Changelog

Source: NEWS.md

MalReBay 0.0.1

This is the first release version of MalReBay! 🎉

• Added a NEWS.md file to track changes to the package.

• Functions:

  • MalReBay()
  • import_data()
  • plot_likelihood_diagnostics()
  • plot_probability_histogram()
  • plot_moi()
  • plot_markers_diversity()

• Example data:

  • Angola_2021_TES_7NMS.xlsx — genotyping data from a Therapeutic Efficacy Study conducted in Angola in 2021. Contains 70 patients from three sites (Benguela, Lunda Sul, Zaire) genotyped at 7 microsatellite markers.

  • Amplicon_Sequencing.xlsx — example amplicon sequencing dataset for demonstrating the ampseq workflow.

  • makers_details.xlsx — marker metadata file containing marker IDs, binning methods, and repeat lengths required by import_data().

  • default_mcmc_config.xlsx — default MCMC configuration file with recommended settings for n_chains, iter, burn_in_frac, adapt_delta, and random_seed.

  All files can be accessed via:

  system.file("extdata", "filename.xlsx", package = "MalReBay")

• Vignettes:

  • Getting started