letsR (version 1.0)

lets.presab: Shapefiles into a presence-absence matrix

Description

Convert species shapefiles into a presence-absence matrix.

Usage

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"), cover=0, presence=NULL,
origin=NULL, seasonal=NULL, count=FALSE)

Arguments

shapes

Object of class SpatialPolygonsDataFrame (see function readShapePoly to open these files). Species name should be in a column (within the .DBF table of the shapefile) called BINOMIAL or bi

xmx

Maximun longitude used to construct the grid in which the matrix will be based (i.e. the [gridded] geographic domain of interest)

xmn

Minimun longitude 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)

ymn

Minimun 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 shown.

crs

Character representign the PROJ.4 type description of a Coordinate Reference System (map projection).

cover

Porcentage 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 http://www.iucnredlist.org/technical-documents/spatial-data).

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 counting window will open.

Value

• The result is an 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 option 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.birds lets.shFilter

Examples

data(Phyllomedusa)  # Spatial distribution polygons of south american frogs of genus Phyllomedusa.
PAM <- lets.presab(Phyllomedusa, xmn=-93, xmx=-29, ymn= -57, ymx=15)
summary(PAM)
plot(PAM)  # Species richness map
plot(PAM, name="Phyllomedusa nordestina")  # Map of the specific species