fernphy/ftol_data

Fern Tree of Life (FTOL) phylogeny and associated data files

ftol_data

Home of Fern Tree of Life (FTOL) phylogeny and associated data files.

The data in this repo are automatically generated by the ftol repo (https://github.com/fernphy/ftol).

These files should not be edited by hand. Rather, the snapshot_ftol_data.R script should be run to commit changes and automatically push to the remote repository.

Use release.R to generate new releases.

For more information, please see the accompanying paper:

• Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. An open and continuously updated fern tree of life (FTOL) https://doi.org/10.1101/2022.03.31.486640

Data format

For information about data files, see ftol_data_README.txt.

Commit messages

The commit messages in this repo have a special format. They have three parts: code, data_, and docker. Each is followed by an equals sign and a string.

• For code, the string is a commit hash in the ftol repo.
• For data_, the string is the hash digest for an input file.
• The docker, the string is the docker image used to run the code.

Together, these specify the version of code, input data, and computing environment used to generate a given data file.

For example, files with the commit

code=b43256a6faa2521bdb00da9b262d9b2e2ac26eac
data_ref_aln=hash://sha256/388b53201a8626d4b41851e716505e7904d24ee3730de25310cb82cd3a1e6e71
data_restez_sql_db=hash://sha256/8059a845c6570eeffb6fe08c29e178a9dc223ab6f929a1b6c6b374e160f21410
docker=joelnitta/ftol:1.1.0

were generated by this code in the ftol docker containter with the tag 1.1.0.

URLs for the data files can be obtained by providing the hash digest to the sources() function of the contentid R package:

> contentid::sources("hash://sha256/8059a845c6570eeffb6fe08c29e178a9dc223ab6f929a1b6c6b374e160f21410")

                                           source                date                                                                                                                                                                      
1 https://figshare.com/ndownloader/files/36005606 2022-06-23 07:35:04

Note that code commit hashes correspond to the earliest (oldest) commit in ftol that generates the file with that commit; more recent commits that don't result in a change to the file will not show up as a new commit here.

ftolr R package

These data are also available via the ftolr R package, which allows direct loading into R and more options for subsetting and formatting.

Citing

If you use this dataset, please cite it! Here is a recommended citation:

FTOL working group. (2022). Fern Tree of Life (FTOL) data v1.0.0. https://doi.org/10.5281/zenodo.6413219

Please also cite the paper describing how the data were generated:

Nitta JH, Schuettpelz E, Ramírez-Barahona S, Iwasaki W. An open and continuously updated fern tree of life (FTOL) https://doi.org/10.1101/2022.03.31.486640 

License

• CC0