Package index
Full pipeline
Run the complete analysis, from importing the genotyping data to saving the posterior probabilities and plots, in a single call.
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MalReBay() - Run the MalReBay malaria recrudescence classification pipeline
Pipeline steps
Run the individual stages of the analysis separately, for example to inspect intermediate results or to rerun the classification with different settings.
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import_data() - Import Genotyping Data from Excel
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classify_infections() - Classify malaria infections using Bayesian MCMC
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summarise_results() - Summarise MCMC Classification Results
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save_results() - Save Classification Results and Generate Plots
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data_quality_check() - Check dataset viability per site
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compute_locus_comparability() - Compute locus comparability per patient
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detect_msp_variants() - Identify which locinames belong to the MSP1/MSP2 families
Convergence diagnostics
Assess whether the MCMC sampling has converged before interpreting the results.
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check_mcmc_diagnostics() - Check MCMC sampler diagnostics and report plain-language guidance
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plot_likelihood_diagnostics() - Plot MCMC Likelihood Diagnostics
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plot_probability_histogram() - Plot Posterior Probability Histogram
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plot_comparison_heatmap() - Plot Match-Counting vs MalReBay Comparison Heatmap
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plot_moi() - Plot Multiplicity of Infection (MOI)
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plot_markers_diversity() - Generate and Save Diversity Pie Charts
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plot_allele_distribution() - Plot Allele Distribution