Title: Phylogenetic Tree Simulation Package
Author: Jason T. Weir <weir@zoology.ubc.ca>, Dolph Schluter <schluter@zoology.ubc.ca>
Maintainer: Jason T. Weir <weir@zoology.ubc.ca>
Description: PhySim contains functions to simulate phylogenetic trees under a virth death model. Functions are provided to model a lag-time to speciation and extract sister species ages.
Packaged: Sun Jan 28 20:12:06 2007; hornik

Title: A Fast, Flexible Tool for Sorting Phylogenetic Trees
Authors@R: c(person("Timothy", "Stephens", email = "timothy.stephens1@uqconnect.edu.au", role = c("aut", "cre", "trl"), comment = "R port"),
person("Debashish", "Bhattacharya", email = "Bhattacharya@AESOP.Rutgers.edu", role = c("aut")),
person("Mark", "Ragan", email = "m.ragan@imb.uq.edu.au", role = c("aut")),
person("Cheong Xin", "Chan", email = "c.chan1@uq.edu.au", role = c("aut", "cph"), comment = "Original Perl implementation"))
Description: Screens and sorts phylogenetic trees in both traditional and
extended Newick format. Allows for the fast and flexible screening (within
a tree) of Exclusive clades that comprise only the target taxa and/or Non-
Exclusive clades that includes a defined portion of non-target taxa.
Author: Timothy Stephens [aut, cre, trl] (R port),
Cheong Xin Chan [aut, cph] (Original Perl implementation)

Description: Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non-Exclusive clades that includes a defined portion of non-target taxa.
Packaged: 2015-12-21 01:09:32 UTC; timothy.stephens

Packaged: 2016-03-22 11:30:26 UTC; timothy.stephens

Packaged: 2016-05-16 06:27:00 UTC; timothy.stephens

Packaged: 2018-07-20 00:23:12 UTC; timothy.stephens

Package: PhyloMeasures
Type: Package
Title: Fast and Exact Algorithms for Computing Phylogenetic
Biodiversity Measures
Version: 1.0
Date: 2015-03-26
Authors@R: c(person("Constantinos", "Tsirogiannis", role = c("aut", "cre"),
email = "analekta@gmail.com"),
person("Brody", "Sandel", role = "aut"))
Author: Constantinos Tsirogiannis [aut, cre], Brody Sandel [aut]
Maintainer: Constantinos Tsirogiannis <analekta@gmail.com>
Description: Given a phylogenetic tree T and a sample S of species represented as
a subset of tips in T, we want to compute a measure of the diversity
of the species in S with respect to T. The current package offers the
implementations of efficient algorithms for several such measures.
Most importantly, the package includes algorithms for computing exactly and
efficiently the expectation and the variance of these measures, which are
essential for null model comparisons. Efficient computation of
richness-standardized versions of these metrics, such as the net
relatedness index (NRI), nearest taxon index (NTI), phylogenetic
diversity index (PDI), and the corresponding indices of two-sample measures
are also available in this package. The package also introduces a new
single-sample measure, the Core Ancestor Cost (CAC); the package provides
functions for computing the value and the standardised index of the CAC and,
more than that, there is an extra function available that can compute exactly
any statistical moment of the measure.
License: GPL-3
Imports: ape
LazyLoad: yes
Packaged: 2015-04-02 11:13:51 UTC; constant
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2015-04-03 01:46:13