bdc_coordinates_transposed: Identify transposed geographic coordinates

In brunobrr/bdc: Biodiversity Data Cleaning

Identify transposed geographic coordinates

Description

This function flags and corrects records when latitude and longitude appear to be transposed.

Usage

bdc_coordinates_transposed(
  data,
  id = "database_id",
  sci_names = "scientificName",
  lat = "decimalLatitude",
  lon = "decimalLongitude",
  country = "country",
  countryCode = "countryCode",
  border_buffer = 0.2,
  save_outputs = FALSE
)

Arguments

data	data.frame. Containing a unique identifier for each record, geographical coordinates, and country names. Coordinates must be expressed in decimal degrees and WGS84.
id	character string. The column name with a unique record identifier. Default = "database_id".
sci_names	character string. The column name with species scientific name. Default = "scientificName".
lat	character string. The column name with latitude. Coordinates must be expressed in decimal degrees and WGS84. Default = "decimalLatitude".
lon	character string. The column with longitude. Coordinates must be expressed in decimal degrees and WGS84. Default = "decimalLongitude".
country	character string. The column name with the country assignment of each record. Default = "country".
countryCode	character string. The column name with an ISO-2 country code.
border_buffer	numeric >= 0. A distance in decimal degrees used to created a buffer around the country. Records within a given country and at a specified distance from the border will be not be corrected. Default = 0.2 (~22 km at the equator).
save_outputs	logical. Should a table containing transposed coordinates saved for further inspection? Default = FALSE.

Details

This test identifies transposed coordinates resulted from mismatches between the country informed for a record and coordinates. Transposed coordinates often fall outside of the indicated country (i.e., in other countries or in the sea). Different coordinate transformations are performed to correct country/coordinates mismatches. Importantly, verbatim coordinates are replaced by the corrected ones in the returned database. A database containing verbatim and corrected coordinates is created in "Output/Check/01_coordinates_transposed.csv" if save_outputs == TRUE. The columns "country" and "countryCode" can be retrieved by using the function bdc_country_standardized.

Value

A data.frame containing the column "coordinates_transposed" indicating if verbatim coordinates were not transposed (TRUE). Otherwise records are flagged as (FALSE) and, in this case, verbatim coordinates are replaced by corrected coordinates.

See Also

Other prefilter: bdc_basisOfRecords_notStandard(), bdc_coordinates_country_inconsistent(), bdc_coordinates_empty(), bdc_coordinates_from_locality(), bdc_coordinates_outOfRange(), bdc_country_standardized(), bdc_scientificName_empty()

Examples

## Not run: 
id <- c(1, 2, 3, 4)
scientificName <- c(
  "Rhinella major", "Scinax ruber",
  "Siparuna guianensis", "Psychotria vellosiana"
)
decimalLatitude <- c(63.43333, -14.43333, -41.90000, -46.69778)
decimalLongitude <- c(-17.90000, -67.91667, -13.25000, -13.82444)
country <- c("BOLIVIA", "bolivia", "Brasil", "Brazil")

x <- data.frame(
  id, scientificName, decimalLatitude,
  decimalLongitude, country
)

# Get country code
x <- bdc_country_standardized(data = x, country = "country")

bdc_coordinates_transposed(
  data = x,
  id = "id",
  sci_names = "scientificName",
  lat = "decimalLatitude",
  lon = "decimalLongitude",
  country = "country_suggested",
  countryCode = "countryCode",
  border_buffer = 0.2,
  save_outputs = FALSE 
) 

## End(Not run)

brunobrr/bdc documentation built on Nov. 21, 2024, 4:18 a.m.