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diversitree: comparative phylogenetic analyses of diversification
R TeX FORTRAN C C++ CSS Other
branch: master
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R Try again with asr.
doc Ladderise tree to make figure prettier
inst Update staticdocs
man Support for exponential decay in time-dependent models.
pub Update MEE scripts to work with current diversitree.
src Support for exponential decay in time-dependent models.
www Move logo within the website.
.Rbuildignore Update build process
.gitignore Update staticdocs
.travis.yml Update travis script to (hopefully) work
CONTRIBUTORS.md Keep track of contributions.
ChangeLog Move diversitree to top level, as is usual for github projects
DESCRIPTION Extra things thrown up by check with --as-cran
Makefile Fix running the tests (2nd time lucky)
NAMESPACE Untested support for asr on bisse.split models
README.md Set up Travis for continuous integration
TODO Move diversitree to top level, as is usual for github projects
cleanup Move diversitree to top level, as is usual for github projects
configure Move diversitree to top level, as is usual for github projects
configure.ac Move diversitree to top level, as is usual for github projects
configure.win Move diversitree to top level, as is usual for github projects
push-www.sh New examples section for website (not yet linked)
run_tests.R Tidy up tests

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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