RPANDA is another recently developed R package that allows us to fit different models of rate variation through time and select the best fitting model using maximum likelihood analysis.
RPANDA shows basically two main differences from BAMM:
In RPANDA, the user must inform which models are going to be tested, whereas in BAMM the program itself will average among the rates for each clade;
In RPANDA, the user must know a priori which are the clades that might show a particular diversification regime, while BAMM will estimate where rate shifts are positioned using a rjMCMC algorithm.
The package also contains some simuation functions as well as datasets. You can find more details on CRAN.
For this exercise, we will test four different scenarios with all combinations of constant and variable speciation and extinction rates as follows (based on Morlon et al. 2011, PNAS)
Read in the whale tree
library(ape)
library(RPANDA)## Loading required package: picante## Loading required package: vegan## Loading required package: permute## Loading required package: lattice## This is vegan 2.4-0## Loading required package: nlmewhales <- read.tree("whaletree.tre")
plot(whales, cex = 0.35)
nodelabels(cex = 0.5)