| backward | Probability Calculation using the Backward Algorithm for Hidden Markov Models |
| compute_joint_state | Posterior Joint Probability Calculation for Hidden States in a Hidden Markov Model |
| compute_loglikelihood | Log-Likelihood Calculation for Hidden Markov Models (Forward Algorithm) |
| compute_state | Posterior Probability Estimation for Hidden States in Hidden Markov Models |
| forward | Forward Algorithm for Probability Calculation in Hidden Markov Models |
| forward_backward | Probability Calculation in Hidden Markov Models using Forward-Backward Algorithm |
| HMM | Fitting Hidden Markov Models using Expectation-Maximization (EM) Algorithm |
| HMM_C_raw | Fit Hidden Markov Model (HMM) |
| HMM_one_step | Single EM Iteration for Fitting Hidden Markov Models (HMM) |
| IRLS_EM | Iterative Reweighted Least Squares for the EM algorithm |
| print.HMM | Print Outputs from a Hidden Markov Model (HMM) |
| rHMM | Fit Regularized Hidden Markov Models (rHMM) with Modified CCD |
| rHMM_one_step | Single Iteration of EM Algorithm for Fitting Regularized Hidden Markov Model (rHMM) |
| simulate_HMM_data | Simulate Hidden Markov Model (HMM) Data |