To test, set this value at some smaller level than current sampling rate, i.e., 25 (default = NULL)
age_samples: If set at a value, tests reductions (and increases) in survey-level number of ages collected. To test, set at a proportion of ages collected, i.e., 0.8 or 1.2 (default = NULL)
plus_len: If set at a value, computes length expansion with a plus-length group (default = FALSE)
plus_age: If set at a value, computes age expansion with a plus-age group (default = FALSE)
by_strata: Boolean. Should length/age pop'n values be computed at stratum level? (default = FALSE)
global: Boolean. Fill in missing length bins with global age-lenth key? (default = FALSE)

Value

List with dataframes of population numbers at length (.lpop) and age (.apop).