An overview of executing searches and generating citations using occCite

Hannah L. Owens

Cory Merow

Brian Maitner

Jamie M. Kass

Vijay Barve

Robert Guralnick

2021-02-02

Introduction

We have entered the age of data-intensive scientific discovery. As data sets increase in complexity and heterogeneity, we must preserve the cycle of data citation from primary data sources to aggregating databases to research products and back to primary data sources. The citation cycle keeps science transparent, but it is also key to supporting primary providers by documenting the use of their data. The Global Biodiversity Information Facility (GBIF), Botanical Information and Ecology Network (BIEN), and other data aggregators have made great strides in harvesting citation data from research products and linking them back to primary data providers. However, this only works if those that publish research products cite primary data sources in the first place. We developed occCite, a set of R-based tools for downloading, managing, and citing biodiversity data, to advance toward the goal of closing the data provenance cycle. These tools preserve links between occurrence data and primary providers once researchers download aggregated data, and facilitate the citation of primary data providers in research papers.

The occCite workflow follows a three-step process. First, the user inputs one or more taxonomic names (or a phylogeny). occCite then rectifies these names by checking them against one or more taxonomic databases, which can be specified by the user (see the Global Names List). The results of the taxonomic rectification are then kept in an occCiteData object in local memory. Next, occCite takes the occCiteData object and user-defined search parameters to query BIEN (through rbien) and/or GBIF(through rGBIF) for records. The results are appended to the occCiteData object, along with metadata on the search. Finally, the user can pass the occCiteData object to occCitation, which compiles citations for the primary providers, database aggregators, and R packages used to build the dataset.

Future iterations of occCite will track citation data through the data cleaning process and provide a series of visualizations on raw query results and final data sets. It will also provide data citations in a format congruent with best-practice recommendations for large biodiversity data sets. Based on these data citation tools, we will also propose a new set of standards for citing primary biodiversity data in published research articles that provides due credit to contributors and allows them to track the use of their work. Keep checking back!

Setup

If you plan to query GBIF, you will need to provide them with your user login information. We have provided a dummy login below to show you the format. You will need to provide actual account information. This is because you will actually be downloading all of the records available for the species using occ_download(), instead of getting results from occ_search(), which has a hard limit of 200,000 occurrences.

library(occCite);
#Creating a GBIF login
GBIFLogin <- GBIFLoginManager(user = "occCiteTester",
                              email = "****@yahoo.com",
                              pwd = "12345")

Advanced features

Loading data from previous GBIF searches

Querying GBIF can take quite a bit of time, especially for multiple species and/or well-known species. In this case, you may wish to access previously-downloaded data sets from your computer by specifying the general location of your downloaded .zip files. occQuery will crawl through your specified GBIFDownloadDirectory to collect all the .zip files contained in that folder and its subfolders. It will then import the most recent downloads that match your taxon list. These GBIF data will be appended to a BIEN search the same as if you do the simple real-time search (if you chose BIEN as well as GBIF), as was shown above. checkPreviousGBIFDownload is TRUE by default, but if loadLocalGBIFDownload is TRUE, occQuery will ignore checkPreviousDownload. It is also worth noting that occCite does not currently support mixed data download sources. That is, you cannot do GBIF queries for some taxa, download previously-prepared data sets for others, and load the rest from local data sets on your computer.

# Simple load
myOldOccCiteObject <- occQuery(x = "Protea cynaroides", 
                                  datasources = c("gbif", "bien"), 
                                  GBIFLogin = NULL, 
                                  GBIFDownloadDirectory = system.file('extdata/', package='occCite'),
                                  loadLocalGBIFDownload = T,
                                  checkPreviousGBIFDownload = F)
## Warning in taxonRectification(taxName = targets[[count]], datasources =
## datasources): Following sources not found in Global Names Index source list:
## NCBI
## Warning in taxonRectification(taxName = targets[[count]], datasources =
## datasources): No valid taxonomic data sources supplied. Populating default list
## from all available sources.

Here is the result. Look familiar?

#GBIF search results
head(myOldOccCiteObject@occResults$`Protea cynaroides`$GBIF$OccurrenceTable);
##                name longitude  latitude day month year
## 1 Protea cynaroides  18.40540 -33.95891   4     1 2015
## 2 Protea cynaroides  18.42350 -33.96619  20     6 2019
## 3 Protea cynaroides  22.99340 -34.05478  16     6 2019
## 4 Protea cynaroides  18.40232 -34.08405   9     6 2019
## 5 Protea cynaroides  19.44807 -34.52123  13     6 2019
## 6 Protea cynaroides  18.39757 -34.07418   9     6 2019
##                                   Dataset                           DatasetKey
## 1 iNaturalist research-grade observations 50c9509d-22c7-4a22-a47d-8c48425ef4a7
## 2 iNaturalist research-grade observations 50c9509d-22c7-4a22-a47d-8c48425ef4a7
## 3 iNaturalist research-grade observations 50c9509d-22c7-4a22-a47d-8c48425ef4a7
## 4 iNaturalist research-grade observations 50c9509d-22c7-4a22-a47d-8c48425ef4a7
## 5 iNaturalist research-grade observations 50c9509d-22c7-4a22-a47d-8c48425ef4a7
## 6 iNaturalist research-grade observations 50c9509d-22c7-4a22-a47d-8c48425ef4a7
##   DataService
## 1        GBIF
## 2        GBIF
## 3        GBIF
## 4        GBIF
## 5        GBIF
## 6        GBIF
#The full summary
summary(myOldOccCiteObject)
##  
##  OccCite query occurred on: 02 February, 2021
##  
##  User query type: User-supplied list of taxa.
##  
##  Sources for taxonomic rectification: NCBI
##      
##  
##  Taxonomic cleaning results:     
## 
##          Input Name        Best Match
## 1 Protea cynaroides Protea cynaroides
##                                                                                                                                     Taxonomic Databases w/ Matches
## 1 National Center for Biotechnology Information; Freebase; Encyclopedia of Life; CU*STAR; uBio NameBank; Arctos; Open Tree of Life Reference Taxonomy; iNaturalist
##  
##  Sources for occurrence data: gbif, bien
##      
##             Species Occurrences Sources
## 1 Protea cynaroides         828      15
##  
##  GBIF dataset DOIs:  
## 
##             Species GBIF Access Date           GBIF DOI
## 1 Protea cynaroides       2019-07-15 10.15468/dl.iqnra2

