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Sampling settings

Source: R/spec_oem.R
oem_settings.Rd

Collects every setting of the observation model. Arguments that can differ by fleet take one value or a vector named by fleet. Catch and effort cover all years of the operating model; CPUE, length frequencies and biological samples cover the last tail years of each fleet (or years).

Usage

oem_settings(
  fishery,
  tail = 10,
  catch_cv = 0.1,
  catch_bias = 0,
  effort_cv = 0.1,
  effort_days = 1000,
  cpue_cv = 0.2,
  cpue_rho = 0.3,
  cpue_creep = TRUE,
  cpue_beta = 1,
  lfd_ess_age = 30,
  lfd_ess_len = 300,
  lfd_bin = NULL,
  lfd_cv = 0.1,
  bio_n = 100,
  bio_p_aged = 0.5,
  bio_age_scheme = c("random", "stratified"),
  bio_n_per_bin = 5,
  age_cv = 0.1,
  wt_cv = 0.1,
  mat_L95 = 1.15,
  catch_bias_from = NULL,
  cpue_q_step = NULL,
  bio_age_bias = 0,
  survey = survey_settings(),
  years = NULL,
  seasons = season_design(4)
)

Arguments

fishery

a fishery() (or a floss_om / floss_oms).

tail

number of most recent years with CPUE, length and biological samples, per fleet.

catch_cv, catch_bias

catch CV and under-reporting (0.1 = 10% under).

effort_cv

effort-index CV.

effort_days

fishing days per year of a fleet at relative effort 1 (per fleet): observed effort is reported in fishing days.

cpue_cv, cpue_rho

CPUE CV and residual autocorrelation.

cpue_creep

does CPUE carry effort creep (rising catchability)?

cpue_beta

proportionality exponent, \(I = qB^\beta\): 1 = proportional, < 1 hyperstable (e.g. range contraction), > 1 hyperdepletion.

lfd_ess_age, lfd_ess_len

stage-1 (clusters) and stage-2 (fish measured) sample sizes.

lfd_bin

length bin (cm); NULL picks about Linf/40 per species.

lfd_cv

CV of length-at-age.

bio_n, bio_p_aged

fish per year and share aged (random ageing).

bio_age_scheme

"random" (a share bio_p_aged of fish aged) or "stratified" (length-stratified subsample: at most bio_n_per_bin fish aged per length bin, source and year, as FLRef::alk.sample()).

bio_n_per_bin

otoliths per length bin for the stratified scheme.

age_cv, wt_cv

ageing-error CV and weight CV.

mat_L95

length at 95% maturity relative to lm (L50).

catch_bias_from

year from which catch_bias applies, per fleet (default: all years); an artefact such as under-reporting that starts with a new quota.

cpue_q_step

artefact: named list by fleet of c(year, mult), the fleet's catchability changes by mult from year (e.g. new electronics), or NULL.

bio_age_bias

proportional ageing bias (default 0 = unbiased); a planted data problem when not 0, e.g. -0.1 = fish are aged 10% too young (typical of old fish read from whole otoliths).

survey

survey_settings() or NULL for no survey.

years

optional named list by fleet of c(first, last) years, overriding tail.

seasons

seasonal sampling of the fleets' length and biological samples: a season_design() for all fleets, or a named list of designs by fleet. Default: four seasons, balanced. season_design(1) gives one annual sample at mid-year.

Value

a list of class floss_oem.

Details

  • Catch by fleet: true catch x (1 - bias) x lognormal error.

  • Effort index by fleet: nominal effort x lognormal error (effort creep is not visible).

  • CPUE by fleet: vulnerable biomass x efficiency (if cpue_creep) with lognormal AR1 residuals, \(\epsilon_y = \rho\,\epsilon_{y-1} + \sqrt{1-\rho^2}\,\delta_y\). Use \(\rho > 0\) for non-random (clustered) sampling of the fleet.

  • Length frequencies: the two-stage FLRef protocol (FLRef::lfd.sim()): lfd_ess_age clusters drawn from the fleet's catch-at-age, then lfd_ess_len fish measured through the gear's length key.

  • Biological samples: bio_n fish per fleet and year with length (mm), age (with ageing error; aged at random or length-stratified), weight (g, with error) and maturity (0/1).

Examples

oem_settings(reef_fishery(), tail = c(traps = 5, gillnet = 10, linefish = 15))
#> FLOSS sampling settings
#>     fleet     years catch_cv bias effort_cv cpue_cv cpue_rho ess_age ess_len
#>     traps 2021-2025      0.1    0       0.1     0.2      0.3      30     300
#>   gillnet 2016-2025      0.1    0       0.1     0.2      0.3      30     300
#>  linefish 2011-2025      0.1    0       0.1     0.2      0.3      30     300
#>  bio_n
#>    100
#>    100
#>    100
#> survey: 2001-2025  timing 0  cv 0.25  rho 0  + length samples 
#> seasons traps : 4 (0.25/0.25/0.25/0.25) 
#> seasons gillnet : 4 (0.25/0.25/0.25/0.25) 
#> seasons linefish : 4 (0.25/0.25/0.25/0.25)