lets.presab.birds: Create a presence-absence matrix of species' geographic...
In BrunoVilela/letsR: Data Handling and Analysis in Macroecology

lets.presab.birds

R Documentation

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

Description

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`	Minimun 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`	Maximun 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`	Minimun 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`	Maximun 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.

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).

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.

Author(s)

Bruno Vilela & Fabricio Villalobos

Examples

## Not run: 
# 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")


## End(Not run)

BrunoVilela/letsR documentation built on March 31, 2024, 11:25 p.m.