compute_ML_rho | Maximum likelihood of recombination rate |
compute_mu | Compute emission probabilities for HMM |
compute_Px | Compute hidden state transition kernel |
count_changepoints | Count changepoints |
count_runs | Count runs |
d_seq | Generate discretization timepoints |
forward_algorithm | Forward algorithm |
forward_algorithm_logspace | Forward algorithm in logspace |
likelihood_Y | Marginal likelihood of Y |
log_likelihood_Y | Marginal log-likelihood of Y |
log_sum_exp | Compute log-sum-exp |
log_sum_exp_lower_bound | Approximate log-sum-exp from below |
log_sum_exp_upper_bound | Approximate log-sum-exp from above |
sample_X | Sample hidden states |
sample_XandY | Sample full model |
sample_YgivenX | Sample emissions |
theta_watterson | Watterson's estimator |
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