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diversitree: comparative phylogenetic analyses of diversification

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Octocat-spinner-32 R Extra things thrown up by check with --as-cran February 20, 2014
Octocat-spinner-32 doc Ladderise tree to make figure prettier June 12, 2012
Octocat-spinner-32 inst Don't actually need ggplot2 here February 20, 2014
Octocat-spinner-32 man Trim long lines February 20, 2014
Octocat-spinner-32 pub Update MEE scripts to work with current diversitree. August 05, 2013
Octocat-spinner-32 src Fix a few compiler warnings February 20, 2014
Octocat-spinner-32 www Move logo within the website. February 20, 2014
Octocat-spinner-32 .Rbuildignore Extra things thrown up by check with --as-cran February 20, 2014
Octocat-spinner-32 .gitignore Move diversitree to top level, as is usual for github projects February 20, 2014
Octocat-spinner-32 .travis.yml Update travis script to (hopefully) work February 20, 2014
Octocat-spinner-32 ChangeLog Move diversitree to top level, as is usual for github projects February 20, 2014
Octocat-spinner-32 DESCRIPTION Extra things thrown up by check with --as-cran February 20, 2014
Octocat-spinner-32 Makefile Simplify build/test February 20, 2014
Octocat-spinner-32 NAMESPACE Avoid the Rcpp/gc/methods bunfight February 20, 2014
Octocat-spinner-32 README.md Set up Travis for continuous integration February 20, 2014
Octocat-spinner-32 TODO Move diversitree to top level, as is usual for github projects February 20, 2014
Octocat-spinner-32 cleanup Move diversitree to top level, as is usual for github projects February 20, 2014
Octocat-spinner-32 configure Move diversitree to top level, as is usual for github projects February 20, 2014
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Octocat-spinner-32 configure.win Move diversitree to top level, as is usual for github projects February 20, 2014
Octocat-spinner-32 push-www.sh New examples section for website (not yet linked) May 09, 2012
Octocat-spinner-32 run_tests.R Tidy up tests February 20, 2014
README.md

diversitree: comparative phylogenetic analyses of diversification

Build Status

This repository contains "diversitree". It is my experimental sources though, and may not compile or work for you. You may prefer the released version from CRAN:

> install.packages("diversitree")

The interesting directories are:

  • inst/tests: testing functions that exercise most of the package's main features. Running ./run_tests.R will run the tests. These take too long to run on CRAN (over a minute), so are not set up in the usual way.
  • doc: Vignettes, and their required data files.

Installing diversitree

Clone the repository with

git clone git://github.com/richfitz/diversitree.git

The package should then be installable the usual way. You'll need a C, C++ and Fortran compiler.

To install and specify the location of the fftw library in a non-standard place, a line like this is required: R CMD INSTALL diversitree --configure-args='--with-fftw=/path/to/fftw' where the path will be the path so that the files /path/to/fftw/include/fftw3.h /path/to/fftw/lib/lib/fftw3.so exist.

On Windows, set the environment variable LIB_FFTW to point to the directory that contains include/fftw.h, and install the package.

If fftw is not found, installation will continue, but the (relatively) fast C based QuaSSE integration will not be available. The R based fft integrator and the method-of-lines integrator will be available.

Branches

The "master" branch contains the bleeding edge version of diversitree. It may or may not work for you. The "release" branch contains stable releases.

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