lets.presab.points: Create a presence-absence matrix based on species' point...

In letsR: Data Handling and Analysis in Macroecology

Description

Convert species' occurrences into a presence-absence matrix based on a user-defined grid.

Usage

lets.presab.points(
  xy,
  species,
  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"),
  count = FALSE
)

Arguments

xy	A matrix with geographic coordinates of species occurrences, first column is the longitude (or x), and the second latitude (or y).
species	Character vector with species names, in the same order as the coordinates.
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 points.
count	Logical, if TRUE a counting window will open.

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 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 optional argument show.matrix.

Author(s)

Bruno Vilela & Fabricio Villalobos

See Also

plot.PresenceAbsence

lets.presab.birds

lets.presab

lets.shFilter

Examples

## Not run: 
species <- c(rep("sp1", 100), rep("sp2", 100),
             rep("sp3", 100), rep("sp4", 100))
x <- runif(400, min = -69, max = -51)
y <- runif(400, min = -23, max = -4)
xy <- cbind(x, y)
PAM <- lets.presab.points(xy, species, xmn = -93, xmx = -29, 
                          ymn = -57, ymx = 15)
summary(PAM)
# Species richness map
plot(PAM, xlab = "Longitude", ylab = "Latitude",
     main = "Species richness map (simulated)")

# Map of the specific species  
plot(PAM, name = "sp1")  

## End(Not run)

letsR documentation built on Oct. 27, 2020, 1:07 a.m.