cladoRcpp - C++ Implementations of Phylogenetic Cladogenesis Calculations
Various cladogenesis-related calculations that are slow in
pure R are implemented in C++ with Rcpp. 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.