Getting citation data works the exact same way with previously-downloaded data as it does from a fresh data set.

#Get citations
myOldOccCitations <- occCitation(myOldOccCiteObject)
print(myOldOccCitations)
## Warning in utils::citation(pkg): no date field in DESCRIPTION file of package
## 'occCite'
## Warning in utils::citation(pkg): could not determine year for 'occCite' from
## package DESCRIPTION file
## Ignoring entry titled "occCite: Querying and Managing Large Biodiversity Occurrence Datasets" because owensocccite: A bibentry of bibtype 'Manual' has to specify the field: c("year", "date")
## Writing 4 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Cameron E, Auckland Museum A M (2021). Auckland Museum Botany Collection. Version 1.56. Auckland War Memorial Museum. https://doi.org/10.15468/mnjkvv. Accessed via GBIF on 2019-07-15.
## Capers R (2014). CONN. University of Connecticut. https://doi.org/10.15468/w35jmd. Accessed via GBIF on 2019-07-15.
## Chamberlain, S., Barve, V., Mcglinn, D., Oldoni, D., Desmet, P., Geffert, L., Ram, K. (2021). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.4.2. https://CRAN.R-project.org/package=rgbif.
## Chamberlain, S., Boettiger, C. (2017). R Python, and Ruby clients for GBIF species occurrence data. PeerJ PrePrints.
## Fatima Parker-Allie, Ranwashe F (2018). PRECIS. South African National Biodiversity Institute. https://doi.org/10.15468/rckmn2. Accessed via GBIF on 2019-07-15.
## MNHN, Chagnoux S (2021). The vascular plants collection (P) at the Herbarium of the Muséum national d'Histoire Naturelle (MNHN - Paris). Version 69.196. MNHN - Museum national d'Histoire naturelle. https://doi.org/10.15468/nc6rxy. Accessed via GBIF on 2019-07-15.
## MNHN. https://doi.org/10.15468/dl.fpwlzt. Accessed via BIEN on 2018-08-14.
## Magill B, Solomon J, Stimmel H (2021). Tropicos Specimen Data. Missouri Botanical Garden. https://doi.org/10.15468/hja69f. Accessed via GBIF on 2019-07-15.
## Maitner, B. (2020). BIEN: Tools for Accessing the Botanical Information and Ecology. R package version 1.2.4. https://CRAN.R-project.org/package=BIEN.
## Missouri Botanical Garden,Herbarium. Accessed via BIEN on NA.
## NSW. https://doi.org/10.15468/dl.fpwlzt. Accessed via BIEN on 2018-08-14.
## R Core Team. (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
## Ranwashe F (2019). BODATSA: Botanical Collections. Version 1.4. South African National Biodiversity Institute. https://doi.org/10.15468/2aki0q. Accessed via GBIF on 2019-07-15.
## SANBI. https://doi.org/10.15468/dl.fpwlzt. Accessed via BIEN on 2018-08-14.
## Senckenberg (2020). African Plants - a photo guide. https://doi.org/10.15468/r9azth. Accessed via GBIF on 2019-07-15.
## Tela Botanica. Carnet en Ligne. https://doi.org/10.15468/rydcn2. Accessed via GBIF on 2019-07-15.
## UConn. https://doi.org/10.15468/dl.fpwlzt. Accessed via BIEN on 2018-08-14.
## Ueda K (2021). iNaturalist Research-grade Observations. iNaturalist.org. https://doi.org/10.15468/ab3s5x. Accessed via GBIF on 2019-07-15.
## naturgucker.de. naturgucker. https://doi.org/10.15468/uc1apo. Accessed via GBIF on 2019-07-15.

Note that you can also load multiple species using either a vector of species names or a phylogeny (provided you have previously downloaded data for all of the species of interest), and you can load occurrences from non-GBIF data sources (e.g. BIEN) in the same query.

occCite with a Phylogeny

Here is an example of how such a search is structured, using an unpublished phylogeny of billfishes.

