Package: phybase
Type: Package
Title: Basic functions for phylogenetic analysis
Version: 1.1
Date: 2008-03-25
Author: Liang Liu
Maintainer: Liang Liu <lliu@oeb.harvard.edu>
Depends: Matrix, ape
Description: This package provides functions to read, write,
manipulate, estimate, and summarize phylogenetic trees
including species trees which contain not only the topology and
branch lengths but also population sizes. The input/output
functions can read tree files in which trees are presented in
parenthetic format. The trees are read in as a string and then
transformed to a matrix which describes the relationship of
nodes and branch lengths. The nodes matrix provides an easy
access for developers to further manipulate the tree, while the
tree string provides interface with other phylogenetic R
packages such as "ape". The input/output functions can also be
used to change the format of tree files between NEXUS and
PHYLIP. Some basic functions have already been established in
the package for manipulating trees such as deleting and
swapping nodes, rooting and unrooting trees, changing the root
of the tree. The package also includes functions such as
"consensus", "coaltime, "popsize", "treedist" for summarizing
phylogenetic trees, calculating the coalescence time,
population size, and tree distance. The function maxtree is
built in the package to esimtate the species tree from multiple
gene trees.
License: GPL (>= 2)
Packaged: 2012-10-29 08:59:26 UTC; ripley
Repository: CRAN
Date/Publication: 2012-10-29 08:59:26

Title: Analysis of Outbreaks with Sequence Data
email = "don@xs4all.nl", role = c("aut", "cre"))
Description: Implementation the outbreak analysis method described by
Simulate outbreaks, analyse datasets by creating samples from the
posterior distribution with a Markov-Chain Monte Carlo sampler,
Imports: Rcpp (>= 0.12.1), methods, stats, utils

Klinkenberg et al (2017) <doi:10.1371/journal.pcbi.1005495>.
Imports: Rcpp (>= 0.12.1), methods, stats, stringr, utils
Suggests: coda, phytools, OutbreakTools, testthat, knitr, rmarkdown