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The Bien R Package: A tool to access the Botanical Information and Ecology Network (BIEN) database

1. There is an urgent need for large-scale botanical data to improve our understanding
of community assembly, coexistence, biogeography, evolution, and many other
fundamental biological processes. Understanding these processes is critical for predicting
and handling human-biodiversity interactions and global change dynamics
such as food and energy security, ecosystem services, climate change, and species
invasions.
2. The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented
wealth of cleaned and standardised botanical data, containing roughly
81 million occurrence records from c. 375,000 species, c. 915,000 trait observations
across 28 traits from c. 93,000 species, and co-occurrence records from
110,000 ecological plots globally, as well as 100,000 range maps and 100 replicated
phylogenies (each containing 81,274 species) for New World species. Here,
we describe an r package that provides easy access to these data.
3. The bien r package allows users to access the multiple types of data in the BIEN
database. Functions in this package query the BIEN database by turning user inputs
into optimised PostgreSQL functions. Function names follow a convention designed
to make it easy to understand what each function does. We have also developed
a protocol for providing customised citations and herbarium acknowledgements
for data downloaded through the bien r package.
4. The development of the BIEN database represents a significant achievement in biological
data integration, cleaning and standardization. Likewise, the bien r package
represents an important tool for open science that makes the BIEN database freely
and easily accessible to everyone.