library(ape)
#Get tree
treeFile <- system.file("extdata/Fish_12Tax_time_calibrated.tre", package='occCite')
phylogeny <- ape::read.nexus(treeFile)
tree <- ape::extract.clade(phylogeny, 18)
#Query databases for names
myPhyOccCiteObject <- studyTaxonList(x = tree, 
                                     datasources = "National Center for Biotechnology Information")
#Query GBIF for occurrence data
myPhyOccCiteObject <- occQuery(x = myPhyOccCiteObject, 
                            datasources = "gbif",
                            GBIFDownloadDirectory = system.file('extdata/', package='occCite'),
                            loadLocalGBIFDownload = T,
                            checkPreviousGBIFDownload = F)
# What does a multispecies query look like?
summary(myPhyOccCiteObject)
##  
##  OccCite query occurred on: 02 February, 2021
##  
##  User query type: User-supplied phylogeny.
##  
##  Sources for taxonomic rectification: National Center for Biotechnology Information
##      
##  
##  Taxonomic cleaning results:     
## 
##                   Input Name                 Best Match
## 1           Istiompax_indica           Istiompax indica
## 2             Kajikia_albida             Kajikia albida
## 3              Kajikia_audax              Kajikia audax
## 4 Tetrapturus_angustirostris Tetrapturus angustirostris
## 5         Tetrapturus_belone         Tetrapturus belone
## 6        Tetrapturus_georgii        Tetrapturus georgii
## 7      Tetrapturus_pfluegeri      Tetrapturus pfluegeri
##                  Taxonomic Databases w/ Matches
## 1 National Center for Biotechnology Information
## 2 National Center for Biotechnology Information
## 3 National Center for Biotechnology Information
## 4 National Center for Biotechnology Information
## 5 National Center for Biotechnology Information
## 6 National Center for Biotechnology Information
## 7 National Center for Biotechnology Information
##  
##  Sources for occurrence data: gbif
##      
##                      Species Occurrences Sources
## 1           Istiompax indica         468      23
## 2             Kajikia albida         167      16
## 3              Kajikia audax        6721      22
## 4 Tetrapturus angustirostris         174      22
## 5         Tetrapturus belone           9       6
## 6        Tetrapturus georgii          62       4
## 7      Tetrapturus pfluegeri         409       7
##  
##  GBIF dataset DOIs:  
## 
##                      Species GBIF Access Date           GBIF DOI
## 1           Istiompax indica       2019-07-04 10.15468/dl.crapuf
## 2             Kajikia albida       2019-07-04 10.15468/dl.lnwf6a
## 3              Kajikia audax       2019-07-04 10.15468/dl.txromp
## 4 Tetrapturus angustirostris       2019-07-04 10.15468/dl.mumi5e
## 5         Tetrapturus belone       2019-07-04 10.15468/dl.q2nxb1
## 6        Tetrapturus georgii       2019-07-04 10.15468/dl.h860up
## 7      Tetrapturus pfluegeri       2019-07-04 10.15468/dl.qjidbs

When you have results for multiple species, as in this case, you can also plot the summary figures either for the whole search…

plot(myPhyOccCiteObject)

or you can plot the results by species!

plot(myPhyOccCiteObject, bySpecies = T)

And then you can print out the citations, separated by species (or not, but in this example, they’re separate).

#Get citations
myPhyOccCitations <- occCitation(myPhyOccCiteObject)

