Exercise 11: State dependent diversification analysis using diversitree

In the following we will use the MuSSE method - a multi-state character extension of the BiSSE model - to test various hypotheses about diversification in the fish family Terapontidae.

First, we can load the packages that we will be using today. These consist of ape, diversitree, phytools, and geiger.

library(ape)
library (diversitree)
library(phytools)
## Loading required package: maps
library(geiger)

Next, download the two files we will be using for today’s exercise:

  1. Terapontidae.tre (the tree file).
  2. SSE.csv (the data file).
phy<-read.tree("Terapontidae.tre")
phy
## 
## Phylogenetic tree with 38 tips and 37 internal nodes.
## 
## Tip labels:
##  Terapon_jarbua, Pelsartia_humeralis, Mesopristes_cancellatus, Mesopristes_argenteus, Rhyncopelates_oxyrhynchus, Terapon_puta, ...
## 
## Rooted; includes branch lengths.
plotTree(phy,ftype="i")