phylopomp, an R package for POMP inference on genealogies

Installation

You can install phylopomp in one of three ways:

1. At the R prompt, run install.packages("phylopomp",repos="https:kingaa.github.io").
2. Visit the latest release and download the archive appropriate for your platform. Then install locally, e.g., by running install.packages(<path/to/local/file>,repos=NULL) at the R command prompt.
3. Use devtools.

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:

• pomp
• circumstance

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/