#Print citations as text with accession dates.
print(myPhyOccCitations, bySpecies = T)
## Warning in utils::citation(pkg): no date field in DESCRIPTION file of package
## 'occCite'
## Warning in utils::citation(pkg): could not determine year for 'occCite' from
## package DESCRIPTION file
## Ignoring entry titled "occCite: Querying and Managing Large Biodiversity Occurrence Datasets" because owensocccite: A bibentry of bibtype 'Manual' has to specify the field: c("year", "date")
## Writing 5 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Istiompax indica 
## 
## Australian Museum (2020). Australian Museum provider for OZCAM. https://doi.org/10.15468/e7susi. Accessed via GBIF on 2019-07-04.
## BARDE Julien N, Inventaire National du Patrimoine Naturel (2019). Programme Ecoscope: données d'observations des écosystèmes marins exploités (Réunion). Version 1.1. UMS PatriNat (OFB-CNRS-MNHN), Paris. https://doi.org/10.15468/elttrd. Accessed via GBIF on 2019-07-04.
## Barde J (2011). ecoscope_observation_database. IRD - Institute of Research for Development. https://doi.org/10.15468/dz1kk0. Accessed via GBIF on 2019-07-04.
## CSIRO - Arafura Sea shark surveys (Rachel cruises 1984-1985) https://doi.org/10.15468/yickr6. Accessed via GBIF on 2019-07-04.
## CSIRO National Collections and Marine Infrastructure (NCMI) Information and Data Centre (IDC): Pelagic fish food web linkages, Queensland, Australia (2003-2005) https://doi.org/10.15468/yy5wdp. Accessed via GBIF on 2019-07-04.
## Catania D, Fong J (2021). CAS Ichthyology (ICH). Version 150.255. California Academy of Sciences. https://doi.org/10.15468/efh2ib. Accessed via GBIF on 2019-07-04.
## Cauquil P, Barde J (2011). observe_tuna_bycatch_ecoscope. IRD - Institute of Research for Development. https://doi.org/10.15468/23m361. Accessed via GBIF on 2019-07-04.
## Chamberlain, S., Barve, V., Mcglinn, D., Oldoni, D., Desmet, P., Geffert, L., Ram, K. (2021). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.4.2. https://CRAN.R-project.org/package=rgbif.
## Chamberlain, S., Boettiger, C. (2017). R Python, and Ruby clients for GBIF species occurrence data. PeerJ PrePrints.
## Elías Gutiérrez M, Comisión nacional para el conocimiento y uso de la biodiversidad C (2020). Códigos de barras de la vida en peces y zooplancton de México. Version 1.7. Comisión nacional para el conocimiento y uso de la biodiversidad. https://doi.org/10.15468/xmbkgo. Accessed via GBIF on 2019-07-04.
## European Nucleotide Archive (EMBL-EBI) (2019). Geographically tagged INSDC sequences. https://doi.org/10.15468/cndomv. Accessed via GBIF on 2019-07-04.
## Feeney R (2019). LACM Vertebrate Collection. Version 18.7. Natural History Museum of Los Angeles County. https://doi.org/10.15468/77rmwd. Accessed via GBIF on 2019-07-04.
## McLean, M.W. (2014). Straightforward Bibliography Management in R Using the RefManager Package. NA, NA. https://arxiv.org/abs/1403.2036.
## McLean, M.W. (2017). RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.
## Ministry for Primary Industries (2014). New Zealand research tagging database. Southwestern Pacific OBIS, National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand, 411926 records, Online http://nzobisipt.niwa.co.nz/resource.do?r=mpi_tag released on November 5, 2014. https://doi.org/10.15468/i66xdm. Accessed via GBIF on 2019-07-04.
## Museum and Art Gallery of the Northern Territory (2019). Northern Territory Museum and Art Gallery provider for OZCAM. https://doi.org/10.15468/giro3a. Accessed via GBIF on 2019-07-04.
## Museums Victoria (2020). Museums Victoria provider for OZCAM. https://doi.org/10.15468/lp1ctu. Accessed via GBIF on 2019-07-04.
## Pozo de la Tijera M D C, Comisión nacional para el conocimiento y uso de la biodiversidad C (2020). Fortalecimiento de las colecciones de ECOSUR. Primera fase (Ictioplancton Chetumal). Version 1.3. Comisión nacional para el conocimiento y uso de la biodiversidad. https://doi.org/10.15468/orx3mk. Accessed via GBIF on 2019-07-04.
## Queensland Museum (2020). Queensland Museum provider for OZCAM. https://doi.org/10.15468/lotsye. Accessed via GBIF on 2019-07-04.
## R Core Team. (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
## Raiva R, Santana P (2019). Diversidade e ocorrência de peixes em Inhambane (2009-2017). Version 1.4. National Institute of Fisheries Research (IIP) – Mozambique. https://doi.org/10.15468/4fj2tq. Accessed via GBIF on 2019-07-04.
## Raiva R, Viador R, Santana P (2019). Diversidade e ocorrência de peixes na Zambézia (2003-2016). National Institute of Fisheries Research (IIP) – Mozambique. https://doi.org/10.15468/mrz36h. Accessed via GBIF on 2019-07-04.
## Robins R (2021). UF FLMNH Ichthyology. Version 117.297. Florida Museum of Natural History. https://doi.org/10.15468/8mjsel. Accessed via GBIF on 2019-07-04.
## Sánchez González S, Comisión nacional para el conocimiento y uso de la biodiversidad C (2020). Taxonomía y sistemática de la Ictiofauna de la Bahía de Banderas del Estado de Nayarit, México. Comisión nacional para el conocimiento y uso de la biodiversidad. https://doi.org/10.15468/uhrwsl. Accessed via GBIF on 2019-07-04.
## The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). https://doi.org/10.15468/inygc6. Accessed via GBIF on 2019-07-04.
## Uchifune Y, Yamamoto H (2020). Asia-Pacific Dataset. Version 1.33. National Museum of Nature and Science, Japan. https://doi.org/10.15468/vjeh1p. Accessed via GBIF on 2019-07-04.
## Ueda K (2021). iNaturalist Research-grade Observations. iNaturalist.org. https://doi.org/10.15468/ab3s5x. Accessed via GBIF on 2019-07-04.
## Western Australian Museum (2019). Western Australian Museum provider for OZCAM. https://doi.org/10.15468/5qt0dm. Accessed via GBIF on 2019-07-04.
## Warning in utils::citation(pkg): no date field in DESCRIPTION file of package
## 'occCite'

