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phylopomp, an R package for POMP inference on genealogies

Project Status: WIP - Initial development is in progress, but there has not yet been a stable, usable release suitable for the public. Development Release R-CMD-check binary-build test-coverage codecov manual pdf-manual doxygen

Publications

“Exact Phylodynamic Likelihood via Structured Markov Genealogy Processes” (arXiv:2405.17032, 2024)
 

“Markov Genealogy Processes” (Theoretical Population Biology 143:77–91, 2022)

Related packages:

Checklist for adding a new model

  • create and edit yaml/<model>.yml
  • in yaml/, run Rscript add_model.R
  • cp yaml/src/* src
  • cp yaml/R/* R
  • optionally edit R/<model>.R and src/<model>.cc for style and documentation
  • add examples to examples/<model.R>
  • add tests to tests/