Convert species' ranges (in shapefile format) into a presence-absence matrix based on a user-defined grid system
lets.presab(
shapes,
xmn = -180,
xmx = 180,
ymn = -90,
ymx = 90,
resol = 1,
remove.cells = TRUE,
remove.sp = TRUE,
show.matrix = FALSE,
crs = CRS("+proj=longlat +datum=WGS84"),
crs.grid = crs,
cover = 0,
presence = NULL,
origin = NULL,
seasonal = NULL,
count = FALSE
)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.
Minimun longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest)
Maximun longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest)
Minimun latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest)
Maximun latitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest)
Numeric vector of length 1 or 2 to set the grid resolution.
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).
Logical, if TRUE the final matrix will not contain species that
do not match any cell in the grid.
Logical, if TRUE only the presence-absence matrix will be returned.
Character representign the PROJ.4 type description of a Coordinate Reference System (map projection) of the polygons.
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.
Porcentage of the cell covered by the shapefile that will be considered for presence (values between 0 and 1).
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).
A vector with the code numbers for the origin type to be considered in the process (for IUCN spatial data).
A vector with the code numbers for the seasonal type to be considered in the process (for IUCN spatial data).
Logical, if TRUE a counting window will open.
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.
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).
# 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")
# }
# NOT RUN {
# }
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