# Plots results from the selectSpecies function This function plots results (species probabilities/optimum solutions) from the selectSpecies() function ```r 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() ## Returns 2D barplot of probabilities for each species or 3D barplot that illustrates probabilities of species located within a 2D trait space ## Examples ```r ### 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)) ```

plotProbs function