Calculate Half-Sibling Pair (HSP) Likelihood (Version 1)

Usage

get_HSP_like_v1(
  hsp_switch,
  hsp_obs,
  hsp_q,
  hsp_false_negative,
  number_ysa,
  phi_ya,
  M_a,
  spawning_biomass_y,
  hrate_ysa
)

hsp_switch: An integer scalar, switch to turn on (>0) or off (0) the HSP likelihood.
hsp_obs: A numeric matrix with columns: cmin, cmax, cdiff, nC, nK.
hsp_q: A numeric scalar, HSP catchability parameter.
hsp_false_negative: A numeric scalar, false negative rate adjustment.
number_ysa: A numeric array of dimensions \[n_year + 1, n_season, n_age\], numbers-at-age.
phi_ya: A numeric matrix of dimensions \[n_year + 1, n_age\], reproductive output-at-age.
M_a: A numeric vector of length n_age, natural mortality-at-age.
spawning_biomass_y: A numeric vector of length n_year + 1, spawning biomass by year.
hrate_ysa: A numeric array of dimensions \[n_year + 1, n_season, n_age\], harvest rate.

A numeric vector of negative log-likelihood values for each HSP observation.