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.
See the manual, hutan-manual.pdf
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 )
To find out how to cite hutan, run the following in R:
citation("hutan")
First, install the devtools package. Then, run the following in R:
library(devtools)
install_github('caseywdunn/hutan')
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
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)