This package originated as a copy of phylodyn, an R package with the purpose of facilitating phylodynamic inference and analyses. phylodyn2 has reduced, specific functionality compared to phylodyn, and it implements methodology developed for accounting for reporting delays, by incorporating reporting probabilities in the preferential sampling model for real-time phylodynamic analyses.

The manuscript describing the methodolody is available at https://arxiv.org/abs/2407.18432 and the repository with code to reproduce the manuscript is available at https://github.com/CatalinaMedina/reporting-delays-in-phylodynamics-paper.

# install.packages("devtools")
devtools::install_github("CatalinaMedina/phylodyn2")