Packaged: Mon Aug  1 16:38:54 2005; pwang

Package: cladoRcpp
Type: Package
Title: C++ implementations of phylogenetic calculations
Version: 0.1
Date: 2013-02-19
Author: Nicholas J. Matzke, Dept. of Integrative Biology, U.C. Berkeley
Maintainer: Nicholas J. Matzke <matzke@berkeley.edu>
Depends: methods, Rcpp (>= 0.9.10), RcppArmadillo
LinkingTo: Rcpp, RcppArmadillo
Description: 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.
License: GPL
ByteCompile: true
Packaged: 2013-04-04 00:11:49 UTC; nickm
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-04-04 07:31:55

Package: cladoRcpp
Type: Package
Title: C++ implementations of phylogenetic calculations
Version: 0.11
Date: 2013-04-09
Authors@R: c(person("Nicholas J.", "Matzke", email =
"matzke@berkeley.edu", role = c("aut", "cre", "cph")))
Maintainer: Nicholas J. Matzke <matzke@berkeley.edu>
Depends: methods, Rcpp (>= 0.9.10), RcppArmadillo
LinkingTo: Rcpp, RcppArmadillo
Description: 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.
License: GPL (>= 2)
LazyLoad: yes
ByteCompile: true
Packaged: 2013-04-11 09:55:40 UTC; nickm
Author: Nicholas J. Matzke [aut, cre, cph]
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2013-04-11 12:19:46