## Warning in utils::citation(pkg): could not determine year for 'occCite' from
## package DESCRIPTION file
## Ignoring entry titled "occCite: Querying and Managing Large Biodiversity Occurrence Datasets" because owensocccite: A bibentry of bibtype 'Manual' has to specify the field: c("year", "date")
## Writing 5 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Kajikia albida 
## 
## BARDE Julien N, Inventaire National du Patrimoine Naturel (2019). Programme Ecoscope: données d'observations des écosystèmes marins exploités. Version 1.1. UMS PatriNat (OFB-CNRS-MNHN), Paris. https://doi.org/10.15468/gdrknh. Accessed via GBIF on 2019-07-04.
## Barde J (2011). ecoscope_observation_database. IRD - Institute of Research for Development. https://doi.org/10.15468/dz1kk0. Accessed via GBIF on 2019-07-04.
## Bentley A (2020). KUBI Ichthyology Collection. Version 17.68. University of Kansas Biodiversity Institute. https://doi.org/10.15468/mgjasg. Accessed via GBIF on 2019-07-04.
## Bentley A (2020). KUBI Ichthyology Tissue Collection. Version 18.56. University of Kansas Biodiversity Institute. https://doi.org/10.15468/jmsnwg. Accessed via GBIF on 2019-07-04.
## Casassovici A, Brosens D (2021). Diveboard - Scuba diving citizen science observations. Version 54.33. Diveboard. https://doi.org/10.15468/tnjrgy. Accessed via GBIF on 2019-07-04.
## Cauquil P, Barde J (2011). observe_tuna_bycatch_ecoscope. IRD - Institute of Research for Development. https://doi.org/10.15468/23m361. Accessed via GBIF on 2019-07-04.
## Chamberlain, S., Barve, V., Mcglinn, D., Oldoni, D., Desmet, P., Geffert, L., Ram, K. (2021). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.4.2. https://CRAN.R-project.org/package=rgbif.
## Chamberlain, S., Boettiger, C. (2017). R Python, and Ruby clients for GBIF species occurrence data. PeerJ PrePrints.
## Elías Gutiérrez M, Comisión nacional para el conocimiento y uso de la biodiversidad C (2020). Códigos de barras de la vida en peces y zooplancton de México. Version 1.7. Comisión nacional para el conocimiento y uso de la biodiversidad. https://doi.org/10.15468/xmbkgo. Accessed via GBIF on 2019-07-04.
## European Nucleotide Archive (EMBL-EBI) (2019). Geographically tagged INSDC sequences. https://doi.org/10.15468/cndomv. Accessed via GBIF on 2019-07-04.
## Feeney R (2019). LACM Vertebrate Collection. Version 18.7. Natural History Museum of Los Angeles County. https://doi.org/10.15468/77rmwd. Accessed via GBIF on 2019-07-04.
## Frable B (2019). SIO Marine Vertebrate Collection. Version 1.7. Scripps Institution of Oceanography. https://doi.org/10.15468/ad1ovc. Accessed via GBIF on 2019-07-04.
## Harvard University M, Morris P J (2021). Museum of Comparative Zoology, Harvard University. Version 162.247. Museum of Comparative Zoology, Harvard University. https://doi.org/10.15468/p5rupv. Accessed via GBIF on 2019-07-04.
## McLean, M.W. (2014). Straightforward Bibliography Management in R Using the RefManager Package. NA, NA. https://arxiv.org/abs/1403.2036.
## McLean, M.W. (2017). RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.
## Millen B (2019). Ichthyology Collection - Royal Ontario Museum. Version 18.7. Royal Ontario Museum. https://doi.org/10.15468/syisbx. Accessed via GBIF on 2019-07-04.
## Orrell T, Informatics Office (2021). NMNH Extant Specimen Records. Version 1.40. National Museum of Natural History, Smithsonian Institution. https://doi.org/10.15468/hnhrg3. Accessed via GBIF on 2019-07-04.
## Pozo de la Tijera M D C, Comisión nacional para el conocimiento y uso de la biodiversidad C (2020). Fortalecimiento de las colecciones de ECOSUR. Primera fase (Ictioplancton Chetumal). Version 1.3. Comisión nacional para el conocimiento y uso de la biodiversidad. https://doi.org/10.15468/orx3mk. Accessed via GBIF on 2019-07-04.
## R Core Team. (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
## Robins R (2021). UF FLMNH Ichthyology. Version 117.297. Florida Museum of Natural History. https://doi.org/10.15468/8mjsel. Accessed via GBIF on 2019-07-04.
## The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). https://doi.org/10.15468/inygc6. Accessed via GBIF on 2019-07-04.
## Warning in utils::citation(pkg): no date field in DESCRIPTION file of package
## 'occCite'

