Package: OccurrenceCleaner
Title: Fast Quality Checks for Species Occurrence Records
Version: 0.2.0
Authors@R: 
    person("Gilles", "Colling", , "gilles.colling051@gmail.com",
           role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0003-3070-6066"))
Description: An extension of 'CoordinateCleaner' (Zizka et al. 2019
        <doi:10.1111/2041-210X.13152>) tailored to large-scale species
        occurrence data. Flags common problems in occurrence records,
        such as coordinates at country centroids, capitals or
        biodiversity institutions, zero or equal coordinates, records
        at sea, in the wrong country or outside the species range,
        duplicates, outliers within a species, and datasets with
        converted or gridded coordinates, with the test definitions and
        default buffers of 'CoordinateCleaner' apart from documented
        differences. It also reads the quality warnings GBIF attaches
        to each record, the basis of record and the establishment
        means, and checks records at sea or on land against the habitat
        of their genus from the Interim Register of Marine and
        Nonmarine Genera. Records are flagged and kept, and users
        choose afterwards which flags to filter on. Data frames of a
        few million records are flagged in seconds, and GBIF snapshots
        of billions of records are processed by reading Parquet files
        in chunks.
License: MIT + file LICENSE
URL: https://gillescolling.com/OccurrenceCleaner/,
        https://github.com/gcol33/OccurrenceCleaner
BugReports: https://github.com/gcol33/OccurrenceCleaner/issues
Depends: R (>= 4.1.0)
Imports: graphics, grDevices, Rcpp, tools, utils, vectra (>= 0.13.0)
LinkingTo: Rcpp
Suggests: CoordinateCleaner, geosphere, ggplot2, knitr, maps,
        rmarkdown, rnaturalearth, rnaturalearthdata, sf, svglite,
        terra, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.1.0
Collate: 'OccurrenceCleaner-package.R' 'RcppExports.R' 'group.R'
        'flag.R' 'clean.R' 'columns.R' 'data.R' 'flag_tests.R'
        'habitat.R' 'methods.R' 'progress.R' 'pyrate.R' 'reference.R'
        'shapefile.R' 'spatialvalid.R' 'store.R' 'stream.R' 'tally.R'
        'test-docs.R'
Repository: https://gcol33.r-universe.dev
Date/Publication: 2026-10-17 09:59:47 UTC
RemoteUrl: https://github.com/gcol33/OccurrenceCleaner
RemoteRef: HEAD
RemoteSha: 2cd91fa1c7c56cb661564ea680c4c4350115df2a
NeedsCompilation: yes
Packaged: 2026-10-17 14:00:08 UTC; root
Author: Gilles Colling [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-3070-6066>)
Maintainer: Gilles Colling <gilles.colling051@gmail.com>