Package: CoordinateCleaner 3.0.1

Alexander Zizka

CoordinateCleaner: Automated Cleaning of Occurrence Records from Biological Collections

Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.

Authors:Alexander Zizka [aut, cre], Daniele Silvestro [ctb], Tobias Andermann [ctb], Josue Azevedo [ctb], Camila Duarte Ritter [ctb], Daniel Edler [ctb], Harith Farooq [ctb], Andrei Herdean [ctb], Maria Ariza [ctb], Ruud Scharn [ctb], Sten Svanteson [ctb], Niklas Wengstrom [ctb], Vera Zizka [ctb], Alexandre Antonelli [ctb], Bruno Vilela [ctb], Irene Steves [rev], Francisco Rodriguez-Sanchez [rev]

CoordinateCleaner_3.0.1.tar.gz
CoordinateCleaner_3.0.1.zip(r-4.5)CoordinateCleaner_3.0.1.zip(r-4.4)CoordinateCleaner_3.0.1.zip(r-4.3)
CoordinateCleaner_3.0.1.tgz(r-4.4-any)CoordinateCleaner_3.0.1.tgz(r-4.3-any)
CoordinateCleaner_3.0.1.tar.gz(r-4.5-noble)CoordinateCleaner_3.0.1.tar.gz(r-4.4-noble)
CoordinateCleaner_3.0.1.tgz(r-4.4-emscripten)CoordinateCleaner_3.0.1.tgz(r-4.3-emscripten)
CoordinateCleaner.pdf |CoordinateCleaner.html
CoordinateCleaner/json (API)
NEWS

# Install CoordinateCleaner in R:
install.packages('CoordinateCleaner', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

Datasets:
  • aohi - Artificial Hotspot Occurrence Inventory
  • buffland - Global Coastlines buffered by 1 degree
  • buffsea - Global Coastlines buffered by -1 degree
  • countryref - Country Centroids and Country Capitals
  • institutions - Global Locations of Biodiversity Institutions
  • pbdb_example - Example data from the Paleobiologydatabase

On CRAN:

25 exports 77 stars 4.38 score 66 dependencies 7 dependents 1.3k downloads

Last updated 4 months agofrom:ebd2b669d6b98369f98ff1e01d5970a5def53979 (via master)

Exports:cc_aohicc_capcc_cencc_councc_duplcc_equcc_gbifcc_instcc_iucncc_outlcc_seacc_urbcc_valcc_zerocd_ddmmcd_roundcf_agecf_equalcf_outlcf_rangeclean_coordinatesclean_datasetclean_fossilsis.spatialvalidwrite_pyrate

Dependencies:askpassclassclassIntclicolorspacecrulcurldata.tableDBIdplyre1071fansifarvergenericsgeosphereggplot2gluegtablehttpcodehttrisobandjsonliteKernSmoothlabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeoaiopensslpillarpkgconfigplyrproxyR6RColorBrewerRcpprgbifrlangrnaturalearths2scalessfspstringistringrsysterratibbletidyselecttriebeardunitsurltoolsutf8vctrsviridisLitewhiskerwithrwkxml2

Cleaning fossil data for the use in biogeography and palaeontology

Rendered fromCleaning_PBDB_fossils_with_CoordinateCleaner.Rmdusingknitr::rmarkdownon Jun 03 2024.

Last update: 2023-08-31
Started: 2018-06-05

Cleaning GBIF data for the use in biogeography

Rendered fromCleaning_GBIF_data_with_CoordinateCleaner.Rmdusingknitr::rmarkdownon Jun 03 2024.

Last update: 2023-10-24
Started: 2018-07-16

Comparison of CoordinateCleaner to other tools

Rendered fromComparison_other_software.Rmdusingknitr::rmarkdownon Jun 03 2024.

Last update: 2023-09-30
Started: 2020-10-09

Using customized gazetteers

Rendered fromUsing_custom_gazetteers.Rmdusingknitr::rmarkdownon Jun 03 2024.

Last update: 2023-08-31
Started: 2020-08-18

Readme and manuals

Help Manual

Help pageTopics
Artificial Hotspot Occurrence Inventoryaohi
Global Coastlines buffered by 1 degreebuffland
Global Coastlines buffered by -1 degreebuffsea
Identify Coordinates in Artificial Hotspot Occurrence Inventorycc_aohi
Identify Coordinates in Vicinity of Country Capitals.cc_cap
Identify Coordinates in Vicinity of Country and Province Centroidscc_cen
Identify Coordinates Outside their Reported Countrycc_coun
Identify Duplicated Recordscc_dupl
Identify Records with Identical lat/loncc_equ
Identify Records Assigned to GBIF Headquarterscc_gbif
Identify Records in the Vicinity of Biodiversity Institutionscc_inst
Identify Records Outside Natural Rangescc_iucn
Identify Geographic Outliers in Species Distributionscc_outl
Identify Non-terrestrial Coordinatescc_sea
Identify Records Inside Urban Areascc_urb
Identify Invalid lat/lon Coordinatescc_val
Identify Zero Coordinatescc_zero
Identify Datasets with a Degree Conversion Errorcd_ddmm
Identify Datasets with Rasterized Coordinatescd_round
Identify Fossils with Outlier Agecf_age
Identify Fossils with equal min and max agecf_equal
Identify Outlier Records in Space and Timecf_outl
Identify Fossils with Extreme Age Rangescf_range
Geographic Cleaning of Coordinates from Biologic Collectionsclean_coordinates summary.spatialvalid
Coordinate Cleaning using Dataset Propertiesclean_dataset
Geographic and Temporal Cleaning of Records from Fossil Collectionsclean_fossils
Country Centroids and Country Capitalscountryref
Global Locations of Biodiversity Institutionsinstitutions
Check spatialvalid objectis.spatialvalid
Example data from the Paleobiologydatabasepbdb_example
Plot Method for Class Spatialvalidplot.spatialvalid
Create Input Files for PyRatewrite_pyrate