README.md

occCite

IMPORTANT NOTE

The taxize package, which occCite uses for taxonRectification(), has been archived. To prevent occCite from being archived, which would result in downstream problems, we have disabled external taxonomic rectification as an option. If taxize comes back, or we identify an alternative, we will reinstate this feature.

Summary

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.

Please cite occCite. Run the following to get the appropriate citation for the version you’re using:

citation(package = "occCite")

## 
## Owens H, Merow C, Maitner B, Kass J, Barve V, Guralnick R (2024).
## _occCite: Querying and Managing Large Biodiversity Occurrence
## Datasets_. doi: 10.5281/zenodo.4726676 (URL:
## https://doi.org/10.5281/zenodo.4726676), R package version 0.5.9,
## <URL: https://CRAN.R-project.org/package=occCite>.
## 
## A BibTeX entry for LaTeX users is
## 
##   @Manual{,
##     title = {occCite: Querying and Managing Large Biodiversity Occurrence Datasets},
##     author = {Hannah Owens and Cory Merow and Brian Maitner and Jamie Kass and Vijay Barve and Robert Guralnick},
##     year = {2024},
##     note = {R package version 0.5.9},
##     url = {https://CRAN.R-project.org/package=occCite},
##     doi = {10.5281/zenodo.4726676},
##   }

Installation:

install.packages("occCite")

Or, install via r-universe

install.packages("occCite", repos = "https://ropensci.r-universe.dev")

Or, install github development version:

devtools::install_github("ropensci/occCite")

After using one of these options, you can load the package into your environment using:

library("occCite")

Getting Started

• occCite introduction vignette (https://ropensci.github.io/occCite/articles/a_Simple.html)
• occCite advanced feature vignette (https://ropensci.github.io/occCite/articles/b_Advanced.html)
• Function reference https://ropensci.github.io/occCite/reference/index.html
• YouTube tutorial (https://www.youtube.com/watch?v=7qSCULN_VjY&t=17s)
• Software note in Ecography (https://doi.org/10.1111/ecog.05618)

Meta

• Please adhere to the ROpenSci code of conduct.
• Please report any issues or bugs.
• We encourage you to contribute to occCite! See the contributor guide for more information.
• License: GPL-3
• Get citation information for occCite in R using citation(package = 'occCite')

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