cladoRcpp: C++ implementations of phylogenetic cladogenesis calculations

This package implements in C++/Rcpp various cladogenesis-related calculations that are slow in pure R. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events. Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state). This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue. C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="cladoRcpp") to get the citation information.

Version: 0.14.4
Imports: Rcpp
LinkingTo: Rcpp, RcppArmadillo
Published: 2014-05-18
Author: Nicholas J. Matzke [aut, cre, cph]
Maintainer: Nicholas J. Matzke <matzke at berkeley.edu>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: http://phylo.wikidot.com/biogeobears
NeedsCompilation: yes
Materials: NEWS
CRAN checks: cladoRcpp results

Downloads:

Reference manual: cladoRcpp.pdf
Package source: cladoRcpp_0.14.4.tar.gz
Windows binaries: r-devel: cladoRcpp_0.14.4.zip, r-release: cladoRcpp_0.14.4.zip, r-oldrel: cladoRcpp_0.14.4.zip
OS X Snow Leopard binaries: r-release: cladoRcpp_0.14.4.tgz, r-oldrel: cladoRcpp_0.14.4.tgz
OS X Mavericks binaries: r-release: cladoRcpp_0.14.4.tgz
Old sources: cladoRcpp archive

Reverse dependencies:

Reverse depends: BioGeoBEARS