getCoord: Get Working Geographical Coordinates

In LimaRAF/plantR: Managing Species Records from Biological Collections

Get Working Geographical Coordinates

Description

This function assess the availability and precision of the original geographical coordinates of the occurrence and it replaces missing coordinates by the coordinates obtained from the gazetteer.

Usage

getCoord(
  x,
  lat.orig = "decimalLatitude",
  lon.orig = "decimalLongitude",
  lat.gazet = "latitude.gazetteer",
  lon.gazet = "longitude.gazetteer",
  res.gazet = "resolution.gazetteer",
  lat.new = "decimalLatitude.new",
  lon.new = "decimalLongitude.new",
  rm.gazet = FALSE
)

Arguments

x	a data.frame containing the original coordinates and the coordinates obtained from a gazetteer.
lat.orig	character. The name of the column containing the latitude. Default to "decimalLatitude".
lon.orig	character. The name of the column containing the longitude. Default to "decimalLongitude".
lat.gazet	character. The name of the column containing the latitude from the gazetteer. Default to "latitude.gazetteer".
lon.gazet	character. The name of the column containing the longitude from the gazetteer. Default to "longitude.gazetteer".
res.gazet	character. The name of the column containing the resolution of the locality information from which the gazetteer coordinates were obtained.
lat.new	character. The name of the column containing the edited latitude, combining the coordinates from the source data and the gazetteer. Default to "decimalLatitude.new".
lon.new	character. The name of the column containing the working longitude combining the coordinates from the source data and the gazetteer. Default to "decimalLongitude.new".
rm.gazet	logical. Should the coordinates form the gazetteer be removed from the data after the replacement of missing coordinates? Default to FALSE.

Details

The function was initially designed as part of a routine to edit and validate geographical coordinates of plant occurrence data. It is possible to use it separately, but it may be easier to use it under the workflow presented in plantR tutorial (see functions getLoc and prepCoord). If used separately, users should provide a data frame preferably with the following six columns (the defaults): 'decimalLatitude', 'decimalLongitude', 'latitude.gazetteer', 'longitude.gazetteer', 'resolution.gazetteer', 'decimalLatitude.new' and 'decimalLongitude.new') or to specify the respective columns in the input data.

The columns lat.new and lon.new are the columns containing the working coordinates that may have been already edited by prepCoord(). It is also the columns were the function will store the coordinates from the gazetteer in the case of missing coordinates. If these columns are not provided in the input data, they are assumed to be equal to lat.orig and lon.orig and they are created internally.

The precision of the geographical coordinates are classified as: "degrees", "minutes", "seconds" and "miliseconds". This classification is performed for the latitude and longitude of each record and the worst precision retrieved is assigned to both of them (i.e. if lat = "minutes" and lon= "seconds", the precision = "minutes"). For simplicity, all latitude/longitude not classified as "degrees", "minutes" or "seconds" are classified as "miliseconds".

The function implicitly assumes that NA coordinates are missing and they are replaced by the coordinates coming from the gazetteer. See the examples below.

Value

The data frame x with the columns 'decimalLatitude.new' and 'decimalLongitude.new' containing the geographical coordinates at the best locality resolution (i.e. 'administrative level') available. The function also returns the precision of the coordinates.

Author(s)

Renato A. F. de Lima

See Also

getLoc and prepCoord.

Examples

(coords <- data.frame(decimalLatitude = c(-23.5, -23.475389, NA),
                     decimalLongitude = c(-47.166667, -47.123768, NA),
                     latitude.gazetteer = c(-23.524052, -23.524052, -23.524052),
                     longitude.gazetteer = c(-47.122207, -47.122207, -47.122207),
                     resolution.gazetteer = c("county", "county", "county"),
                     decimalLatitude.new = c(-23.5, -23.475389, NA),
                     decimalLongitude.new = c(-47.166667,-47.123768, NA)
                     ))

getCoord(coords)

LimaRAF/plantR documentation built on Jan. 1, 2023, 10:18 a.m.