Create a presence-absence matrix of species' geographic ranges within a grid

Convert species' ranges (in shapefile format) into a presence-absence matrix based on a user-defined grid system

Usage

lets.presab(
  shapes,
  xmn = NULL,
  xmx = NULL,
  ymn = NULL,
  ymx = NULL,
  resol = NULL,
  remove.cells = TRUE,
  remove.sp = TRUE,
  show.matrix = FALSE,
  crs = "+proj=longlat +datum=WGS84",
  crs.grid = crs,
  cover = 0,
  presence = NULL,
  origin = NULL,
  seasonal = NULL,
  count = FALSE
)

Arguments

shapes: Object of class SpatVect or Spatial (see packages terra and sf to read these files) containing the distribution of one or more species. Species names should be stored in the object as BINOMIAL/binomial or SCINAME/sciname.
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.
crs.grid: Character representing the PROJ.4 type description of a Coordinate Reference System (map projection) for the grid. Note that when you change this options you may probably change the extent coordinates and the resolution.
cover: Percentage of the cell covered by the shapefile that will be considered for presence (values between 0 and 1).
presence: A vector with the code numbers for the presence type to be considered in the process (for IUCN spatial data https://www.iucnredlist.org/resources/spatial-data-download, see metadata).
origin: A vector with the code numbers for the origin type to be considered in the process (for IUCN spatial data).
seasonal: A vector with the code numbers for the seasonal type to be considered in the process (for IUCN spatial data).
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

This function creates the presence-absence matrix based on a raster object. 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 to display the progress (i.e. the polygon/shapefile that the function is working on). Note that the number of polygons is not the same as the number of species (i.e. a species may have more than one polygon/shapefiles).

Author

Bruno Vilela & Fabricio Villalobos

Examples

if (FALSE) { # \dontrun{
# Spatial distribution polygons of South American frogs
# of genus Phyllomedusa.
data(Phyllomedusa)
PAM <- lets.presab(Phyllomedusa)
summary(PAM)
# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Phyllomedusa species richness")
# Map of individual species
plot(PAM, name = "Phyllomedusa nordestina")
} # }