fuzzySim (version 3.7)

gridRecords: Grid (or thin) point occurrence records to the resolution of a raster map

Description

This function takes a Raster* or SpatRaster object and a set of spatial coordinates of a species' presence (and optionally absence) records, and returns a data frame with the presences and absences as well as the corresponding values of the rasters in the grid of pixels (cells). This is analogous to removing duplicates and thinning the points with a distance equal to the raster pixel size. If absences = TRUE (the default) and absence coordinates are not supplied, all pixels without any presence point are returned as absences.

Usage

gridRecords(rst, pres.coords, abs.coords = NULL, absences = TRUE, na.rm = TRUE)

Arguments

rst

a Raster* or SpatRaster object (the latter is processed faster) with the desired spatial resolution and extent for the species presence-absence data, and the layer(s) whose values to extract for those data.

pres.coords

a matrix or data frame with two columns containing, respectively, the x and y, or longitude and latitude coordinates (in this order, and in the same coordinate reference system as 'rst') of the points where species presence was detected.

abs.coords

(optional) same as 'pres.coords' but for points where the species was not detected. If NULL (the default), all pixels that are not intersected by 'pres.coords' will be output as absence cells.

absences

logical value indicating whether pixels without presence records should be returned as absences. The default is TRUE.

na.rm

Logical value indicating whether pixels without values in any of the 'rst' layers should be removed from the resulting data frame. The default is TRUE.

Value

This function returns a data frame with the following columns:

'presence'

integer, 1 for the cells (pixels) with at least one presence point, and 0 for the cells without any presence point (if absences = TRUE) or with at least one absence point (if 'abs.coords' are provided) AND with no presence points

'x', 'y'

centroid coordinates of each cell (pixel))

'cell'

the pixel identifier in 'rst'

one column for each layer in 'rst'

value of each pixel for each layer.

Details

See e.g. Baez et al. (2020), where this function was used to get unique presences and absences from point occurrence data at the spatial resolution of marine raster variables.

References

Baez J.C., Barbosa A.M., Pascual P., Ramos M.L. & Abascal F. (2020) Ensemble modelling of the potential distribution of the whale shark in the Atlantic Ocean. Ecology and Evolution, 10: 175-184

See Also

'extract' in package raster or in package terra

Examples

# NOT RUN {
# you can run the following code if you have the 'raster' package installed

# import a system raster with 3 layers and crop it to a smaller extent:
require(raster)
rst <- stack(system.file("external/rlogo.grd", package = "raster"))
ext <- extent(c(0, 15, 25, 40))
rst <- crop(rst, ext)
plot(rst)
plot(rst[[1]])

# generate some random presence and absence points:
set.seed(123)
presences <- sp::spsample(as(ext, "SpatialPolygons"), 50, type = "random")
absences <- sp::spsample(as(ext, "SpatialPolygons"), 50, type = "random")
points(presences, pch = 20, cex = 0.2, col = "black")
points(absences, pch = 20, cex = 0.2, col = "white")

# use 'gridRecords' on these random points:
gridded_pts <- gridRecords(rst, coordinates(presences), coordinates(absences))
head(gridded_pts)  # 'red', 'green' and 'blue' are the names of the layers in 'rst'

# plot them to check the result:
pres_coords <- gridded_pts[gridded_pts$presence == 1, c("x", "y")]
abs_coords <- gridded_pts[gridded_pts$presence == 0, c("x", "y")]
points(gridded_pts[ , c("x", "y")], pch = 4, cex = 0.6, col = gridded_pts$presence)

# you can also do it with only presence (no absence) records:
gridded_pres <- gridRecords(rst, coordinates(presences))
head(gridded_pres)
plot(rst[[1]])
points(presences, pch = 20, cex = 0.2, col = "black")
pres_coords <- gridded_pres[gridded_pres$presence == 1, c("x", "y")]
abs_coords <- gridded_pres[gridded_pres$presence == 0, c("x", "y")]
points(gridded_pres[ , c("x", "y")], pch = 4, cex = 0.6, col = gridded_pres$presence)
# }