## Warning in utils::citation(pkg): could not determine year for 'occCite' from
## package DESCRIPTION file
## Ignoring entry titled "occCite: Querying and Managing Large Biodiversity Occurrence Datasets" because owensocccite: A bibentry of bibtype 'Manual' has to specify the field: c("year", "date")
## Writing 5 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Kajikia audax 
## 
## Australian Museum (2020). Australian Museum provider for OZCAM. https://doi.org/10.15468/e7susi. Accessed via GBIF on 2019-07-04.
## BARDE Julien N, Inventaire National du Patrimoine Naturel (2019). Programme Ecoscope: données d'observations des écosystèmes marins exploités (Réunion). Version 1.1. UMS PatriNat (OFB-CNRS-MNHN), Paris. https://doi.org/10.15468/elttrd. Accessed via GBIF on 2019-07-04.
## BARDE Julien N, Inventaire National du Patrimoine Naturel (2019). Programme Ecoscope: données d'observations des écosystèmes marins exploités. Version 1.1. UMS PatriNat (OFB-CNRS-MNHN), Paris. https://doi.org/10.15468/gdrknh. Accessed via GBIF on 2019-07-04.
## Barde J (2011). ecoscope_observation_database. IRD - Institute of Research for Development. https://doi.org/10.15468/dz1kk0. Accessed via GBIF on 2019-07-04.
## Cauquil P, Barde J (2011). observe_tuna_bycatch_ecoscope. IRD - Institute of Research for Development. https://doi.org/10.15468/23m361. Accessed via GBIF on 2019-07-04.
## Chamberlain, S., Barve, V., Mcglinn, D., Oldoni, D., Desmet, P., Geffert, L., Ram, K. (2021). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.4.2. https://CRAN.R-project.org/package=rgbif.
## Chamberlain, S., Boettiger, C. (2017). R Python, and Ruby clients for GBIF species occurrence data. PeerJ PrePrints.
## Chiang W (2014). Taiwan Fisheries Research Institute – Digital archives of coastal and offshore specimens. TELDAP. https://doi.org/10.15468/xvxngy. Accessed via GBIF on 2019-07-04.
## Commonwealth Scientific and Industrial Research Organisation (2020). CSIRO Ichthyology provider for OZCAM. https://doi.org/10.15468/azp1pf. Accessed via GBIF on 2019-07-04.
## European Nucleotide Archive (EMBL-EBI) (2019). Geographically tagged INSDC sequences. https://doi.org/10.15468/cndomv. Accessed via GBIF on 2019-07-04.
## Feeney R (2019). LACM Vertebrate Collection. Version 18.7. Natural History Museum of Los Angeles County. https://doi.org/10.15468/77rmwd. Accessed via GBIF on 2019-07-04.
## Frable B (2019). SIO Marine Vertebrate Collection. Version 1.7. Scripps Institution of Oceanography. https://doi.org/10.15468/ad1ovc. Accessed via GBIF on 2019-07-04.
## González Acosta A F, Comisión nacional para el conocimiento y uso de la biodiversidad C (2020). Ampliación de la base de datos de la ictiofauna insular del Golfo de California. Version 1.7. Comisión nacional para el conocimiento y uso de la biodiversidad. https://doi.org/10.15468/p5ovq7. Accessed via GBIF on 2019-07-04.
## Grant S, McMahan C (2020). Field Museum of Natural History (Zoology) Fish Collection. Version 13.12. Field Museum. https://doi.org/10.15468/alz7wu. Accessed via GBIF on 2019-07-04.
## McLean, M.W. (2014). Straightforward Bibliography Management in R Using the RefManager Package. NA, NA. https://arxiv.org/abs/1403.2036.
## McLean, M.W. (2017). RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.
## Ministry for Primary Industries (2014). New Zealand research tagging database. Southwestern Pacific OBIS, National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand, 411926 records, Online http://nzobisipt.niwa.co.nz/resource.do?r=mpi_tag released on November 5, 2014. https://doi.org/10.15468/i66xdm. Accessed via GBIF on 2019-07-04.
## Museum and Art Gallery of the Northern Territory (2019). Northern Territory Museum and Art Gallery provider for OZCAM. https://doi.org/10.15468/giro3a. Accessed via GBIF on 2019-07-04.
## Orrell T, Informatics Office (2021). NMNH Extant Specimen Records. Version 1.40. National Museum of Natural History, Smithsonian Institution. https://doi.org/10.15468/hnhrg3. Accessed via GBIF on 2019-07-04.
## Queensland Museum (2020). Queensland Museum provider for OZCAM. https://doi.org/10.15468/lotsye. Accessed via GBIF on 2019-07-04.
## R Core Team. (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
## Robins R (2021). UF FLMNH Ichthyology. Version 117.297. Florida Museum of Natural History. https://doi.org/10.15468/8mjsel. Accessed via GBIF on 2019-07-04.
## SWPRON (2014). Marine biological observation data from coastal and offshore surveys around New Zealand. Southwestern Pacific OBIS, National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand, 9092 records, Online http://nzobisipt.niwa.co.nz/resource.do?r=mbis_nz released on January 16, 2018. https://doi.org/10.15468/pzpgop. Accessed via GBIF on 2019-07-04.
## The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). https://doi.org/10.15468/inygc6. Accessed via GBIF on 2019-07-04.
## Uchifune Y, Yamamoto H (2020). Asia-Pacific Dataset. Version 1.33. National Museum of Nature and Science, Japan. https://doi.org/10.15468/vjeh1p. Accessed via GBIF on 2019-07-04.
## Ueda K (2021). iNaturalist Research-grade Observations. iNaturalist.org. https://doi.org/10.15468/ab3s5x. Accessed via GBIF on 2019-07-04.
## University of Washington Ichthyology Collection (UWFC) https://doi.org/10.15468/vvp7gr. Accessed via GBIF on 2019-07-04.
## Warning in utils::citation(pkg): no date field in DESCRIPTION file of package
## 'occCite'

