plotProbs {Select}

Plots results from the selectSpecies function

Description

This function plots results (species probabilities/optimum solutions) from the selectSpecies() function

Usage

plotProbs(result, traits, colors = c("lightblue", "blue"), xlim = NULL,
  ylim = NULL, xlab = NULL, ylab = NULL, zlab = "Probability",
  distance = 0.3, cex.lab = 1.5, box.col = "transparent", xbase = 0.5,
  ybase = 0.5, ...)

Arguments

result

A saved object from function selectSpecies()

traits

A matrix of trait values where traits are columns and rows are species. If one trait is provided, then the function creates a 2D barplot of probabilities for each species. If two traits are provided, then the function creates a 3D barplot that illustrates probabilities of species located within a 2D trait space.

colors

An optional vector of colors for plotting that must include at least two valid color names. The default color scheme is a ramp palette of lightblue to blue.

xlim

Vector of two numbers denoting limits on x-axis.

ylim

Vector of two numbers denoting limits on y-axis.

xlab

Character string to describe x-axis.

ylab

Character string to describe y-axis.

zlab

Character string to describe z-axis. The default axis names is "Probabilities".

distance

An optional number denoting distance between bars in 3d plot.

cex.lab

An optional number denoting the size of the labels. The default is set to 1.5.

box.col

An optional setting for the color of the box. The default setting is transparent.

xbase

The length of the base of each 3d bar along the x-axis

ybase

The length of the base of each 3d bar along the y-axis

...

Additional arguments to pass to barplot() or lattice::cloud()

Value

2D barplot of probabilities for each species or 3D barplot that illustrates probabilities of species located within a 2D trait space

Examples

### 1 trait constraint with maximum functional diversity and entropy
Spp <- 5 #S = number of species
trait <- as.matrix(data.frame(trait=c(1:Spp)))
rownames(trait) <- c(letters[1:nrow(trait)])
result1 <- selectSpecies(t2c=trait, constraints=c(3.5), t2d=trait, obj="QH", capd=FALSE)
plotProbs(result1,trait, xlab="Trait")

##### 2 traits: Constrain trait X to value 2.5, diversify trait Y
traitX <- matrix(c(rep(1,3),rep(2,3),rep(3,3)))
traitY <- matrix(c(rep(c(1,2,3),3)))
rownames(traitX) <- c(letters[1:9]); colnames(traitX) <- c("traitX")
rownames(traitY) <- c(letters[1:9]); colnames(traitY) <- c("traitY")
result2 <- selectSpecies(t2c=traitX,constraints=c(traitX=2.5),t2d=traitY,capd=TRUE,obj="QH")
plotProbs(result2,traits = cbind(traitX, traitY))