Man pages for bobverity/MALECOT
Joint estimation of COI and population structure for malaria genetic data
| active_set | Change the active set of a MALECOT project |
| bind_data_biallelic | Bind bi-allelic data to project |
| bind_data_multiallelic | Bind multi-allelic format data to project |
| check_MALECOT_loaded | Check that MALECOT package has loaded successfully |
| delete_set | Delete parameter set |
| get_ESS | Get ESS |
| get_group_order | Match grouping against q-matrix |
| is.malecot_project | Determine if object is of class malecot_project |
| MALECOT | MALECOT package |
| malecot_file | Import file |
| malecot_project | Define empty malecot_project object |
| more_colours | Expand series of colours by interpolation |
| new_set | Create new MALECOT parameter set |
| plot_acf | Produce MCMC autocorrelation plot |
| plot_COI | Plot COI 95% credible intervals |
| plot_COI_mean | Plot COI_mean 95% credible intervals |
| plot_coupling | Plot Metropolis-coupling acceptance rates |
| plot_density | Produce MCMC density plot |
| plot_e | Plot error rate 95% credible intervals |
| plot_GTI_path | Plot GTI path of current active set |
| plot_logevidence_K | Plot log-evidence estimates over K |
| plot_logevidence_model | Plot log-evidence estimates over parameter sets |
| plot_loglike | Plot loglikelihood 95% credible intervals |
| plot_loglike_dignostic | Produce diagnostic plots of log-likelihood |
| plot_p | Plot allele frequency 95% credible intervals |
| plot_posterior_K | Plot posterior K |
| plot_posterior_model | Plot posterior model |
| plot_prior_COI | Plot prior on COI |
| plot_prior_p | Plot prior on allele frequencies |
| plot_structure | Posterior allocation plot |
| plot_trace | Produce MCMC trace plot |
| print_full | Ordinary print function for class malecot_project |
| print.malecot_project | Custom print function for class malecot_project |
| recalculate_evidence | Recalculate evidence and posterior estimates |
| run_mcmc | Run main MCMC |
| sim_data | Simulate genetic data |
| sim_data_safe | Simulate genetic data subject to constraints |
| summary.malecot_project | Print summary for class malecot_project |
