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Software

R packages from the Maitner Lab at USF St. Petersburg for accessing and cleaning biodiversity data (BIEN, TNRS, GNRS, NSR, GVS), species distribution modeling (S4DM), plant trait analysis, and Open Science.

We develop and maintain R packages for working with biodiversity data: 13 are on CRAN, with more than 631,000 downloads from the RStudio CRAN mirror as of November 2026. CRAN packages install with install.packages(). More code from the lab is on the Maitner Lab GitHub.

Biodiversity data access

  • BIEN: tools for accessing the Botanical Information and Ecology Network database: plant occurrences, traits, plots, and range maps. CRAN · GitHub · paper
  • OpenRange: access open species range maps. CRAN · GitHub
  • BIENapi: API access to the BIEN database (in development). GitHub
  • occCite (co-developed): querying biodiversity occurrence data with reproducible citation of sources. CRAN · paper

Biodiversity data cleaning

R interfaces to the BIEN data-cleaning services:

  • TNRS: Taxonomic Name Resolution Service, which corrects and standardizes plant names. CRAN · GitHub
  • GNRS: Geographic Name Resolution Service, which standardizes country, state, and county names. CRAN · GitHub · paper
  • NSR: Native Status Resolver, which flags whether a species is native or introduced in a region. CRAN · GitHub
  • GVS: Geocoordinate Validation Service, which checks occurrence coordinates for common errors. CRAN · GitHub

Analysis

  • S4DM: species distribution modeling with small sample sizes. CRAN · GitHub · paper
  • traitstrap (co-developed): bootstrapping trait distributions from community data. CRAN · GitHub · paper
  • occTest (co-developed): characterizing and filtering species occurrence data. GitHub
  • wallace (contributor): a modular platform for reproducible modeling of species niches and distributions. CRAN · paper

Open Science

  • citeR: finds the R packages used in your code so you can cite them (in development). GitHub
  • rangeModelMetadata (co-developed): metadata standards for documenting species range models. CRAN · paper

Color palettes

Color palettes for scientific figures, with ggplot2 scales and helpers that screen palettes for color-blind-safe, sequential, or diverging use.

  • glyospalettes: palettes drawn from Glyos toy colorways. CRAN
  • transformerpalettes: palettes drawn from Transformers toys, cartoons, and comics. CRAN · website