plotSuitabilityToProba: Visualise the function that was used to transform...

In virtualspecies: Generation of Virtual Species Distributions

Visualise the function that was used to transform environmental suitability into probability of occurrence

Description

This function plots the relationships between the environmental suitability and the probability of occurrence, which is used to generate the presence- absence distribution. It requires the output from convertToPA.

Usage

plotSuitabilityToProba(sp, add = FALSE, ...)

Arguments

sp	the output from convertToPA.
add	TRUE or FALSE. If TRUE, the relationship will be added to the currently active graph.
...	further arguments to be passed to plot. See plot and par.

Author(s)

Boris Leroy [e-mail]

Examples

# Create an example stack with two environmental variables
a <- matrix(rep(dnorm(1:100, 50, sd = 25)), 
            nrow = 100, ncol = 100, byrow = TRUE)
env <- c(rast(a * dnorm(1:100, 50, sd = 25)),
         rast(a * 1:100))
names(env) <- c("variable1", "variable2")

parameters <- formatFunctions(variable1 = c(fun = 'dnorm', mean = 1e-04, 
                                             sd = 1e-04),
                              variable2 = c(fun = 'linearFun', a = 1, b = 0))
# Generation of the virtual species
sp1 <- generateSpFromFun(env, parameters)
sp1


# Converting to presence-absence, probablistic method, logistic conversion
# A species with a low prevalence:

sp1.lowprev <- convertToPA(sp1, species.prevalence = 0.1)
plotSuitabilityToProba(sp1.lowprev)

# A species with a high prevalence:

sp1.highprev <- convertToPA(sp1, species.prevalence = 0.9)
plotSuitabilityToProba(sp1.lowprev)

# Converting to presence-absence, probablistic method, linear conversion
# A species with a low prevalence:

sp1.lowprev <- convertToPA(sp1, species.prevalence = 0.1,
                           prob.method = "linear")
plotSuitabilityToProba(sp1.highprev)

# A species with a high prevalence:

sp1.highprev <- convertToPA(sp1, species.prevalence = 0.9,
                           prob.method = "linear")
plotSuitabilityToProba(sp1.highprev)

virtualspecies documentation built on Sept. 27, 2023, 1:06 a.m.