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Open Sustainable Technology

A curated list of open technology projects to sustain a stable climate, energy supply, biodiversity and natural resources.

diversitree

Includes a number of comparative phylogenetic methods, mostly focussing on analysing diversification and character evolution.
https://github.com/richfitz/diversitree

Category: Biosphere
Sub Category: Biodiversity Analysis and Metrics

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geos

Last synced: about 12 hours ago
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Repository metadata

diversitree: comparative phylogenetic analyses of diversification

README.md

diversitree: comparative phylogenetic analyses of diversification

R-CMD-check

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.

Owner metadata

GitHub Events

Total
Last Year

Committers metadata

Last synced: 7 days ago

Total Commits: 526
Total Committers: 8
Avg Commits per committer: 65.75
Development Distribution Score (DDS): 0.561

Commits in past year: 13
Committers in past year: 1
Avg Commits per committer in past year: 13.0
Development Distribution Score (DDS) in past year: 0.0

Name Email Commits
Rich FitzJohn f****n@z****a 231
Rich FitzJohn r****n@g****m 231
Rich FitzJohn r****n@i****k 45
Emma Goldberg e****g@u****u 13
Jonathan Chang me@j****g 3
Emma Goldberg e****a@s****k 1
Gustavo Burin Ferreira a****o@g****m 1
Shinya Uryu s****7@g****m 1

Committer domains:

Issue and Pull Request metadata

Last synced: 1 day ago

Total issues: 27
Total pull requests: 18
Average time to close issues: 4 months
Average time to close pull requests: 20 days
Total issue authors: 11
Total pull request authors: 4
Average comments per issue: 0.96
Average comments per pull request: 0.22
Merged pull request: 17
Bot issues: 0
Bot pull requests: 0

Past year issues: 0
Past year pull requests: 1
Past year average time to close issues: N/A
Past year average time to close pull requests: 26 days
Past year issue authors: 0
Past year pull request authors: 1
Past year average comments per issue: 0
Past year average comments per pull request: 0.0
Past year merged pull request: 1
Past year bot issues: 0
Past year bot pull requests: 0

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/richfitz/diversitree

Top Issue Authors

  • richfitz (11)
  • jamie-thompson (3)
  • ghost (3)
  • nhcooper123 (2)
  • sdwfrost (2)
  • mwpennell (1)
  • szhan (1)
  • emmaday (1)
  • KYPpa (1)
  • rgarciasandoval (1)
  • LiliyaSerbina (1)

Top Pull Request Authors

  • richfitz (12)
  • eeg (3)
  • jonchang (2)
  • uribo (1)

Top Issue Labels

  • bug (2)

Top Pull Request Labels

Dependencies

.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite

Score: 5.950642552587727