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