Man pages for Cronjaeger/HotBirdHMM
Find Recombination Hoitspots using a Hidden Markov Model
| 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 |
