The Probability of Transmission Given Phylogenetic Linkage
c(person("John R", "Giles", role=c("aut", "ctb"), email="jrgiles@uw.edu"),
person("Shirlee", "Wohl", role=c("aut", "ctb"), email="swohl@jhu.edu"),
person("Justin", "Lessler", role=c("aut", "cre"), email="jlessler@unc.edu"))
Implements novel tools that estimate the probability of true transmission between two cases given
phylogenetic linkage and the expected number of true transmission links in a sample. Methods described in
Wohl, Giles, and Lessler (2021) <doi:10.1371/journal.pcbi.1009182>.
John R Giles [aut, ctb],
Shirlee Wohl [aut, ctb],
Justin Lessler [aut, cre]

Graph-Based Permutation Tests for Microbiome Data
Provides functions for graph-based multiple-sample
testing and visualization of microbiome data, in particular data
stored in 'phyloseq' objects. The tests are based on those
described in Friedman and Rafsky (1979)
<http://www.jstor.org/stable/2958919>, and the tests are described
in more detail in Callahan et al. (2016)
<doi:10.12688/f1000research.8986.1>.

Exploring the Phylogenetic Signal in Continuous Traits
A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.
Rcpp (>= 0.11.0), adephylo, igraph, ape, phylobase, boot,
RCurl, graphics, grDevices, methods, stats, utils

Rcpp (>= 0.11.0), adephylo, igraph, ape, phylobase, boot, DBI,
graphics, grDevices, methods, stats, utils

R packge for simulating biological sequence evolution
Botond Sipos <sbotond@ebi.ac.uk>, Gregory Jordan
<greg@ebi.ac.uk>
PhyloSim is an extensible object-oriented framework for
the Monte Carlo simulation of sequence evolution written in 100
percent R. It is built on the top of the R.oo and ape packages
and uses Gillespie's direct method to simulate substitutions,
insertions and deletions.