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Create a presence-absence matrix of species' geographic ranges within a grid for the Birdlife spatial data

Source: R/lets_presab_birds.R
lets.presab.birds.Rd

Convert species' ranges (in shapefile format and stored in particular folders) into a presence-absence matrix based on a user-defined grid. This function is specially designed to work with BirdLife Intl. shapefiles (https://www.birdlife.org). (Notice that new versions of birds spatial data are in a similar format to other groups and should be run using the lets.presab function. We will keep this function in case someone needs to use on the previous data format.)

Usage

lets.presab.birds(
  path,
  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

path

Path location of folders with one or more species' individual shapefiles. Shapefiles with more than one species will not work on this function. To use multi-species shapefiles see lets.presab.

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

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).

See also

plot.PresenceAbsence

lets.presab

lets.shFilter

Author

Bruno Vilela & Fabricio Villalobos

Examples

if (FALSE) { # \dontrun{
# Constructing a Presence/Absence matrix for birds
# Attention: For your own files, omit the 'system.file'
# and 'package="letsR"', these are just to get the path
# to files installed with the package.
path.Ramphastos <- system.file("extdata", package = "letsR")
PAM <- lets.presab.birds(path.Ramphastos, xmn = -93, xmx = -29,
                         ymn = -57, ymx = 25)

# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Ramphastos species Richness")

} # }