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CoordinateCleaner (version 1.0-7)

Automated Cleaning of Occurrence Records from Biological Collections

Description

Automated cleaning of geographic species occurrence records by automated flagging of problems common to biodiversity data from biological collections. 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. See for more details and tutorials.

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Version

Install

install.packages('CoordinateCleaner')

Monthly Downloads

1,292

Version

1.0-7

License

GPL-3

Maintainer

Last Published

March 23rd, 2018

Functions in CoordinateCleaner (1.0-7)

cc_cap

Flag Coordinates in Vicinity of Country Capitals.
CleanCoordinates

Geographic Cleaning of Coordinates from Biologic Collections
cc_dupl

Flag Duplicated Records
CleanCoordinatesDS

Geographic Coordinate Cleaning based on Dataset Properties
cc_cen

Flag Coordinates in Vicinity of Country and Province Centroids
cc_sea

Flag Non-terrestrial Coordinates
cc_coun

Flag Coordinates Outside their Reported Country
CoordinateCleaner-package

CoordinateCleaner
WritePyRate

Create Input Files for PyRate
cc_equ

Flag Records with Identical lat/lon
cc_urb

Flag Records Inside Urban Areas
cc_gbif

Flag Records Assigned to GBIF Headquarters
countryref

Country Centroids and Country Capitals
capitals

Global Capital Locations
cc_inst

Flag Records in the Vicinity of Biodiversity Institutions
centroids

Global Country and Province Centroids
cc_val

Check Coordinate Validity in lat/lon
CleanCoordinatesFOS

Geographic and Temporal Cleaning of Records from Fossil Collections
cc_outl

Flag Geographic Outliers in Species Distributions
cc_zero

Flag Zero Coordinates
tc_range

Flag Fossils with Extreme Age Ranges
tc_equal

Flag Fossils with equal min and max age
tc_outl

Flag Fossil Outlier Records in Space and Time
plot.spatialvalid

Plot Method for Class Spatialvalid
dc_ddmm

Flag Datasets with a Degree Conversion Error
institutions

Global Locations of Biodiversity Institutions
dc_round

Flags Datasets with Rasterized Coordinates
landmass

Global Coastlines