Removes or flags 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",
species = "species",
buffer = 100,
geod = TRUE,
ref = NULL,
verify = FALSE,
verify_mltpl = 10,
value = "clean",
verbose = TRUE
)Arguments
- x
data.frame. Containing geographical coordinates and species names.
- lon
character string. The column with the longitude coordinates. Default = “decimallongitude”.
- lat
character string. The column with the latitude coordinates. Default = “decimallatitude”.
- species
character string. The column with the species identity. Only required if verify = TRUE.
- buffer
numerical. The buffer around each institution, where records should be flagged as problematic, in decimal degrees. Default = 100m.
- geod
logical. If TRUE the radius around each capital is calculated based on a sphere, buffer is in meters and independent of latitude. If FALSE the radius is calculated assuming planar coordinates and varies slightly with latitude, in this case buffer is in degrees. Default = TRUE. See https://seethedatablog.wordpress.com/ for detail and credits.
- ref
SpatialPointsDataFrame. Providing the geographic gazetteer. Can be any SpatialPointsDataFrame, but the structure must be identical to
institutions. Default =institutions- verify
logical. If TRUE, records close to institutions are only flagged, if there are no other records of the same species in the greater vicinity (a radius of buffer * verify_mltpl).
- verify_mltpl
numerical. indicates the factor by which the radius for verify exceeds the radius of the initial test. Default = 10, which might be suitable if geod is TRUE, but might be too large otherwise.
- value
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 (“flagged”), with TRUE = test passed and FALSE = test failed/potentially problematic . Default = “clean”.
Details
Note: the buffer radius is in degrees, thus will differ slightly between different latitudes.
Examples
x <- data.frame(species = letters[1:10],
decimallongitude = runif(100, -180, 180),
decimallatitude = runif(100, -90,90))
#large buffer for demonstration, using geod = FALSE for shorter runtime
cc_inst(x, value = "flagged", buffer = 10, geod = FALSE)
#> Testing biodiversity institutions
#> Warning: GEOS support is provided by the sf and terra packages among others
#> Warning: Spatial object is not projected; GEOS expects planar coordinates
#> Flagged 47 records.
#> 1 2 3 4 5 6 7 8 9 10 11 12 13
#> TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
#> 14 15 16 17 18 19 20 21 22 23 24 25 26
#> TRUE FALSE FALSE TRUE FALSE FALSE FALSE FALSE TRUE TRUE FALSE TRUE TRUE
#> 27 28 29 30 31 32 33 34 35 36 37 38 39
#> TRUE TRUE FALSE FALSE FALSE TRUE TRUE FALSE TRUE FALSE TRUE FALSE TRUE
#> 40 41 42 43 44 45 46 47 48 49 50 51 52
#> FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE
#> 53 54 55 56 57 58 59 60 61 62 63 64 65
#> TRUE FALSE FALSE FALSE TRUE TRUE FALSE FALSE FALSE FALSE TRUE FALSE TRUE
#> 66 67 68 69 70 71 72 73 74 75 76 77 78
#> TRUE FALSE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE FALSE
#> 79 80 81 82 83 84 85 86 87 88 89 90 91
#> FALSE TRUE TRUE FALSE TRUE TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE
#> 92 93 94 95 96 97 98 99 100
#> TRUE TRUE FALSE TRUE TRUE TRUE FALSE FALSE FALSE
if (FALSE) {
#' cc_inst(x, value = "flagged", buffer = 50000) #geod = T
}