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},
## }
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")
occCite
! See the
contributor guide
for more information.occCite
in R using
citation(package = 'occCite')
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