Title: Single Transferable Vote Counting
person("John", "Emerson", email = "john.emerson@yale.edu", role = c("cre", "aut")),
person("Saksham", "Chandra", role = "aut"),
person("Efim", "Abrikosov", role = "ctb"),
person("Shadie", "Khubba", role = "ctb"),
person("William", "Meyerson", role = "ctb"),
person("Shylee", "Ezroni", role = "ctb"),
Description: Implementations of the Single Transferable Vote counting
system. By default, it uses the Cambridge method for surplus allocation
and Droop method for quota calculation.  Fractional surplus allocation
and the Hare quota are available as options.

Title: Enumeration and Uniform Sampling of Transmission Trees for a
Authors@R: c(person("Matthew", "Hall", email = "matthew.hall@bdi.ox.ac.uk", role = c("aut", "cre")), person("Caroline", "Colijn", role = c("ctb")))
Description: 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.
Imports: ape, phangorn, igraph, gmp, ggplot2, ggtree (>= 1.14.6),

Imports: ape, phangorn, igraph, gmp, ggplot2, ggtree (>= 2.0.0),

Description: 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 <doi:10.1101/160812> for methodology.
Imports: ape, phangorn, igraph, gmp, gtools, ggplot2, ggtree (>=

Description: This is a package for the subsampling method of robust