ppg

This repo houses the Pteridophyte Phylogeny Group (PPG) taxonomic database for ferns and lycophytes.

Issues are used to discuss taxonomic proposals by the PPG community, which are voted on monthly. All proposals are relative to PPG I (2016). To propose a taxonomic change, use the taxonomic proposal template. Proposals that pass by a 2/3 majority will be implemented in the taxonomic database.

For more information about PPG, see the PPG webpage.

IMPORTANT: if you want to participate, please read the Project Guidelines first.

Format

The database is provided as a CSV file in the Darwin Core (DwC) format for taxonomic data.

A human readable summary of the same data is available as a plain text file in Markdown format.

Versioning

As of v2.0.0, this repository contains the official PPG II taxonomic system, reflecting changes to the classification of ferns and lycophytes since PPG I (2016). See the PPG II publication for details. (citation to be added)

Version numbers follow a four-part scheme, MAJOR.GENUS.SPECIES.DEV:

• MAJOR — a wholesale revision of the classification, such as the transition from PPG I to PPG II.
• GENUS — bumped when a release changes the accepted classification at genus rank or above (e.g., a genus is added, merged, split, or resurrected from synonymy).
• SPECIES — bumped when a release includes at least one change at species rank or below (new species, synonymy changes, name corrections, etc.) without any genus-or-above change.
• DEV — identifies an in-progress development version between full releases; it is dropped from the version number once a release is issued (e.g. v0.0.0.9009 was a dev version; v2.0.0 is a release).

Most commits on main are automated daily data updates and are not individually version-tagged; issuing a new version is a separate, manual decision.

Contributing

All taxonomic decisions are made by the PPG community.

Taxonomic proposals should be submitted as issues, which will be voted on monthly. Proposals may be commented upon in the issue tracker. Voting is carried out separately via a Google Form survey circulated on the PPG mailing list. Any proposal receiving >2/3 support will be approved and implemented in the data.

Anybody is welcome to contribute. All participants must adhere to the Code of Conduct. Please read the Project Guidelines before contributing.

Automated updates

The data are refreshed daily by the Update PPG data GitHub Actions workflow (.github/workflows/update-ppg.yml), which runs the targets pipeline and commits any changed data files back to main. It can also be triggered manually from the Actions tab, or via gh workflow run update-ppg.yml.

Running with Docker

The Docker image is only for local, interactive development; it is not used by the automated update.

Mount gitconfig and ssh for authentication:

docker run --rm -dt \
  -v ${PWD}:/wd \
  -v $HOME/.gitconfig:/home/user/.gitconfig:ro \
  -v $HOME/.ssh:/home/user/.ssh:ro \
  -w /wd \
  joelnitta/ppg:latest bash

Then attach to the container:

docker exec -it $(docker ps -q --filter ancestor=joelnitta/ppg:latest) bash

Data sources

Original data were kindly provided by Michael Hassler.

References

Pteridophyte Phylogeny Group I (2016) A community-derived classification for extant lycophytes and ferns. Journal of Systematics and Evolution 54:563–603. https://doi.org/10.1111/jse.12229

License

Data (files in data_raw/ and data/) are made available under the CC BY 4.0 license.

Code is under the MIT license.