https://github.com/richfitz/diversitree

diversitree: comparative phylogenetic analyses of diversification
https://github.com/richfitz/diversitree

Last synced: 11 days ago
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diversitree: comparative phylogenetic analyses of diversification

• Host: GitHub
• URL: https://github.com/richfitz/diversitree
• Owner: richfitz
• Created: 2012-03-20T20:29:11.000Z (over 12 years ago)
• Default Branch: master
• Last Pushed: 2023-12-20T15:47:06.000Z (11 months ago)
• Last Synced: 2024-06-11T18:21:57.427Z (5 months ago)
• Language: R
• Homepage: http://www.zoology.ubc.ca/prog/diversitree
• Size: 13.2 MB
• Stars: 30
• Watchers: 5
• Forks: 9
• Open Issues: 16
• Metadata Files:
  • Readme: README.md
  • Changelog: ChangeLog

Awesome Lists containing this project

• open-sustainable-technology - diversitree - Includes a number of comparative phylogenetic methods, mostly focussing on analysing diversification and character evolution. (Biosphere / Biodiversity Analysis and Metrics)

README

        
# diversitree: comparative phylogenetic analyses of diversification

[![R-CMD-check](https://github.com/richfitz/diversitree/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/richfitz/diversitree/actions/workflows/R-CMD-check.yaml)

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.

## Unresolved clades

As of version 0.10.0, diversitree can no longer work with unresolved clades (FitzJohn, Maddison and Otto 2009's method), due to the package being long in retirement from development and difficulties adapting the Fortran code to meet CRAN's requirements.  Users can install an older package from github (e.g., with `remotes::install_github("mrc-ide/diversitree@e587755")` to install the last released version that contained this code). This will require a working Fortran compiler. Alternatively, a suitably motivated person could restore the code (reverting changes contained in `aaaa`) and patch the code to work with the current version of `flang` as used by CRAN.

## 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.