Man pages for mirjamlaager/mrsamcmc
An Implementation of Data Augmented MCMC for Inference on MRSA Transmission
| col_pop | Count the number of colonised patients |
| count_false_negative_tests | Count false negative tests |
| count_tests_forward_simulations | Count positive and negative tests |
| count_true_positive_tests | Count true positive tests. |
| daily_col_prob_precalculated | Compute the probability of acquisition |
| generate_configuration | Generate configuration. |
| generate_priors | Generate priors. |
| log_lik_importation | Log likelihood of importation |
| log_lik_overall | Overall log likelihood for one patient |
| log_lik_overall_with_types | Overall log likelihood for one patient |
| log_lik_rho | Log likelihood of test sensitivity |
| log_lik_sources | Log likelihood of sources |
| log_lik_transmission | Log likelihood of transmission |
| onward_check | Get last possible day for colonisation |
| patient_data_simulated | Simulated patient data. |
| posterior_predictive_checks | Run forward simulations |
| run_forward_simulations | Run forward simulations |
| run_mcmc | Run data augmented MCMC |
| run_mcmc_with_types | Run data augmented MCMC with discrete typing data. |
| update_onward_transmission | Get first onward transmission of a patient |
