CoordinateCleaner (version 1.0-7)

cc_inst: Flag Records in the Vicinity of Biodiversity Institutions

Description

Flag records assigned to the location of zoos, botanical gardens, herbaria, universities and museums, based on a global database of ~10,000 such biodiversity institutions. Coordinates from these locations can be related to data-entry errors, false automated geo-reference or individuals in captivity/horticulture.

Usage

cc_inst(x, lon = "decimallongitude", lat = "decimallatitude", 
        buffer = 0.001, ref = NULL, value = "clean", verbose = TRUE)

Arguments

x

a data.frame. Containing geographical coordinates and species names.

lon

a character string. The column with the longitude coordinates. Default = “decimallongitude”.

lat

a character string. The column with the longitude coordinates. Default = “decimallatitude”.

buffer

numerical. The buffer around each province or country centroid, where records should be flagged as problematic, in decimal degrees. Default = 0.001 (= ~ 100m).

ref

a SpatialPointsDataframe. Providing the geographic gazetteer. Can be any SpatialPointsDataframe, but the structure must be identical to institutions. Default = institutions

value

a character string. Defining the output value. See value.

verbose

logical. If TRUE reports the name of the test and the number of records flagged.

Value

Depending on the ‘value’ argument, either a data.frame containing the records considered correct by the test (“clean”) or a logical vector, with TRUE = test passed and FALSE = test failed/potentially problematic (“flags”). Default = “clean”.

Details

Note: the buffer radius is in degrees, thus will differ slightly between different latitudes.

Examples

# NOT RUN {
x <- data.frame(species = letters[1:10], 
                decimallongitude = runif(100, -180, 180), 
                decimallatitude = runif(100, -90,90))
                
cc_inst(x, buffer = 5)#large buffer for demonstration
cc_inst(x, value = "flags", buffer = 5)
# }