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.
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.
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.
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.
Launch a container in the background:
docker run \
--rm \
-dt \
-v ${PWD}:/wd \
-w /wd \
--user root \
joelnitta/ppg:latest bash
Specify user and git files, otherwise you won't have permission to make changes to the git cache.
docker run --rm -dt \
--user $(id -u):$(id -g) \
-v ${PWD}:/wd \
-v $HOME/.gitconfig:/home/user/.gitconfig:ro \
-v $HOME/.ssh:/home/user/.ssh:ro \
-w /wd \
joelnitta/ppg:latest bash
Run as root to enable the cron job, which will run the targets workflow once per day.
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
Original data were kindly provided by Michael Hassler.
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
Data (files in data_raw/ and data/) are made available under the CC BY 4.0 license.
Code is under the MIT license.