BIEN - Tools for Accessing the Botanical Information and Ecology Network Database

Provides Tools for Accessing the Botanical Information and Ecology Network Database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <https://bien.nceas.ucsb.edu/bien/> for more Information). This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.

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6.29 score 5 dependents 237 scripts 5.5k downloads

S4DM - Small Sample Size Species Distribution Modeling

Implements a set of distribution modeling methods that are suited to species with small sample sizes (e.g., poorly sampled species or rare species). While these methods can also be used on well-sampled taxa, they are united by the fact that they can be utilized with relatively few data points. More details on the currently implemented methodologies can be found in Maitner et al. (2026) <doi:10.1002/ecog.08112>, Drake and Richards (2018) <doi:10.1002/ecs2.2373>, Drake (2015) <doi:10.1098/rsif.2015.0086>, and Drake (2014) <doi:10.1890/ES13-00202.1>.

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open-sciencerange-modellingrare-speciesspecies-distribution-modelingspecies-distribution-modelling

5.25 score 4 stars 44 scripts 183 downloads

TNRS - Taxonomic Name Resolution Service

Provides access to the Taxonomic Name Resolution Service <https://github.com/ojalaquellueva/tnrsapi> through R. The user supplies plant taxonomic names and the package returns resolved taxonomic names along with information on decisions. Optionally, the package can also be used to parse taxonomic names.

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3.81 score 65 scripts 317 downloads

GVS - 'Geocoordinate Validation Service'

The 'Geocoordinate Validation Service' (GVS) runs checks of coordinates in latitude/longitude format. It returns annotated coordinates with additional flags and metadata that can be used in data cleaning. Additionally, the package has functions related to attribution and metadata information. More information can be found at <https://github.com/ojalaquellueva/gvs/tree/master/api>.

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2.70 score 2 scripts 397 downloads

OpenRange - Code to Access Open Access Species Range Maps

Allows access to a proof-of-concept database containing Open Access species range models and relevant metadata. Access to the database is via both 'PostgreSQL' connection and API <https://github.com/EnquistLab/Biendata-Frontend>, allowing diverse use-cases.

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2.70 score 4 scripts 180 downloads

NSR - 'Native Status Resolver'

Provides access to the 'Native Status Resolver' (NSR) <https://github.com/ojalaquellueva/nsr> API through R. The user supplies plant taxonomic names and political divisions and the package returns information about their likely native status (e.g., native, non-native,endemic), along with information on how those decisions were made.

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2.70 score 1 stars 4 scripts 98 downloads

GNRS - Access the 'Geographic Name Resolution Service'

Provides tools for interacting with the 'geographic name resolution service' ('GNRS') API <https://github.com/ojalaquellueva/gnrs> and associated functionality. The 'GNRS' is a batch application for resolving & standardizing political division names against standard name in the geonames database <http://www.geonames.org/>. The 'GNRS' resolves political division names at three levels: country, state/province and county/parish. Resolution is performed in a series of steps, beginning with direct matching to standard names, followed by direct matching to alternate names in different languages, followed by direct matching to standard codes (such as ISO and FIPS codes). If direct matching fails, the 'GNRS' attempts to match to standard and then alternate names using fuzzy matching, but does not perform fuzzing matching of political division codes. The 'GNRS' works down the political division hierarchy, stopping at the current level if all matches fail. In other words, if a country cannot be matched, the 'GNRS' does not attempt to match state or county.

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2.70 score 8 scripts 255 downloads