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Filter GBIF Records by Grid Cell

Source: R/obs_filter.R
obs_filter.Rd

Reduce the spatial density of a getGBIF object by retaining a single record per grid cell and, optionally, removing cells with too few records.

Usage

obs_filter(gbifs, grid, threshold = NULL)

Arguments

gbifs

getGBIF object containing one or more species.

grid

Raster. Defining the target spatial resolution and extent. Accepted classes are SpatRaster, RasterLayer, RasterBrick, and RasterStack.

threshold

Optional integer. Specifying the minimum number of records a cell must contain to be retained.

Value

A data frame with the columns Species, x, and y, representing the filtered coordinates.

Details

The function first collapses each species to one occurrence per grid cell. If threshold is supplied, cells with fewer than that many original records are then discarded.

Examples

if (FALSE) { # \dontrun{
# Load data
shp.path <- paste0(
  system.file(package = "gbif.range"),
  "/extdata/shp_lonlat.shp"
)
shp.lonlat <- terra::vect(shp.path)
rst.path <- paste0(
  system.file(package = "gbif.range"),
  "/extdata/rst_enl.tif"
)
rst <- terra::rast(rst.path)

# Download observations for two plant species in the European Alps
obs.arcto <- get_gbif(
  sp_name = "Arctostaphylos alpinus",
  geo = shp.lonlat
)
obs.saxi <- get_gbif(
  sp_name = "Saxifraga cernua",
  geo = shp.lonlat
)

# Test plot
terra::plot(shp.lonlat)
graphics::points(
  obs.arcto[, c("decimalLongitude","decimalLatitude")],
  pch = 20,
  col = "#238b4550",
  cex = 1
)
graphics::points(
  obs.saxi[, c("decimalLongitude","decimalLatitude")],
  pch = 20,
  col = "#99000d50",
  cex = 1
)

# Combine both datasets
both.sp <- rbind(obs.arcto,obs.saxi)

# Run function
obs.filt <- obs_filter(gbifs = both.sp, grid = rst, threshold = 4)

# Check new points
terra::plot(shp.lonlat)
graphics::points(
  obs.filt[obs.filt$Species%in%"Arctostaphylos alpinus",c("x","y")],
  pch = 20,
  col = "#238b4550",
  cex = 1
)
graphics::points(
  obs.filt[obs.filt$Species%in%"Saxifraga cernua",c("x","y")],
  pch = 20,
  col = "#99000d50",
  cex = 1
)
} # }