Description Usage Arguments Details Value Author(s) See Also Examples
Convert species' ranges (in shapefile format) into a presence-absence matrix based on a user-defined grid system
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
shapes |
Object of class |
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 |
remove.sp |
Logical, if |
show.matrix |
Logical, if |
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). |
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 |
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).
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
.
Bruno Vilela & Fabricio Villalobos
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## 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)
|
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