## Warning in utils::citation(pkg): could not determine year for 'occCite' from
## package DESCRIPTION file
## Ignoring entry titled "occCite: Querying and Managing Large Biodiversity Occurrence Datasets" because owensocccite: A bibentry of bibtype 'Manual' has to specify the field: c("year", "date")
## Writing 5 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Tetrapturus angustirostris 
## 
## Australian Museum (2020). Australian Museum provider for OZCAM. https://doi.org/10.15468/e7susi. Accessed via GBIF on 2019-07-04.
## BARDE Julien N, Inventaire National du Patrimoine Naturel (2019). Programme Ecoscope: données d'observations des écosystèmes marins exploités (Réunion). Version 1.1. UMS PatriNat (OFB-CNRS-MNHN), Paris. https://doi.org/10.15468/elttrd. Accessed via GBIF on 2019-07-04.
## BARDE Julien N, Inventaire National du Patrimoine Naturel (2019). Programme Ecoscope: données d'observations des écosystèmes marins exploités. Version 1.1. UMS PatriNat (OFB-CNRS-MNHN), Paris. https://doi.org/10.15468/gdrknh. Accessed via GBIF on 2019-07-04.
## Barde J (2011). ecoscope_observation_database. IRD - Institute of Research for Development. https://doi.org/10.15468/dz1kk0. Accessed via GBIF on 2019-07-04.
## Catania D, Fong J (2021). CAS Ichthyology (ICH). Version 150.255. California Academy of Sciences. https://doi.org/10.15468/efh2ib. Accessed via GBIF on 2019-07-04.
## Cauquil P, Barde J (2011). observe_tuna_bycatch_ecoscope. IRD - Institute of Research for Development. https://doi.org/10.15468/23m361. Accessed via GBIF on 2019-07-04.
## Chamberlain, S., Barve, V., Mcglinn, D., Oldoni, D., Desmet, P., Geffert, L., Ram, K. (2021). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.4.2. https://CRAN.R-project.org/package=rgbif.
## Chamberlain, S., Boettiger, C. (2017). R Python, and Ruby clients for GBIF species occurrence data. PeerJ PrePrints.
## Chiang W (2014). Taiwan Fisheries Research Institute – Digital archives of coastal and offshore specimens. TELDAP. https://doi.org/10.15468/xvxngy. Accessed via GBIF on 2019-07-04.
## European Nucleotide Archive (EMBL-EBI) (2019). Geographically tagged INSDC sequences. https://doi.org/10.15468/cndomv. Accessed via GBIF on 2019-07-04.
## Feeney R (2019). LACM Vertebrate Collection. Version 18.7. Natural History Museum of Los Angeles County. https://doi.org/10.15468/77rmwd. Accessed via GBIF on 2019-07-04.
## Frable B (2019). SIO Marine Vertebrate Collection. Version 1.7. Scripps Institution of Oceanography. https://doi.org/10.15468/ad1ovc. Accessed via GBIF on 2019-07-04.
## Harvard University M, Morris P J (2021). Museum of Comparative Zoology, Harvard University. Version 162.247. Museum of Comparative Zoology, Harvard University. https://doi.org/10.15468/p5rupv. Accessed via GBIF on 2019-07-04.
## McLean, M.W. (2014). Straightforward Bibliography Management in R Using the RefManager Package. NA, NA. https://arxiv.org/abs/1403.2036.
## McLean, M.W. (2017). RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.
## Ministry for Primary Industries (2014). New Zealand research tagging database. Southwestern Pacific OBIS, National Institute of Water and Atmospheric Research (NIWA), Wellington, New Zealand, 411926 records, Online http://nzobisipt.niwa.co.nz/resource.do?r=mpi_tag released on November 5, 2014. https://doi.org/10.15468/i66xdm. Accessed via GBIF on 2019-07-04.
## National Museum of Nature and Science, Japan (2020). Fish specimens of Kagoshima University Museum. https://doi.org/10.15468/vcj3j8. Accessed via GBIF on 2019-07-04.
## Queensland Museum (2020). Queensland Museum provider for OZCAM. https://doi.org/10.15468/lotsye. Accessed via GBIF on 2019-07-04.
## R Core Team. (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
## Raiva R, Santana P (2019). Diversidade e ocorrência de peixes em Inhambane (2009-2017). Version 1.4. National Institute of Fisheries Research (IIP) – Mozambique. https://doi.org/10.15468/4fj2tq. Accessed via GBIF on 2019-07-04.
## Raiva R, Viador R, Santana P (2019). Diversidade e ocorrência de peixes na Zambézia (2003-2016). National Institute of Fisheries Research (IIP) – Mozambique. https://doi.org/10.15468/mrz36h. Accessed via GBIF on 2019-07-04.
## Robins R (2021). UF FLMNH Ichthyology. Version 117.297. Florida Museum of Natural History. https://doi.org/10.15468/8mjsel. Accessed via GBIF on 2019-07-04.
## South Australian Museum (2020). South Australian Museum Australia provider for OZCAM. https://doi.org/10.15468/wz4rrh. Accessed via GBIF on 2019-07-04.
## The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). https://doi.org/10.15468/inygc6. Accessed via GBIF on 2019-07-04.
## Uchifune Y, Yamamoto H (2020). Asia-Pacific Dataset. Version 1.33. National Museum of Nature and Science, Japan. https://doi.org/10.15468/vjeh1p. Accessed via GBIF on 2019-07-04.
## Ueda K (2021). iNaturalist Research-grade Observations. iNaturalist.org. https://doi.org/10.15468/ab3s5x. Accessed via GBIF on 2019-07-04.
## Western Australian Museum (2019). Western Australian Museum provider for OZCAM. https://doi.org/10.15468/5qt0dm. Accessed via GBIF on 2019-07-04.
## Warning in utils::citation(pkg): no date field in DESCRIPTION file of package
## 'occCite'

## Warning in utils::citation(pkg): could not determine year for 'occCite' from
## package DESCRIPTION file
## Ignoring entry titled "occCite: Querying and Managing Large Biodiversity Occurrence Datasets" because owensocccite: A bibentry of bibtype 'Manual' has to specify the field: c("year", "date")
## Writing 5 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Tetrapturus belone 
## 
## Bentley A (2020). KUBI Ichthyology Collection. Version 17.68. University of Kansas Biodiversity Institute. https://doi.org/10.15468/mgjasg. Accessed via GBIF on 2019-07-04.
## Chamberlain, S., Barve, V., Mcglinn, D., Oldoni, D., Desmet, P., Geffert, L., Ram, K. (2021). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.4.2. https://CRAN.R-project.org/package=rgbif.
## Chamberlain, S., Boettiger, C. (2017). R Python, and Ruby clients for GBIF species occurrence data. PeerJ PrePrints.
## European Nucleotide Archive (EMBL-EBI) (2019). Geographically tagged INSDC sequences. https://doi.org/10.15468/cndomv. Accessed via GBIF on 2019-07-04.
## Harvard University M, Morris P J (2021). Museum of Comparative Zoology, Harvard University. Version 162.247. Museum of Comparative Zoology, Harvard University. https://doi.org/10.15468/p5rupv. Accessed via GBIF on 2019-07-04.
## McLean, M.W. (2014). Straightforward Bibliography Management in R Using the RefManager Package. NA, NA. https://arxiv.org/abs/1403.2036.
## McLean, M.W. (2017). RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.
## R Core Team. (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
## Ranz J (2017). Banco de Datos de la Biodiversidad de la Comunitat Valenciana. Biodiversity data bank of Generalitat Valenciana. https://doi.org/10.15468/b4yqdy. Accessed via GBIF on 2019-07-04.
## Robins R (2021). UF FLMNH Ichthyology. Version 117.297. Florida Museum of Natural History. https://doi.org/10.15468/8mjsel. Accessed via GBIF on 2019-07-04.
## UMS PatriNat (OFB-CNRS-MNHN), Paris (2020). Données d'occurrences Espèces issues de l'inventaire des ZNIEFF. Version 1.1. https://doi.org/10.15468/ikshke. Accessed via GBIF on 2019-07-04.
## Warning in utils::citation(pkg): no date field in DESCRIPTION file of package
## 'occCite'

