Length Composition Likelihood

Computes likelihood for observed length compositions using a probability-of-length-at-age (PLA) matrix. Gradients propagate through to growth parameters when they are estimated.

Usage

get_length_like(
  lf_obs_flat,
  lf_obs_ints,
  lf_obs_prop,
  catch_pred_fya,
  pla,
  lf_n_f,
  lf_fishery_f,
  lf_year_fi,
  lf_n_fi,
  lf_minbin,
  lf_maxbin,
  removal_switch_f,
  lf_switch,
  n_len,
  n_lf,
  log_lf_tau
)

Arguments

lf_obs_flat

numeric vector of unrounded length composition counts (used when lf_switch=1).

lf_obs_ints

integer vector of integer length composition counts (used when lf_switch=3).

lf_obs_prop

numeric vector of length composition proportions (used when lf_switch=2).

catch_pred_fya

3D array [n_fishery, n_year, n_age] of predicted catch-at-age from do_dynamics().

pla

matrix [n_len, n_age] probability-of-length-at-age from get_pla(). On the AD tape when growth parameters are estimated.

lf_n_f

integer vector [n_fishery] of number of observations per fishery.

lf_fishery_f

integer vector of fishery indices for each observation group.

lf_year_fi

list of integer vectors of year indices for each observation.

lf_n_fi

list of integer vectors of sample sizes for each observation.

lf_minbin

integer vector [n_fishery] of minimum bin index per fishery.

lf_maxbin

integer vector [n_fishery] of maximum bin index per fishery.

removal_switch_f

integer vector [n_fishery] indicating if fishery is removed (0=included, 1=removed).

lf_switch

integer likelihood type selector (1=multinomial, 2=dirichlet, 3=dirichlet-multinomial).

n_len

integer number of length bins.

n_lf

integer total number of length composition observations.

log_lf_tau

numeric vector [n_fishery] of log-scale variance adjustment parameters.

Value

a numeric vector of negative log-likelihood contributions, one per observation.