Package index

Functions

Run the full Bayesian recrudescence classification pipeline, from importing genotype data to saving posterior probabilities and diagnostic plots.

MalReBay()

Run the MalReBay malaria recrudescence classification pipeline

Data import

Import and validate paired genotyping data from an Excel file, automatically detecting whether the data is length-polymorphic or amplicon sequencing.

import_data()

Import Genotyping Data from Excel

Plotting helpers

Visualize results to help you tune hyperparameters and choose model methods.

plot_likelihood_diagnostics()

Plot MCMC Likelihood Diagnostics

plot_probability_histogram()

Plot Posterior Probability Histogram

plot_moi()

Plot Multiplicity of Infection (MOI)

plot_markers_diversity()

Generate and Save Diversity Pie Charts