Create a presence-absence matrix based on species' point occurrences

Convert species' occurrences into a presence-absence matrix based on a user-defined grid.

Usage

lets.presab.points(
  xy,
  species,
  xmn = NULL,
  xmx = NULL,
  ymn = NULL,
  ymx = NULL,
  resol = NULL,
  remove.cells = TRUE,
  remove.sp = TRUE,
  show.matrix = FALSE,
  crs = "+proj=longlat +datum=WGS84",
  count = FALSE
)

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.
xmn: Minimum longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
xmx: Maximum longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
ymn: Minimum latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
ymx: Maximum latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest). If NULL, limits will be calculated based on the limits of the shapes object.
resol: Numeric vector of length 1 or 2 to set the grid resolution. If NULL, resolution will be equivalent to 1 degree of latitude and longitude.
remove.cells: Logical, if TRUE the final matrix will not contain cells in the grid with a value of zero (i.e. sites with no species present).
remove.sp: Logical, if TRUE the final matrix will not contain species that do not match any cell in the grid.
show.matrix: Logical, if TRUE only the presence-absence matrix will be returned.
crs: Character representing the PROJ.4 type description of a Coordinate Reference System (map projection) of the polygons.
count: Logical, if TRUE a progress bar indicating the processing progress will be shown.

Value

The result is a list object of class PresenceAbsence with the following objects: Presence-Absence Matrix: A matrix of species' presence(1) and absence(0) information. The first two columns contain the longitude (x) and latitude (y) of the cells' centroid (from the gridded domain used); Richness Raster: A raster containing species richness data; Species name: A character vector with species' names contained in the matrix. *But see the optional argument show.matrix.

Details

The function creates the presence-absence matrix based on a raster file. Depending on the cell size, extension used and number of species it may require a lot of memory, and may take some time to process it. Thus, during the process, if count argument is set TRUE, a counting window will open so you can see the progress (i.e. in what polygon the function is working). Note that the number of polygons is not the same as the number of species that you have (i.e. a species may have more than one polygon/shapefiles).

Author

Bruno Vilela & Fabricio Villalobos

Examples

if (FALSE) { # \dontrun{
species <- c(rep("sp1", 100), rep("sp2", 100),
             rep("sp3", 100), rep("sp4", 100))
x <- runif(400, min = -69, max = -51)
y <- runif(400, min = -23, max = -4)
xy <- cbind(x, y)
PAM <- lets.presab.points(xy, species, xmn = -93, xmx = -29,
                          ymn = -57, ymx = 15)
summary(PAM)
# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Species richness map (simulated)")

# Map of the specific species
plot(PAM, name = "sp1")
} # }