Rekyt / automated_trait_retrieval

Collection of software to automatically retrieve species functional trait data from databases. R packages, Python and Julia modules.

Automated Trait Retrieval

Here I compile a list of software that gives programmatic access to species functional trait data. The idea would be to draw the panorama of trait databases available out there, for programmatic functional biogeography (especially for plants).

Many of the tools and databases are referenced at https://opentraits.org/datasets.html

R packages

Package	Release URL	Dev. URL	Taxonomic Group(s)	Database(s)
algaeClassify	https://cran.r-project.org/package=algaeClassify	https://github.com/vppatil/GEISHA_phytoplankton/tree/master/package%20builds/algaeClassify	Algae
arakno	https://cran.r-project.org/package=arakno	NA	spiders	World Spider Trait database
austraits	NA	https://github.com/traitecoevo/austraits	plants	AusTraits
BIEN	https://cran.r-project.org/package=BIEN	https://github.com/bjmaitner/RBIEN	plants (vascular plants + ferns)	BIEN (bien.nceas.ucsb.edu/)
BIFloraExplorer	NA	https://github.com/RBGKew/BIFloraExplorer	plants	trait database for UK and Ireland
frubase	NA	https://github.com/pedroj/FRUBASE	fleshy fruits	FRUBASE
functionaltraits	NA	https://github.com/conservationscience/functionaltraits	many	many
fungaltraits	NA	https://github.com/traitecoevo/fungaltraits	fungi	Fun^fun Fores-Moreno et al. https://doi.org/10.5281/zenodo.1216256
palmtrees	NA	https://github.com/EmilHvitfeldt/palmtrees	palm trees	Kissling et al. 2019 (https://doi.org/10.1038/s41597-019-0189-0)
parrottraits	NA	https://github.com/trashbirdecology/parrottraits	parrots	Burgio et al. 2018
rdataretriever	https://cran.r-project.org/package=rdataretriever	https://github.com/ropensci/rdataretriever	many
rfishbase	https://cran.r-project.org/package=rfishbase	https://github.com/ropensci/rfishbase	fishes and marine organisms	FishBase and SeaLifeBase
rfutres	NA	https://github.com/futres/rfutres	mammals	FuTRES database (https://futres.org/)
Rmosaic	NA	https://github.com/mosaicdatabase/Rmosaic	animals and plants
rtry	NA	https://github.com/MPI-BGC-Functional-Biogeography/rtry	plants	TRY
rYoutheria	https://cran.r-project.org/package=rYoutheria	https://github.com/BiologicalRecordsCentre/rYoutheria	mammals
TR8	https://cran.r-project.org/package=TR8	https://github.com/GioBo/TR8	plants (vascular plants?)
traits	https://cran.r-project.org/package=traits	https://github.com/ropensci/traits	many

Python modules

Modules	Release URL	Dev. URL	Taxonomic Group(s)	Database(s)
retriever	https://pypi.org/project/retriever/	https://github.com/weecology/retriever	many

Julia modules

None to our knowledge

Other

Contributing

If you want to add your preferred package/module to the list feel free to open a PR!