phylomd

This package implements a post-order tree traversal meta-algorithm that computes phylogenetic stochastic mapping moments and likelihood derivatives of any order and scales linearly in the number of phylogeny tips. Utility functions related to simulation-based stochastic mapping and higher-order continuous-time Markov chain (CTMC) moment and derivative calculations are also provided.

Installation

First, install the devtools package (if it isn't already installed) using install.packages("devtools"). Check to make sure you have a working development environment by running devtools::has_devel(). If it returns TRUE, then your development environment is correctly set up; otherwise, you'll need to install additional tools. More information on this subject can be found at https://github.com/hadley/devtools. In addition, a C++11 compliant compiler is needed to build this package. If you're using Mac OS X, please be aware of Rcpp-FAQ question 2.16.

The phylomd package can then be installed from GitHub using the install_github function.

library(devtools)
install_github("dunleavy005/phylomd")

To install the phylomd package with vignettes, run install_github("dunleavy005/phylomd", build_vignettes = TRUE). The vignettes can be accessed by executing browseVignettes("phylomd").

References

1. Nielsen R (2002) "Mapping Mutations on Phylogenies", Systematic Biology, 51(5):729-739.

2. Minin VN and Suchard MA (2008) "Counting labeled transitions in continuous-time Markov models of evolution", Journal of Mathematical Biology, 56(3):391-412.

3. Minin VN and Suchard MA (2008) "Fast, Accurate and Simulation-Free Stochastic Mapping", Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1512):3985-3995.

4. Kenney T and Gu H (2012) "Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications", Statistical Applications in Genetics and Molecular Biology, 11(4).

5. Dhar A and Minin VN (2017) "Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time", Journal of Computational Biology, 24(5):377-399.

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