betydata provides offline access to public data from the BETYdb: Biofuel Ecophysiological Traits and Yields Database. This R data package enables reproducible analyses of plant traits, crop yields, and ecosystem service data without requiring database connectivity.

This package provides a dataset with 16 tables exported from BETYdb.

The traitsview table is a union of traits and yields tables in BETYdb. The unique row identifier is composite key (result_type, id), not id alone; a given id can appear under both result_type = "traits" and result_type = "yields".

These tables provide reference data for species, sites, variables, and other entities linked to the trait observations.

These junction tables connect entities in many-to-many relationships. Use pfts_species to find which species belong to a Plant Functional Type, or managements_treatments to link management practices to experimental treatments.

# install.packages("remotes")
remotes::install_github("PecanProject/betydata")

git clone https://github.com/PecanProject/betydata.git
R CMD INSTALL betydata

library(betydata)
library(dplyr)

# Preview the primary table (columns are ordered for readability)
traitsview

# Count observations by trait
traitsview |>
  count(trait, sort = TRUE)

# Bioenergy crop yields
bioenergy_genera <- c("Miscanthus", "Panicum", "Populus", "Salix", "Saccharum")
traitsview |>
  filter(genus %in% bioenergy_genera) |>
  count(genus, sort = TRUE)

All trait and yield data include a quality control flag:

This package exports only checked >= 0 data. Flagged records (checked = -1) are excluded during data preparation. Records with checked = NA are converted to checked = 0 (unchecked) during the build. All data in this package is public (from BETYdb records with access_level = 4). For restricted or flagged data, access the BETYdb PostgreSQL database directly.

If you find errors in the data or want to report verified records:

• Data corrections: File a data correction issue
• Verified records: Report a verified record

To submit corrections via pull request, edit the relevant CSV file in data-raw/csv/, rebuild with source("data-raw/make-data.R"), and submit a PR using the data correction template.

The traitsview table contains measurements of ecophysiological traits and crop yields:

• SLA -- Specific Leaf Area (m2/kg)
• Vcmax -- Maximum carboxylation rate (umol/m2/s)
• leafN -- Leaf nitrogen content (%)
• height -- Plant height (m)
• LAI -- Leaf Area Index (m2/m2)

• Ayield -- Above-ground yield (Mg/ha)
• AGBiomass -- Above-ground biomass (Mg/ha)

Use the variables table for complete definitions and units:

variables |>
  filter(name %in% c("SLA", "Vcmax", "Ayield")) |>
  select(name, description, units)

Lazy-loaded R data objects, available after library(betydata):

traitsview

Machine-readable metadata following the Frictionless data standard:

// datapackage.json (repo root)
{
  "name": "betydata",
  "title": "BETYdb Plant Traits and Yields Data Package",
  "licenses": [{"name": "ODC-By-1.0", ...}],
  "resources": [...]
}

Detailed tutorials are available as package vignettes:

browseVignettes("betydata")