This package implements in C++/Rcpp various cladogenesisrelated 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 continuoustime 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.
Package details 


Author  Nicholas J. Matzke [aut, cre, cph] 
Date of publication  20130715 07:30:51 
Maintainer  Nicholas J. Matzke <[email protected]> 
License  GPL (>= 2) 
Version  0.14.2 
Package repository  View on GitHub 
Installation 
Install the latest version of this package by entering the following in R:

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