This function will calculate the face extinction and origination values for extinct species following Foote (2005)
First we will load required packages, and simulate a phylogeny with lots of extinct species:
library(diversitree)
library(geiger)
library(phytools)
pars <- c(0.2, 0.2, 0.07, 0.05, 0.03, 0.03)
set.seed(12)
phy <- tree.bisse(pars, max.taxa=150, x0=0, include.extinct=TRUE)The function expects species names that can be distinguished from each other. Due to the way which diversitree labels extinct taxa, we will generate some arbitrary (nonsense) names for our taxa.
for(i in 1:length(phy$tip.label)){
text <- paste("Species_",sample(letters[1:26],1),sample(letters[1:26],1),sample(letters[1:26],1),sample(letters[1:26],1),sample(letters[1:26],1))
text <- gsub(" ","",text)
phy$tip.label[i] <- text
}Now it is possible to load and run the function. Function arguments are: * phy - An object of class phylo or multiphylo. If of class multiphylo average values for origination and extinction will be calculated across from all phylogenies. * bin.size - Interval size in millions of years to estimate origination and extinction values * value - Can either be "origination" or "extinction" respectively
source("base.line.values.R")
extinction.results <- base.line.values(phy, bin.size=2, value="extinction")
origination.results <- base.line.values(phy, bin.size=2, value="origination")Visualizing the results:
plot(extinction.results$bin.age, extinction.results$Face.value.extinction, pch=19, xlab="Age (Mya)",ylab="Relative Rate")
lines(extinction.results$bin.age, extinction.results$Face.value.extinction)
points(origination.results$bin.age, origination.results$Face.value.origination, col="red",pch=19)
lines(origination.results$bin.age, origination.results$Face.value.origination, col="red")
legend("topright",c("Origination Rate","Extinction Rate"), lwd=rep(2,2),col=c("red","black"))
Gaps in the plot are due to periods of time where there are no fossils in the simulated phylogeny.