Parent-Offspring Pairing Likelihood

Computes the negative log-likelihood for observed parent-offspring pairings from genetic samples.

Usage

get_POP_like(pop_switch, pop_obs, phi_ya, paly, spawning_biomass_y)

Arguments

pop_switch

Integer flag for activation (currently unused).

pop_obs

Matrix n,6: capture year, offspring year, adult age/length, type flag (0=age, 1=length), number of pairings, and number of comparisons.

phi_ya

Matrix year, age of reproductive output-at-age.

paly

Array length, age, year of predicted adult distributions at length.

spawning_biomass_y

Vector of spawning biomass by year.

Value

Vector of negative log-likelihood contributions for each observation.