@article{dd67b7529c224a1a818ae152d5763fd3,
title = "The bien r package: A tool to access the Botanical Information and Ecology Network (BIEN) database",
abstract = "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. 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. 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. 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.",
keywords = "R, biodiversity, community plot, ecoinformatics, functional traits, herbarium records, occurrence, phylogeny, plants, presence, range maps",
author = "Maitner, {Brian S.} and Brad Boyle and Nathan Casler and Rick Condit and John Donoghue and Dur{\'a}n, {Sandra M.} and Daniel Guaderrama and Hinchliff, {Cody E.} and J{\o}rgensen, {Peter M.} and Kraft, {Nathan J.B.} and Brian McGill and Cory Merow and Naia Morueta-Holme and Peet, {Robert K.} and Brody Sandel and Mark Schildhauer and Smith, {Stephen A.} and Svenning, {Jens Christian} and Barbara Thiers and Cyrille Violle and Susan Wiser and Enquist, {Brian J.}",
note = "Funding Information: We thank Irena {\v S}Dᴀmofvo{\'a}r input on the manuscript, Scott Chamberlain for valuable comments on R programming, our beta-testers for their input, and our CRAN reviewers for their cheerful comments and assistance. We thank Scott Chamberlain, Robert Freckleton and an anonymous reviewer for their helpful comments on both the manuscript and the r package. N.M.-H. acknowledges support by a Villum Foundation Postdoctoral Fellowship. We gratefully acknowledge the Canada Foundation for Innovation for funding the infrastructure for Canadensys. This work was conducted as a part of the Botanical Information and Ecology Network (BIEN) Working Group (PIs BJE, Richard Condit, B.B., S.M.D., R.K.P.) supported by the National Center for Ecological Analysis and Synthesis (funded by NSF Grant #EF-0553768), the University of California, Santa Barbara, and the State of California. The BIEN Working Group was also supported by iPlant (NSF #DBI-0735191). C.V. was supported by the French Foundation for Research on Biodiversity (FRB; www.fondationbiodiversite.fr) in the context of the CESAB project “Assembling, analysing and sharing data on plant functional diversity to understand the effects of biodiversity on ecosystem functioning: a case study with French Permanent Grasslands” (DIVGRASS), by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Program (DiversiTraits project, no. 221060) and by the European Research Council (ERC) Starting Grant Project “Ecophysiological and biophysical constraints on domestication in crop plants” (Grant ERC-StG-2014-639706-CONSTRAINTS). J.-C.S. was supported by the European Research Council (ERC-2012-StG-310886-HISTFUNC). S.W. was supported by Core funding for Crown Research Institutes from the New Zealand Ministry of Business, Innovation and Employment{\textquoteright}s Science and Innovation Group. We acknowledge the herbaria that contributed data to this work: A, AAH, AAS, AAU, ABH, ACAD, ACOR, AD, ADW, AFS, AHUC, AIMS, AJOU, AK, AKPM, ALCB, ALT, ALTA, ALU, AMD, AMES, AMNH, AMO, ANA, ANGU, ANSM, ANSP, ANUC, ARAN, ARC, ARIZ, ARM, AS, ASDM, ASU, ATCC, AUG, AUT, B, BA, BAA, BAB, BACP, BAF, BAFC, BAI, BAJ, BAL, BARC, BAS, BBB, BBS, BC, BCF, BCMEX, BCN, BCRU, BEREA, BG, BH, BHCB, BHO, BILAS, BIO, BISH, BLA, BM, BO, BOCH, BOG, BOL, BOLV, BONN, BOUM, BPI, BR, BRA, BREM, BRI, BRIT, BRIU, BRLU, BRM, BSB, BSIP, BSN, BTN, BUL, BULU, BUT, C, CALI, CAMU, CAN, CANB, CANL, CAS, CAY, CBG, CBM, CBS, CEN, CEPEC, CESJ, CGE, CHAM, CHAP, CHAPA, CHI, CHL, CHR, CHRB, CIB, CICY, CIIDIR, CIMI, CINC, CIQR, CLEMS, CLF, CM, CMC, CMMEX