README.md

In caseywdunn/hutan: A Collection of Tools for Phylogenetic Tree Manipulation

hutan: An R package for manipulation of phylogenetic trees

There are many excellent R packages for phylogenetic analyses (http://cran.r-project.org/web/views/Phylogenetics.html). Tools for topological analysis and manipulation of trees are, however, relatively limitted. Such methods are required to preprocess data, implement analysis methods, and summarize phylogenetic results. This package provides a variety of functions for topological manipulations and assessments of phylogenetic trees, building on those already present in the ape R package.

Documentation

See the manual, hutan-manual.pdf

Example usage

Create a zero-constrained tree

The following creates a zero-constrained tree as described by Susko 2014 (http://dx.doi.org/10.1093/molbev/msu039):

library(hutan)
data( siphonophore_ml )
data( siphonophore_constraint )

zc <- zero_constrained( siphonophore_ml, siphonophore_constraint )
plot( zc )

Citing

To find out how to cite hutan, run the following in R:

citation("hutan")

Installing

From the git repository

First, install the devtools package. Then, run the following in R:

library(devtools)
install_github('caseywdunn/hutan')

Development

This package is built with the excellent devtools (https://github.com/hadley/devtools). Extensive explanations on using devtools to create R packages is available in the book R Packages.

Development typically involves cding to the package directory, launching R, and running some combination of the following:

options(error=traceback) # Get line numbers for errors
library(devtools)
load_all()
test()
document()
check() # A wrapper for R CMD check, see http://r-pkgs.had.co.nz/check.html#check
build() # Create package bundle, including executed vignettes

To regenerate the pdf manual, run the following shell command in the package directory:

R CMD Rd2pdf . --force --output=hutan-manual.pdf

Funding

This software has been developed with support from the following US National Science Foundation grants:

The evolution of gene expression and functional specialization in Siphonophora (Award Number DEB-1256695)

caseywdunn/hutan documentation built on June 12, 2020, 3:12 a.m.