Zachary Foster

A set of tools for parsing, manipulating, and graphing data classified by a hierarchy (e.g. a taxonomy).

Provides taxonomic classes for groupings of taxonomic names without data, and those with data. Methods provided are "taxonomically aware", in that they know about ordering of ranks, and methods that filter based on taxonomy also filter associated data. This package is described in the publication: "Taxa: An R package implementing data standards and methods for taxonomic data", Zachary S.L. Foster, Scott Chamberlain, Niklaus J. Gr<c3><bc>nwald (2018) <doi:10.12688/f1000research.14013.2>.

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.

Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (<https://www.synbiosys.alterra.nl/turboveg>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.

Species trait data from many different sources, including sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data from 'EOL' 'Traitbank', 'Birdlife' International, and more.