base.line.values - Calculate face extinction and origination values from fossil species

This function will calculate the face extinction and origination values for extinct species following Foote (2005)

Function code can be found here. First we will load required packages, and simulate a phylogeny with lots of extinct species:

library(diversitree)
## Loading required package: deSolve
## Loading required package: ape
## Loading required package: subplex
## Loading required package: Rcpp
library(geiger)
library(phytools)
## Loading required package: maps
## Loading required package: rgl
 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:

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"))

plot of chunk unnamed-chunk-4

Gaps in the plot are due to periods of time where there are no fossils in the simulated phylogeny.