Create a presence-absence matrix based on species' point occurrences within a user's grid shapefile (beta version)

Convert species' occurrences points into a presence-absence matrix based on a grid in shapefile format.

Usage

lets.presab.grid.points(xy, species, grid, sample.unit, remove.sp = TRUE)

Arguments

xy: A matrix with geographic coordinates of species occurrences, first column is the longitude (or x), and the second latitude (or y).
species: Character vector with species names, in the same order as the coordinates.
grid: Object of class SpatVector (see function terra::vect) representing the spatial grid (e.g. regular/irregular cells, political divisions, hexagonal grids, etc). The grid and the shapefiles must be in the same projection.
sample.unit: Object of class character with the name of the column (in the grid) representing the sample units of the presence absence matrix.
remove.sp: Logical, if TRUE the final matrix will not contain species that do not match any cell in the grid.

Value

The result is a list containing two objects:

(I) A matrix the species presence (1) and absence (0) values per sample unity.

(II) The original grid.

Details

This function is an alternative way to create a presence absence matrix when users already have their own grid.

Author

Bruno Vilela & Fabricio Villalobos

Examples

if (FALSE) { # \dontrun{
# Species polygons
data("wrld_simpl")

# Grid
crs = "+proj=longlat +datum=WGS84 +no_defs"
sp.r <- terra::as.polygons(terra::rast(
  resol = 5,
  crs = crs,
  xmin = -93,
  xmax = -29,
  ymin = -57,
  ymax = 15
))
sp.r$ID <- 1:length(sp.r)

# Occurrence Points
N = 20
species <- c(rep("sp1", N), rep("sp2", N),
             rep("sp3", N), rep("sp4", N))
x <- runif(N * 4, min = -69, max = -51)
y <- runif(N * 4, min = -23, max = -4)
xy <- cbind(x, y)

# PAM
resu <- lets.presab.grid.points(xy, species, sp.r, "ID")

# Plot
rich_plus1 <- rowSums(resu$PAM[, -1, drop = FALSE]) + 1
colfunc <- colorRampPalette(c("#fff5f0", "#fb6a4a", "#67000d"))
colors <- c("white", colfunc(max(rich_plus1)))
occs <- terra::vect(xy, crs = crs)
plot(resu$grid, border = "gray40",
     col = colors[rich_plus1])
plot(sf::st_geometry(wrld_simpl), add = TRUE)
plot(occs, cex = 0.5, col = rep(1:4, each = N), add = T)
} # }