plot.speciesLisa: Plot positional uncertainty based on LISA

In babaknaimi/usdm: Uncertainty Analysis for Species Distribution Models

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

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)

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.

Value

plots the bubble plot.

Author(s)

Babak Naimi [e-mail]

https://r-gis.net/

https://www.biogeoinformatics.org/

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))

babaknaimi/usdm documentation built on Oct. 5, 2023, 9:27 p.m.