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.
|Author||Matthew Hall [aut, cre], Caroline Colijn [ctb]|
|Maintainer||Matthew Hall <[email protected]>|
|Package repository||View on CRAN|
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