Computes the negative log-likelihood for half-sibling pair observations based on reproduction and survival.
Usage
get_HSP_like(
hsp_switch,
hsp_obs,
hsp_q,
hsp_false_negative,
number_ysa,
phi_ya,
M_a,
spawning_biomass_y,
hrate_ysa
)Arguments
- hsp_switch
Integer flag for activation.
- hsp_obs
Matrix n,5 with columns: cohort1, cohort2, cohort difference, comparisons, matches.
- hsp_q
Effective sampling fraction of potential parents.
- hsp_false_negative
Probability of detecting a true match (1 – false negative rate).
- number_ysa
3D array year, season, age of numbers-at-age.
- phi_ya
Matrix year, age of reproductive output-at-age.
- M_a
Vector of natural mortality at age.
- spawning_biomass_y
Vector of spawning biomass by year.
- hrate_ysa
3D array year, season, age of harvest rates.