OccurrenceCleaner: fast quality flags for species occurrence records

An extension of CoordinateCleaner (Zizka et al. 2019) tailored to large-scale occurrence data: it runs that package's record tests with the same definitions and default buffers, up to the differences listed in vignette("coordinatecleaner", package = "OccurrenceCleaner"), and keeps every record. Each test writes one flag per record, so a cleaning rule is chosen afterwards as a query over the flags. See flag_occurrences() to flag a data frame or an on-disk table, flag_tests() for the bit each test sets, and tally_flags() to count what each test and rule removes.

Details

CoordinateCleaner by Alexander Zizka and co-authors supplies the record tests and what each one looks for, their default buffers, the outlier statistics and the raster approximation for species with many records, the dataset tests, the fossil tests, the choice of reference sources behind the gazetteers and the spatialvalid output layout; please cite Zizka et al. (2019) together with this package (citation("OccurrenceCleaner") gives both).

References

Zizka A, Silvestro D, Andermann T, et al. (2019) CoordinateCleaner: standardized cleaning of occurrence records from biological collection databases. Methods in Ecology and Evolution 10:744-751. doi:10.1111/2041-210X.13152

See also

Useful links:

• https://gillescolling.com/OccurrenceCleaner/

• https://github.com/gcol33/OccurrenceCleaner

• Report bugs at https://github.com/gcol33/OccurrenceCleaner/issues

Author

Maintainer: Gilles Colling gilles.colling051@gmail.com (ORCID) [copyright holder]

Authors:

• Gilles Colling gilles.colling051@gmail.com (ORCID) [copyright holder]