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Function to thin longitude and latitude data

Source: R/clean_dup.R
clean_dup.Rd

Cleans up duplicated or redundant occurrence records that present overlapping longitude and latitude coordinates. Thinning can be performed using either a geographical distance threshold or a pixel neighborhood approach.

Usage

clean_dup(
  data,
  longitude,
  latitude,
  threshold = 0,
  by_mask = FALSE,
  raster_mask = NULL,
  n_ngbs = 0
)

Arguments

data

A data.frame with longitude and latitude of occurrence records.

longitude

A character vector indicating the column name of the "longitude" variable.

latitude

A character vector indicating the column name of the "latitude" variable.

threshold

A numeric value representing the distance threshold between coordinates to be considered duplicates. Units depend on whether by_mask is T or F. If T, the user needs to specify the number of pixels that define the neighborhood of duplicates (see n_ngbs parameter).

by_mask

Logical. If T, the thinning process will use a raster layer as a mask for defining distance in pixel units.

raster_mask

An object of class SpatRaster that serves as a reference to thin the occurrence data. Required if by_mask is T.

n_ngbs

Number of pixels used to define the neighborhood matrix that helps determine which occurrences are duplicates:

  • 0 removes occurrences within the same pixel, keeping one.

  • 1 considers duplicates all occurrences within a distance of one pixel.

  • n considers duplicates all occurrences within a distance of n pixels.

Value

Returns a data.frame with cleaned occurrence records, excluding duplicates based on the specified criteria.

Details

This function cleans up duplicated occurrences based on the specified distance threshold. If by_mask is T, the distance is interpreted as pixel distance using the provided raster_mask; otherwise, it is interpreted as geographic distance.

Examples

data(abronia)
tempora_layers_dir <- system.file("extdata/bio",package = "tenm")
tenm_mask <- terra::rast(file.path(tempora_layers_dir,"1939/bio_01.tif"))
# Clean duplicates without raster mask (just by distance threshold)
# First check the number of occurrence records
print(nrow(abronia))
#> [1] 106
# Clean duplicated records using a distance of ~ 18 km (0.1666667 grades)
ab_1 <- tenm::clean_dup(data =abronia,
                        longitude = "decimalLongitude",
                        latitude = "decimalLatitude",
                        threshold = terra::res(tenm_mask),
                        by_mask = FALSE,
                        raster_mask = NULL)
# Check number of records
print(nrow(ab_1))
#> [1] 10
# Clean duplicates using a raster mask
ab_2 <- tenm::clean_dup(data =abronia,
                        longitude = "decimalLongitude",
                        latitude = "decimalLatitude",
                        threshold = terra::res(tenm_mask)[1],
                        by_mask = TRUE,
                        raster_mask = tenm_mask,
                        n_ngbs = 1)
# Check number of records
print(nrow(ab_2))
#> [1] 9