Package: occCite 0.5.9

Hannah L. Owens

occCite: Querying and Managing Large Biodiversity Occurrence Datasets

Facilitates the gathering of biodiversity occurrence data from disparate sources. Metadata is managed throughout the process to facilitate reporting and enhanced ability to repeat analyses.

Authors:Hannah L. Owens [aut, cre], Cory Merow [aut], Brian Maitner [aut], Jamie M. Kass [aut], Vijay Barve [aut], Robert P. Guralnick [aut], Damiano Oldoni [rev]

occCite_0.5.9.tar.gz
occCite_0.5.9.zip(r-4.6)occCite_0.5.9.zip(r-4.5)occCite_0.5.9.zip(r-4.4)
occCite_0.5.9.tgz(r-4.5-any)occCite_0.5.9.tgz(r-4.4-any)
occCite_0.5.9.tar.gz(r-4.6-noble)occCite_0.5.9.tar.gz(r-4.5-noble)
occCite_0.5.9.tgz(r-4.4-emscripten)occCite_0.5.9.tgz(r-4.3-emscripten)
occCite.pdf |occCite.html✨
occCite/json (API)
NEWS

# Install 'occCite' in R:

install.packages('occCite', repos = c('https://packages.ropensci.org', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #407

Bug tracker:https://github.com/ropensci/occcite/issues

Pkgdown site:https://docs.ropensci.org

Datasets:

myOccCiteObject - Results of an occCite search for *Protea cynaroides*

On CRAN:

biodiversity-data biodiversity-informatics biodiversity-standards citations museum-collection-specimens museum-collections museum-metadata

7.30 score 23 stars 43 scripts 658 downloads 11 exports 119 dependencies

Last updated 6 months agofrom:c9299147f7 (on main). Checks:1 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Apr 23 2025
R-4.6-win	NOTE	Apr 23 2025
R-4.6-linux	NOTE	Apr 23 2025
R-4.5-win	NOTE	Apr 23 2025
R-4.5-mac	NOTE	Apr 23 2025
R-4.5-linux	NOTE	Apr 23 2025
R-4.4-win	NOTE	Apr 23 2025
R-4.4-mac	NOTE	Apr 23 2025

Exports:GBIFLogin GBIFLoginManager getBIENpoints getGBIFpoints occCitation occCiteData occCiteMap occQuery prevGBIFdownload studyTaxonList taxonRectification

Dependencies:ape askpass backports base64enc bib2df bibtex BIEN bslib cachem class classInt cli codetools colorspace cpp11 crosstalk crul curl data.table DBI digest doParallel dplyr DT e1071 evaluate extrafont extrafontdb fansi farver fastmap fontawesome foreach fs generics ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httpcode httpuv httr humaniformat isoband iterators jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leaflet leaflet.providers lifecycle lubridate magrittr MASS Matrix memoise mgcv mime munsell nlme oai openssl pillar pkgconfig plyr png promises proxy purrr R.methodsS3 R.oo R.utils R6 rappdirs raster RColorBrewer Rcpp RefManageR rgbif rlang rmarkdown RPostgreSQL Rttf2pt1 s2 sass scales sf sp stringi stringr sys terra tibble tidyr tidyselect timechange tinytex triebeard units urltools utf8 vctrs viridis viridisLite waffle whisker withr wk xfun xml2 yaml

Advanced search and citation of occurrences

Hannah L. Owens, Cory Merow, Brian Maitner, Jamie M. Kass, Vijay Barve, Robert Guralnick

Rendered fromb_Advanced.Rmdusingknitr::rmarkdownon Apr 23 2025.

Last update: 2022-03-15
Started: 2022-03-01

Simple search and citation of occurrences

Hannah L. Owens, Cory Merow, Brian Maitner, Jamie M. Kass, Vijay Barve, Robert Guralnick

Rendered froma_Simple.Rmdusingknitr::rmarkdownon Apr 23 2025.

Last update: 2024-10-28
Started: 2022-03-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
GBIFLogin Data Class	GBIFLogin GBIFLogin-class
GBIF Login Manager	GBIFLoginManager
Download occurrence points from BIEN	getBIENpoints
Download occurrences from GBIF	getGBIFpoints
Results of an occCite search for Protea cynaroides	myOccCiteObject
Occurrence Citations	occCitation
occCite Citation Class	occCiteCitation occCiteCitation-class
occCite Data Class	occCiteData occCiteData-class
Generating a map of downloaded points	occCiteMap
Query from Taxon List	occQuery
Plotting summary figures for occCite search results	plot.occCiteData
Download previously-prepared GBIF data sets	prevGBIFdownload
Print occCite citation object	print.occCiteCitation
Study Taxon List	studyTaxonList
Summary for occCite data objects	summary.occCiteData
Taxon Rectification	taxonRectification