R packages by mdhall272

ggarchery - Flexible Segment Geoms with Arrows for 'ggplot2'

Geoms for placing arrowheads at multiple points along a segment, not just at the end; position function to shift starts and ends of arrows to avoid exactly intersecting points.

Last updated 12 months ago

5.28 score 32 stars 1 dependents 40 scripts 745 downloads

STraTUS - Enumeration and Uniform Sampling of Transmission Trees for a Known Phylogeny

For a single, known pathogen phylogeny, provides functions for enumeration of the set of compatible epidemic transmission trees, and for uniform sampling from that set. Optional arguments allow for incomplete sampling with a known number of missing individuals, multiple sampling, and known infection time limits. Always assumed are a complete transmission bottleneck and no superinfection or reinfection. See Hall and Colijn (2019) <doi:10.1093/molbev/msz058> for methodology.

Last updated 5 months ago

3.30 score 4 stars 238 downloads