This R package implements a simulation-free dynamic programming algorithm for calculating higher-order moments of stochastic mapping summaries on a phylogeny [3]. Utility functions related to simulation-based stochastic mapping [1] and first-order moments [2] are also provided.
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, if you're using Mac OS X, you will need to run the following commands in the Terminal.
curl -O http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2
sudo tar fvxz gfortran-4.8.2-darwin13.tar.bz2 -C /
The phylomoments
package can then be installed from GitHub using the install_github
function.
library(devtools)
install_github("dunleavy005/phylomoments")
By default, vignettes are not included in the installation.
To install the phylomoments
package with vignettes, use install_github("dunleavy005/phylomoments", build_vignettes = TRUE)
.
Note that installing phylomoments
with vignettes is a little slower than installing the package without them.
We provide three vignettes that illustrate how to use the functions provided in this package.
- Introductory Examples
- Rate Variation Testing
- Evolutionary Conservation Testing
You can access the phylomoments
vignettes with browseVignettes("phylomoments")
.
-
Nielsen R (2002) "Mapping mutations on phylogenies", Systematic Biology, 51(5):729-739.
-
Minin VN and Suchard MA (2008) "Counting labeled transitions in continuous-time Markov models of evolution", Journal of Mathematical Biology, 56(3):391-412.
-
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.