Run the MalReBay malaria recrudescence classification pipeline

Imports genotype data, runs Bayesian MCMC classification to distinguish recrudescent from reinfection malaria treatment failures, summarises results, and saves output plots and tables.

Usage

MalReBay(
  filepath = system.file("extdata", "Dataset_microsatellite_panel.xlsx", package = "MalReBay"),
  marker_filepath = system.file("extdata", "makers_details.xlsx", package = "MalReBay"),
  additional_filepath = NULL,
  mcmc_config = system.file("extdata", "default_mcmc_config.rds", package = "MalReBay"),
  output_folder = NULL,
  n_workers = 1,
  verbose = TRUE,
  suppress_warnings = TRUE,
  prob_threshold = 0.5,
  plots = TRUE
)

Arguments

filepath

Path to the genotype data Excel file. Defaults to the package example dataset.

marker_filepath

Path to the marker metadata Excel file. Defaults to the package example marker file.

mcmc_config

Path to the MCMC configuration Excel file. Defaults to the package default configuration.

output_folder

Path to a folder for saving results and plots. Set to NULL to skip saving (results are still returned invisibly).

n_workers

Number of parallel workers. For length-polymorphic data this is handled automatically by the sampler; the argument is retained for compatibility with amplicon-sequencing data.

verbose

If TRUE, print progress messages to the console.

suppress_warnings

Logical. If TRUE (default), silences the MCMC sampler's own console warnings about divergent transitions, treedepth, and E-BFMI. See classify_infections for details – these diagnostics remain available afterwards via summary_results$convergence regardless of this setting.

prob_threshold

Numeric in [0, 1]. The posterior probability at or above which a recurrence is classified as "Recrudescence" (below it, "Reinfection"). Defaults to 0.5, the natural cutoff under this model's equal 50/50 prior. See summarise_results for where this is applied.

plots

Logical. If FALSE, skips all plots (descriptive, result and convergence diagnostic plots); convergence diagnostics are still computed and printed. Defaults to TRUE.

Value

A list of per-site summary results (invisibly). See summarise_results() for details of the list structure.

Examples

if (FALSE) { # \dontrun{
# Run on the bundled example data with default settings
results <- MalReBay()

# Run on your own data and save output to a folder
results <- MalReBay(
  filepath      = "path/to/your_data.xlsx",
  output_folder = "path/to/output"
)
} # }