Object of class SpatialPolygonsDataFrame (see function readShapePoly
to open these files) containing the distribution of one or more species.
Species names should be in a column (within the .DBF table of the shapefile)
called BINOMIAL/binomial or SCINAME/sciname.
xmn
Minimun longitude used to construct the grid in which the matrix will be based
(i.e. the [gridded] geographic domain of interest)
xmx
Maximun longitude used to construct the grid in which the matrix will be based
(i.e. the [gridded] geographic domain of interest)
ymn
Minimun latitude used to construct the grid in which the matrix will be based
(i.e. the [gridded] geographic domain of interest)
ymx
Maximun latitude used to construct the grid in which the matrix will be based
(i.e. the [gridded] geographic domain of interest)
resol
Numeric vector of length 1 or 2 to set the grid resolution.
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 representign the PROJ.4 type description of
a Coordinate Reference System (map projection) of the polygons.
crs.grid
Character representign 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
Porcentage of the cell covered by the shapefile that will be considered for presence
(values between 0 and 1). This option is only available when the coordinates
are in degrees (longitude/latitude).
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 counting window will open.
Details
The 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 so you can see the progress
(i.e. in what polygon/shapefile 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
See Also
plot.PresenceAbsence
lets.presab.birds
lets.shFilter
Examples
## Not run:
# Spatial distribution polygons of south american frogs
# of genus Phyllomedusa.
data(Phyllomedusa)
PAM <- lets.presab(Phyllomedusa, xmn = -93, xmx = -29,
ymn = -57, ymx = 15)
summary(PAM)
# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
main = "Phyllomedusa species richness")
# Map of the specific species
plot(PAM, name = "Phyllomedusa nordestina")
## End(Not run)
providing 
.