usdm (version 2.1-7)

plot.speciesLISA: Plot positional uncertainty based on LISA

Description

Plot the values of LISAs at species occurrence locations, which can be used to identify the locations that need positional uncertainty treatment.

Usage

# S4 method for speciesLISA,missing
plot(x, y, ...)
# S4 method for speciesLISA,SpatialPolygons
plot(x, y, ...)
# S4 method for speciesLISA,SpatialPolygonsDataFrame
plot(x, y, ...)

Value

plots the bubble plot.

Arguments

x

an object of class speciesLISA, which is the output of speciesLisa function.

y

optional. Boundary map of the study area, an object of class SpatialPolygons.

...

additional argument (see details)

Author

Babak Naimi

https://r-gis.net/

https://www.biogeoinformatics.org/

Details

This function generates a map (i.e. a bubble plot) in which the species points present the magnitude of LISA in predictors at the location as open or filled circles with different sizes.

Below are additional arguments:

cex the maximum symbol size (circle) in the plot. levels specifies the number of LISA levels at which the points are presented . xyLegend a vector with two numbers, specifying the coordinates of the legend. If missing, the function tries to find the appropriate location for it. ... xlab, ylab and main same as the base plot function.

See Also

speciesLisa, lisa

Examples

file <- system.file("external/predictors.tif", package="usdm")

r <- rast(file) # reading a RasterBrick object including 4 rasters in the Netherlands

r 

plot(r) # visualize the raster layers

sp.file <- system.file("external/species_nl.shp", package="usdm")
sp <- vect(sp.file)


splisa <- speciesLisa(x=r,y=sp,uncertainty=15000,weights=c(0.22,0.2,0.38,0.2))

splisa

plot(splisa)

bnd.file <- system.file("external/boundary.shp", package="usdm")
bnd <- vect(bnd.file) # reading the boundary map

plot(splisa,bnd)

#plot(splisa,bnd,levels=c(2,4,6,8))

#plot(splisa,bnd,levels=c(-5,-3,0,3,5))