The goal of pteridocat is to provide a taxonomic database of pteridophytes that adheres to Darwin Core standards.
You can install pteridocat from GitHub with:
# install.packages("remotes")
remotes::install_github("fernphy/pteridocat")This package consists of a single data object, a taxonomic database of
pteridophytes called pteridocat.
The tibble package is recommended for pretty printing.
library(pteridocat)
library(tibble)
pteridocat
#> # A tibble: 64,657 × 18
#> taxonID parentNameUsageID acceptedNameUsageID taxonomicStatus taxonRank
#> <chr> <chr> <chr> <chr> <chr>
#> 1 DWY5 <NA> DX28 synonym species
#> 2 6RMC9 <NA> DWV4 synonym species
#> 3 3V22X 62YQB <NA> accepted species
#> 4 DWZC <NA> 5M863 synonym species
#> 5 36HMM 465R <NA> accepted species
#> 6 7Y7BL 7PTHT <NA> provisionally accept… species
#> 7 6QFWR 62YQB <NA> accepted species
#> 8 3V2B8 62YQB <NA> accepted species
#> 9 7WYVJ 62YQB <NA> accepted species
#> 10 3V2B7 62YQB <NA> accepted species
#> # … with 64,647 more rows, and 13 more variables: scientificName <chr>,
#> # scientificNameAuthorship <chr>, genericName <chr>,
#> # infragenericEpithet <chr>, specificEpithet <chr>,
#> # infraspecificEpithet <chr>, nomenclaturalCode <chr>,
#> # nomenclaturalStatus <chr>, taxonRemarks <chr>, references <chr>,
#> # modified <chr>, namePublishedIn <chr>, nameAccordingTo <chr>Run help(pteridocat) to see more details about the data.
The data were downloaded from the Catalog of Life and modified under the Creative Commons Attribution (CC BY) 4.0 license. They were originally compiled by Michael Hassler, who maintains the World Ferns database, and generously contributed them to Catalog of Life.
If you use this package, please cite it! Here is an example:
FTOL working group. (2023). pteridocat: A taxonomic database of pteridophytes. https://doi.org/10.5281/zenodo.6388786
The example DOI above is for the overall package.
Here is the latest DOI, which you should cite if you are using the latest version of the package:
You can find DOIs for older versions by viewing the “Releases” menu on the right.
You should also cite the World Ferns
database
(contained in Catalog of Life),
which forms the basis for pteridocat:
Hassler, M. (2021). Checklist of Ferns and Lycophytes of the World. In O. Bánki, Y. Roskov, M. Döring, G. Ower, L. Vandepitte, D. Hobern, D. Remsen, P. Schalk, R. E. DeWalt, M. Keping, J. Miller, T. Orrell, R. Aalbu, R. Adlard, E. Adriaenssens, C. Aedo, E. Aescht, N. Akkari, M. A. Alonso-Zarazaga, et al., Catalogue of Life Checklist (12.8, Dec 2021). https://doi.org/10.48580/d4tm-3dc
pteridocat is generated with a
targets pipeline.
Package dependencies are managed with renv.
To run the pipeline, first install packages with renv::restore(), then
run targets::tar_make().
R scripts needed for the package are in R/. Other R scripts, including
those needed for the pipeline, are in _R/.
Running devtools::check() will take much too long because of the large
directories _targets and renv. Instead, use _R/check.R.