resources

Open-source tools and databases from the Enquist Lab

Software & Open Data

Code and public tools associated with current and ongoing lab projects.

Researcher conducting leaf gas-exchange measurements at an Andean high-altitude field station, cloud-forest slopes visible through the window
High-Andes field station: leaf-level gas-exchange measurements linking plant physiology to ecosystem function.

Additional Lab Resources

BIEN R Package occurrencetraitrange

The BIEN R package provides programmatic access to the Botanical Information and Ecology Network database — ~85 million botanical observations, ~100,000 species range maps, and plant trait data for the New World.

install.packages("BIEN")
library(BIEN)
sp <- BIEN_occurrence_species("Pinus ponderosa")

BIEN Data Portal occurrencespatial

The BIEN GeoSpatial portal provides web-based access to New World plant occurrence, range, and trait data with QA/QC, taxonomic harmonization, and geographic filtering.

Taxonomic Name Resolution Service (TNRS) taxonomy

Computer-assisted standardization of plant scientific names: corrects spelling errors, resolves synonyms, and maps names to accepted taxonomy.

An online tool for the standardization of plant taxonomic names.

BIEN Web Services

These services support a complete biodiversity data QA workflow from names to geography:

TNRS

Taxonomic Name Resolution Service

GNRS

Geographic Name Resolution Service

NSR

Native Species Resolver

GVS

Geocoordinate Validation Service
  • GVS (Geocoordinate Validation Service): validates and corrects geocoordinates and returns political context.

R Vignettes

Native Species Resolver (NSR) taxonomynative status

Uses regional taxonomic checklists to determine whether observations of a species within political divisions (country, state/province, county) are native or introduced.

Hypervolumes R Package traitniche

Estimates the shape and volume of high-dimensional ecological objects (niches, trait distributions) and performs set operations including intersection, union, and overlap. Used for n-dimensional niche measurement and species distribution modeling.

  • CRAN: hypervolume
  • Citation: Blonder et al. (2014) Global Ecology and Biogeography

fluxible fluxtime seriesQA

Processes ecosystem gas flux time series and applies quality assurance workflows for eddy covariance and closed-chamber measurements. Handles CO₂, CH₄, and N₂O flux data from a variety of sensor systems. Core functions include flux calculation from raw concentration–time curves, automatic detection of non-linear or problematic measurements, outlier flagging, and export of QA-annotated summaries.

Designed to integrate with the outputs of standard flux loggers and field datalogger formats, and pairs naturally with the lab’s long-term ecosystem monitoring work at sites including RMBL and tropical elevational transects.

install.packages("fluxible")
library(fluxible)

traitstrap traituncertaintybootstrap

Bootstraps trait distributions to propagate uncertainty from individual-level measurements to community-weighted means and higher-order community trait statistics. Addresses a key challenge in trait-based ecology: raw community-weighted mean (CWM) calculations ignore intraspecific trait variation and sampling uncertainty. traitstrap implements parametric bootstrapping that draws from species-level trait distributions, weighted by abundance, producing CWMs with full uncertainty quantification suitable for downstream modeling.

Works directly with trait data from BIEN, TRY, and comparable databases, and is designed to integrate with the lab’s Trait Driver Theory framework.

install.packages("traitstrap")
library(traitstrap)

netassoc R Package occurrenceco-occurrence

Infers species associations from community co-occurrence matrices using partial correlations and Gaussian graphical models with null modeling.

  • CRAN: netassoc
  • Citation: Morueta-Holme, Blonder et al. Ecography

comclim R Package traitclimate

Computes community climate statistics for volume and mismatch using species’ climate niches, scaled relative to a regional species pool. Used to infer community assembly processes.

  • CRAN: comclim
  • Citation: Blonder et al. (2015) Ecology

Plant-O-Matic

Open software integrating biodiversity layers with mobile APIs to deliver plant identification and occurrence information.

  • Citation: Enquist et al. (2016) Methods in Ecology and Evolution
  • GitHub

OpenTraits Network

We co-lead the OpenTraits Network, which promotes open, standardized, and FAIR (Findable, Accessible, Interoperable, Reusable) trait data across all organisms.

  • Website: opentraits.org
  • Publication: Gallagher et al. (2020) Nature Ecology & Evolution

Trait Driver Theory Tools

Code and tutorials for applying Trait Driver Theory to community data:

Additional Tools & Datasets

Resource Description Link
SALVIAS Plant inventory plots database salvias.net
BIEN Traits Validated plant trait measurements biendata.org
GBIF / TNRS Taxonomic resolution tools tnrs.biendata.org