validateCoord: Spatial Validation of Species Records

In LimaRAF/plantR: Managing Species Records from Biological Collections

Spatial Validation of Species Records

Description

This function performs the crossing of the geographical coordinates with the world and Latin-american maps, and it checks for coordinates falling near the sea shore, open sea and country boundaries. It also test if problematic coordinates are not inverted or swapped. Finally, the function searches for records taken from cultivated individuals and for the presence of spatial outliers for each species.

Usage

validateCoord(
  x,
  lon = "decimalLongitude.new",
  lat = "decimalLatitude.new",
  low.map = "plantR",
  high.map = "plantR",
  country.shape = "NAME_0",
  country.gazetteer = "country.gazet",
  tax.name = "scientificName.new",
  output = "same.col"
)

Arguments

x	a data frame with the species records and their coordinates in decimal degrees.
lon	Name of the column with the longitude to be validated. Default to 'decimalLongitude.new'
lat	Name of the column with the latitude to be validated. Default to 'decimalLatitude.new'
low.map	a sf multipolygon object containing the global administrative map at the lowest level (e.g. country). The default is "plantR", the default map obtained from [GADM]https://gadm.org (see worldMap).
high.map	a sf multipolygon object or a list of sf objects containing the regional map at the highest administrative level (e.g. municipality). The default is "plantR", the map for all Latin American countries and dependent territories obtained [GADM]https://gadm.org (see latamMap).
country.shape	Name of the column with the country name obtained from the world map based on the original record coordinates. Default to 'NAME_0'
country.gazetteer	Name of the column with the country name obtained from the gazetteer, based on the description of the record locality. Default to 'loc.correct'
tax.name	character. Name of the columns containing the species name. Default to "scientificName.new"
output	a character string with the type of output desired: 'new.col' (columns with the new results for each type of validation added to the input data) or 'same.col' (results are stored only in overwritten into column geo.check). Default to 'same.col'.

Details

The function works similarly to a wrapper function, where the individuals steps of the proposed plantR workflow for the validation of the spatial information associated to each record (e.g. geographical coordinates) are performed altogether (see the plantR tutorial for details).

Value

The input data frame, plus the new columns with the results of the geographical coordinates (e.g. 'geo.check').

Author(s)

Andrea Sánchez-Tapia, Sara R. Mortara & Renato A. F. de Lima

See Also

checkCoord, checkBorders, checkShore, checkInverted, checkOut, getCult

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