Advanced execution of occurrence searches and citations generation

Hannah L. Owens

Cory Merow

Brian Maitner

Jamie M. Kass

Vijay Barve

Robert Guralnick

2021-04-27

Advanced features

This vignette demonstrates more advanced features and customization available in occCite. We recommend you read vignette("Simple.Rmd", package = "occCite") first, if you have not already done so.

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)

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: 27 April, 2021
##  
##  User query type: User-supplied list of taxa.
##  
##  Sources for taxonomic rectification: National Center for Biotechnology Information
##      
##  
##  Taxonomic cleaning results:     
## 
##          Input Name        Best Match
## 1 Protea cynaroides Protea cynaroides
##                  Taxonomic Databases w/ Matches
## 1 National Center for Biotechnology Information
##  
##  Sources for occurrence data: gbif, bien
##      
##             Species Occurrences Sources
## 1 Protea cynaroides           0       0
##  
##  GBIF dataset DOIs:  
## 
##             Species GBIF Access Date GBIF DOI
## 1 Protea cynaroides             <NA>     <NA>

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)
## Writing 5 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Warning: `as_data_frame()` was deprecated in tibble 2.0.0.
## Please use `as_tibble()` instead.
## The signature and semantics have changed, see `?as_tibble`.
## Cameron E, Auckland Museum A M (2021). Auckland Museum Botany Collection. Version 1.59. 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 3.5.2. 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 69.206. 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.
## 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.
## Owens, H., Merow, C., Maitner, B., Kass, J., Barve, V., Guralnick, R. (2021). occCite: Querying and Managing Large Biodiversity Occurrence Datasets. R package version 0.4.7. https://CRAN.R-project.org/package=occCite.
## 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.
## Solomon J, Stimmel H (2021). Tropicos Specimen Data. Missouri Botanical Garden. https://doi.org/10.15468/hja69f. 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: 27 April, 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)
## Writing 6 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Istiompax indica 
## 
## Australian Museum (2021). 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 150.267. 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 3.5.2. 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 (2021). Museums Victoria provider for OZCAM. https://doi.org/10.15468/lp1ctu. Accessed via GBIF on 2019-07-04.
## Owens, H., Merow, C., Maitner, B., Kass, J., Barve, V., Guralnick, R. (2021). occCite: Querying and Managing Large Biodiversity Occurrence Datasets. R package version 0.4.7. https://CRAN.R-project.org/package=occCite.
## 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 (2021). 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 117.309. 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.
## Writing 6 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 (2021). KUBI Ichthyology Collection. Version 17.71. University of Kansas Biodiversity Institute. https://doi.org/10.15468/mgjasg. Accessed via GBIF on 2019-07-04.
## Bentley A (2021). KUBI Ichthyology Tissue Collection. Version 18.59. 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 54.36. 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 3.5.2. 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 162.256. 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 1.42. National Museum of Natural History, Smithsonian Institution. https://doi.org/10.15468/hnhrg3. Accessed via GBIF on 2019-07-04.
## Owens, H., Merow, C., Maitner, B., Kass, J., Barve, V., Guralnick, R. (2021). occCite: Querying and Managing Large Biodiversity Occurrence Datasets. R package version 0.4.7. https://CRAN.R-project.org/package=occCite.
## 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 117.309. 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.
## Writing 6 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Kajikia audax 
## 
## Australian Museum (2021). 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 3.5.2. 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 1.42. National Museum of Natural History, Smithsonian Institution. https://doi.org/10.15468/hnhrg3. Accessed via GBIF on 2019-07-04.
## Owens, H., Merow, C., Maitner, B., Kass, J., Barve, V., Guralnick, R. (2021). occCite: Querying and Managing Large Biodiversity Occurrence Datasets. R package version 0.4.7. https://CRAN.R-project.org/package=occCite.
## Queensland Museum (2021). 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 117.309. 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.
## Writing 6 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Tetrapturus angustirostris 
## 
## Australian Museum (2021). 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 150.267. 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 3.5.2. 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 162.256. 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.
## Owens, H., Merow, C., Maitner, B., Kass, J., Barve, V., Guralnick, R. (2021). occCite: Querying and Managing Large Biodiversity Occurrence Datasets. R package version 0.4.7. https://CRAN.R-project.org/package=occCite.
## Queensland Museum (2021). 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 117.309. Florida Museum of Natural History. https://doi.org/10.15468/8mjsel. Accessed via GBIF on 2019-07-04.
## South Australian Museum (2021). 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.
## Writing 6 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Tetrapturus belone 
## 
## Bentley A (2021). KUBI Ichthyology Collection. Version 17.71. 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 3.5.2. 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 162.256. 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.
## Owens, H., Merow, C., Maitner, B., Kass, J., Barve, V., Guralnick, R. (2021). occCite: Querying and Managing Large Biodiversity Occurrence Datasets. R package version 0.4.7. https://CRAN.R-project.org/package=occCite.
## 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 117.309. Florida Museum of Natural History. https://doi.org/10.15468/8mjsel. Accessed via GBIF on 2019-07-04.
## UMS PatriNat (OFB-CNRS-MNHN), Paris (2021). 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.
## Writing 6 Bibtex entries ... OK
## Results written to file 'temp.bib'
## Species: Tetrapturus georgii 
## 
## Bentley A (2021). KUBI Ichthyology Collection. Version 17.71. 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 3.5.2. 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 1.42. National Museum of Natural History, Smithsonian Institution. https://doi.org/10.15468/hnhrg3. Accessed via GBIF on 2019-07-04.
## Owens, H., Merow, C., Maitner, B., Kass, J., Barve, V., Guralnick, R. (2021). occCite: Querying and Managing Large Biodiversity Occurrence Datasets. R package version 0.4.7. https://CRAN.R-project.org/package=occCite.
## 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.
## Writing 6 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 3.5.2. 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.
## Owens, H., Merow, C., Maitner, B., Kass, J., Barve, V., Guralnick, R. (2021). occCite: Querying and Managing Large Biodiversity Occurrence Datasets. R package version 0.4.7. https://CRAN.R-project.org/package=occCite.
## 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 117.309. 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.