Man pages for bobverity/MALECOT
Joint estimation of COI and population structure for malaria genetic data

active_setChange the active set of a MALECOT project
bind_data_biallelicBind bi-allelic data to project
bind_data_multiallelicBind multi-allelic format data to project
check_MALECOT_loadedCheck that MALECOT package has loaded successfully
delete_setDelete parameter set
get_ESSGet ESS
get_group_orderMatch grouping against q-matrix
is.malecot_projectDetermine if object is of class malecot_project
malecot_fileImport file
malecot_projectDefine empty malecot_project object
more_coloursExpand series of colours by interpolation
new_setCreate new MALECOT parameter set
plot_acfProduce MCMC autocorrelation plot
plot_COIPlot COI 95% credible intervals
plot_COI_meanPlot COI_mean 95% credible intervals
plot_couplingPlot Metropolis-coupling acceptance rates
plot_densityProduce MCMC density plot
plot_ePlot error rate 95% credible intervals
plot_GTI_pathPlot GTI path of current active set
plot_logevidence_KPlot log-evidence estimates over K
plot_logevidence_modelPlot log-evidence estimates over parameter sets
plot_loglikePlot loglikelihood 95% credible intervals
plot_loglike_dignosticProduce diagnostic plots of log-likelihood
plot_pPlot allele frequency 95% credible intervals
plot_posterior_KPlot posterior K
plot_posterior_modelPlot posterior model
plot_prior_COIPlot prior on COI
plot_prior_pPlot prior on allele frequencies
plot_structurePosterior allocation plot
plot_traceProduce MCMC trace plot
print_fullOrdinary print function for class malecot_project
print.malecot_projectCustom print function for class malecot_project
recalculate_evidenceRecalculate evidence and posterior estimates
run_mcmcRun main MCMC
sim_dataSimulate genetic data
sim_data_safeSimulate genetic data subject to constraints
summary.malecot_projectPrint summary for class malecot_project
bobverity/MALECOT documentation built on May 13, 2019, 4:01 a.m.