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

The data are currently being updated to reflect changes that have taken place since PPG I (2016). Once this is done, a version number starting with 2 (i.e., PPG II) will be assigned. Therefore, these data should not be taken as the official PPG II system until a version number is assigned >= 2.

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.

Running with Docker

Interactive development

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

Cron job

Run as root to enable the cron service, which will run the targets workflow once per day. The cron jobs execute as a non-root user and the entrypoint automatically fixes file ownership to match, preventing permission issues.

Gitconfig and ssh are needed to commit and push data files to GitHub.

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

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.