Resample data and compute conditional age-at-length

This function resamples cpue and age specimen data, adds ageing error and growth variability, and then computes conditional age-at-length.

srvy_comps_caal(
  specimen_data,
  cpue_data,
  r_t,
  yrs = NULL,
  bin = 1,
  boot_hauls = FALSE,
  boot_ages = FALSE,
  al_var = FALSE,
  al_var_ann = FALSE,
  age_err = FALSE,
  age_samples = NULL,
  plus_len = NULL,
  plus_age = NULL
)

Arguments

specimen_data

age-length specimen input dataframe

cpue_data

catch-per-unit effort 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_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)

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)

Value

List with dataframe of conditional age-at-length (.caal).