jbd_coordCountryInconsistent {BeeBDC}

Flags coordinates that are inconsistent with the stated country name

Description

Compares stated country name in an occurrence record with record's coordinates using rnaturalearth data. The prefix, jbd_ is meant to distinguish this function from the original bdc::bdc_coordinates_country_inconsistent(). This functions will preferably use the countryCode and country_suggested columns generated by bdc::bdc_country_standardized(); please run it on your dataset prior to running this function.

Usage

jbd_coordCountryInconsistent(
  data = NULL,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  scale = 50,
  pointBuffer = 0.01,
  stepSize = 1e+06,
  mc.cores = 1
)

Arguments

data

A data frame or tibble. Occurrence records as input.

lon

Character. The name of the column to use as longitude. Default = "decimalLongitude".

lat

Character. The name of the column to use as latitude. Default = "decimalLatitude".

scale

Numeric or character. To be passed to rnaturalearth::ne_countries()'s scale. Scale of map to return, one of 110, 50, 10 or "small", "medium", "large". Smaller values return higher-resolution maps.

pointBuffer

Numeric. Amount to buffer points, in decimal degrees. If the point is outside of a country, but within this point buffer, it will not be flagged. Default = 0.01.

stepSize

Numeric. The number of occurrences to process in each chunk. Default = 1000000.

mc.cores

Numeric. If > 1, the st_intersects function will run in parallel using mclapply using the number of cores specified. If = 1 then it will be run using a serial loop. NOTE: Windows machines must use a value of 1 (see ?parallel::mclapply). Additionally, be aware that each thread can use large chunks of memory. Default = 1.

Value

The input occurrence data with a new column, .coordinates_country_inconsistent

Examples

if(requireNamespace("rnaturalearthdata")){
beesRaw_out <- jbd_coordCountryInconsistent(
  data = BeeBDC::beesRaw,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  scale = 50,
  pointBuffer = 0.01)
} # END if require