, CNHM, CNPO, CO, COA, COAH, COCA, CODAGEM, COFC, COL, COLO, CONC, CORD, CP, CPAP, CPUN, CR, CRAI, CRP, CS, CSU, CTES, CTESN, CU, CUVC, CUZ, CVRD, CWU, DAO, DAOM, DAV, DBN, DES, DLF, DMNH, DMU, DNA, DR, DS, DUKE, DUSS, E, EA, EAC, EBH, EBUM, ECH, ECU, EIF, EIU, EKY, EM, EMMA, ENCB, ENS, ERA, ESA, ESS, F, FAA, FAU, FB, FBCS, FCME, FCO, FCQ, FEN, FH, FHO, FI, FLAS, FLOR, FM, FR, FRP, FTG, FUEL, FURB, G, GB, GDA, GDAC, GE, GENT, GEO, GES, GH, GI, GJO, GLM, GMNHJ, GOET, GUA, GZU, H, HA, HAC, HAJB, HAL, HAM, HAMAB, HAO, HAS, HAST, HASU, HAW, HB, HBG, HBR, HCIB, HEID, HGI, HIP, HKU, HNHM, HNT, HO, HPL, HRCB, HRP, HSS, HSU, HU, HUA, HUAA, HUAL, HUAZ, HUEFS, HUEM, HUFU, HUSA, HUT, HXBH, HYO, IA, IAA, IAC, IAL, IAN, IB, IBGE, IBUG, ICEL, ICN, IEB, IFO, ILL, ILLS, IMSSM, INB, INEGI, INIF, INM, INPA, IPA, IPRN, ISC, ISL, ISTC, ISU, ITCV, ITMH, IZAC, IZTA, JACA, JBAG, JE, JEPS, JOE, JUA, JYV, K, KANU, KIEL, KMN, KMNH, KOELN, KOR, KPM, KSC, KSTC, KSU, KTU, KU, KUO, KYO, L, LA, LAE, LAF, LAM, LCR, LD, LE, LEB, LEMA, LG, LI, LIL, LINN, LISE, LISI, LISU, LKHD, LL, LM, LOJA, LOMA, LP, LPAG, LPB, LPD, LPS, LSU, LTR, LY, LYJB, LZ, M, MA, MAF, MAIC, MAK, MAN, MARY, MASS, MB, MBK, MBM, MBML, MCM, MCN, MCNS, MEL, MEN, MERL, MEXU, MFA, MFU, MG, MGC, MICH, MIL, MIN, MISS, MJG, MMMN, MNHM, MNHN, MO, MOL, MOR, MOSS, MPU, MPUC, MRSN, MSB, MSC, MSE, MSTR, MSUN, MT, MTMG, MU, MUB, MUCV, MVFA, MVFQ, MVJB, MVM, MY, N, NA, NCSC, NCU, ND, NE, NEB, NHM, NHMC, NHT, NLH, NLU, NMB, NMC, NMCR, NMNL, NMR, NMSU, NMW, NO, NOU, NRCC, NSPM, NSW, NT, NUM, NWOSU, NY, O, OC, OCLA, ODU, OHN, OKL, OKLA, OMA, OS, OSA, OSC, OSH, OSN, OULU, OWU, OXF, P, PACA, PAR, PE, PEL, PENN, PERTH, PEUFR, PFC, PH, PI, PKDC, PLAT, PMA, PMNH, PNH, POLL, POM, PORT, PR, PRC, PRE, PTBG, PVNH, PY, QCA, QCNE, QFA, QM, QMEX, QRS, QUE, R, RAS, RB, RBR, REG, RENO, RFA, RIOC, RM, RNG, ROST, RPM, RSA, RYU, S, SALA, SAM, SAN, SANT, SAPS, SASK, SBT, SD, SEL, SEV, SF, SFSU, SGO, SI, SIM, SING, SIU, SJRP, SLPM, SMB, SMDB, SMF, SNM, SOM, SP, SPF, SPSF, SQF, SRFA, STL, STU, SUVA, SVG, SZU, TAES, TAI, TAIF, TAMU, TAN, TEF, TENN, TEPB, TEX, TFC, TFM, TI, TKPM, TNS, TO, TRA, TRH, TROM, TRT, TRTC, TRTE, TRTS, TS, TSM, TTRS, TU, TULS, TUR, U, UADY, UAM, UAMIZ, UARK, UAS, UAT, UB, UBA, UBC, UC, UCAM, UCBG, UCR, UEC, UESC, UFG, UFMA, UFMT, UFP, UFRJ, UFRN, UFS, UGDA, UH, UI, UJAT, ULM, ULS, UME, UMO, UNA, UNB, UNCC, UNEX, UNL, UNM, UNR, UNSL, UPCB, UPEI, UPNA, UPNG, UPS, US, USAS, USJ, USM, USNC, USON, USP, USZ, UT, UTC, UTEP, UTMC, UV, UVIC, UVSC, UWO, V, VA, VAL, VALD, VDB, VEN, VM, VMSL, VT, W, WAG, WAT, WELT, WFU, WII, WIN, WIS, WMNH, WOH, WRSL, WS, WTU, WU, XAL, Y, YA, YAM, YU, Z, ZMT, ZSS, ZT. Funding Information: National Science Foundation, Grant/Award Number: DBI-0735191 and EF-0553768; Villum Foundation Postdoctoral Fellowship; Canada Foundation for Innovation; National Center for Ecological Analysis and Synthesis; University of California; Santa Barbara; State of California; French Foundation for Research on Biodiversity; European Research Council, Grant/Award Number: ERC-StG-2014-639706-CONSTRAINTS and ERC-2012-StG-310886-HISTFUNC; New Zealand Ministry of Business, Innovation and Employment{\textquoteright}s Science and Innovation Group Publisher Copyright: {\textcopyright} 2017 The Authors. Methods in Ecology and Evolution {\textcopyright} 2017 British Ecological Society",
year = "2018",
month = feb,
day = "1",
doi = "10.1111/2041-210X.12861",
language = "English (US)",
volume = "9",
pages = "373--379",
journal = "Methods in Ecology and Evolution",
issn = "2041-210X",
publisher = "John Wiley and Sons Inc.",
number = "2",
}