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Estimate Stock Composition Using Direct Maximum Likelihood (Theta5)

Source: R/estimate.R
estimate_ml_theta5.Rd

Applies an EM algorithm to obtain the direct Maximum Likelihood Estimate (MLE) of stock proportions (Theta_5 in HISEA). This uses the likelihood of each individual mixed fishery sample fish belonging to each stock. The likelihood maximized is:

Usage

estimate_ml_theta5(
  individual_likelihoods,
  np,
  freq = NULL,
  use_accelerated_em = TRUE,
  ...
)

Arguments

individual_likelihoods

A numeric matrix (N_mixed_samples x NP) where individual_likelihoods[i,j] is $P(Data_i | Stock_j)$, the likelihood of observing the data for mixed sample fish i given it came from stock j.

np

Integer, the number of populations (stocks).

freq

Optional numeric vector of frequencies/weights for each sample (row) in individual_likelihoods. Defaults to rep(1, nrow(individual_likelihoods)).

use_accelerated_em

Logical, if TRUE, uses accel_em_algorithm, otherwise em_algorithm. Default TRUE.

...

Additional arguments passed to the chosen EM algorithm (e.g., max_iter, tol, verbose, save_theta_path).

Value

A numeric vector of estimated stock proportions (Theta5).