R-universe - mdhall272 (Matthew Hall)

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.

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5.53 score 34 stars 1 dependents 66 scripts 877 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.

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3.30 score 4 stars 216 downloads