## Warning in utils::citation(pkg): could not determine year for 'occCite' from
## package DESCRIPTION file
## Ignoring entry titled "occCite: Querying and Managing Large Biodiversity Occurrence Datasets" because owensocccite: A bibentry of bibtype 'Manual' has to specify the field: c("year", "date")
## Writing 5 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Tetrapturus georgii 
## 
## Bentley A (2020). KUBI Ichthyology Collection. Version 17.68. University of Kansas Biodiversity Institute. https://doi.org/10.15468/mgjasg. Accessed via GBIF on 2019-07-04.
## Chamberlain, S., Barve, V., Mcglinn, D., Oldoni, D., Desmet, P., Geffert, L., Ram, K. (2021). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.4.2. https://CRAN.R-project.org/package=rgbif.
## Chamberlain, S., Boettiger, C. (2017). R Python, and Ruby clients for GBIF species occurrence data. PeerJ PrePrints.
## European Nucleotide Archive (EMBL-EBI) (2019). Geographically tagged INSDC sequences. https://doi.org/10.15468/cndomv. Accessed via GBIF on 2019-07-04.
## McLean, M.W. (2014). Straightforward Bibliography Management in R Using the RefManager Package. NA, NA. https://arxiv.org/abs/1403.2036.
## McLean, M.W. (2017). RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.
## Orrell T, Informatics Office (2021). NMNH Extant Specimen Records. Version 1.40. National Museum of Natural History, Smithsonian Institution. https://doi.org/10.15468/hnhrg3. Accessed via GBIF on 2019-07-04.
## R Core Team. (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
## The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). https://doi.org/10.15468/inygc6. Accessed via GBIF on 2019-07-04.
## Warning in utils::citation(pkg): no date field in DESCRIPTION file of package
## 'occCite'

## Warning in utils::citation(pkg): could not determine year for 'occCite' from
## package DESCRIPTION file
## Ignoring entry titled "occCite: Querying and Managing Large Biodiversity Occurrence Datasets" because owensocccite: A bibentry of bibtype 'Manual' has to specify the field: c("year", "date")
## Writing 5 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Tetrapturus pfluegeri 
## 
## BARDE Julien N, Inventaire National du Patrimoine Naturel (2019). Programme Ecoscope: données d'observations des écosystèmes marins exploités (Réunion). Version 1.1. UMS PatriNat (OFB-CNRS-MNHN), Paris. https://doi.org/10.15468/elttrd. Accessed via GBIF on 2019-07-04.
## BARDE Julien N, Inventaire National du Patrimoine Naturel (2019). Programme Ecoscope: données d'observations des écosystèmes marins exploités. Version 1.1. UMS PatriNat (OFB-CNRS-MNHN), Paris. https://doi.org/10.15468/gdrknh. Accessed via GBIF on 2019-07-04.
## Barde J (2011). ecoscope_observation_database. IRD - Institute of Research for Development. https://doi.org/10.15468/dz1kk0. Accessed via GBIF on 2019-07-04.
## Cauquil P, Barde J (2011). observe_tuna_bycatch_ecoscope. IRD - Institute of Research for Development. https://doi.org/10.15468/23m361. Accessed via GBIF on 2019-07-04.
## Chamberlain, S., Barve, V., Mcglinn, D., Oldoni, D., Desmet, P., Geffert, L., Ram, K. (2021). rgbif: Interface to the Global Biodiversity Information Facility API. R package version 3.4.2. https://CRAN.R-project.org/package=rgbif.
## Chamberlain, S., Boettiger, C. (2017). R Python, and Ruby clients for GBIF species occurrence data. PeerJ PrePrints.
## European Nucleotide Archive (EMBL-EBI) (2019). Geographically tagged INSDC sequences. https://doi.org/10.15468/cndomv. Accessed via GBIF on 2019-07-04.
## McLean, M.W. (2014). Straightforward Bibliography Management in R Using the RefManager Package. NA, NA. https://arxiv.org/abs/1403.2036.
## McLean, M.W. (2017). RefManageR: Import and Manage BibTeX and BibLaTeX References in R. The Journal of Open Source Software.
## R Core Team. (2020). R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/.
## Robins R (2021). UF FLMNH Ichthyology. Version 117.297. Florida Museum of Natural History. https://doi.org/10.15468/8mjsel. Accessed via GBIF on 2019-07-04.
## The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). https://doi.org/10.15468/inygc6. Accessed via GBIF on 2019-07-04.