`"diversitree"`

(FitzJohn 2012)

*Example 1: the simple BiSSE model*

The binary-state speciation and extinction (BiSSE) model is a powerful framework to model and analyze diversification where the speciation and extinction rates vary with respect to a binary trait (taking values 0 or 1) which itself evolves under a Markov model (see detailed description in the book). We define the parameter values such that the speciation rate is the same for both states (λ = 0.1), the extinction rate (μ) is larger for species in state 0 (0.05) than in state 1 (0.01), and the transition from 0 → 1 is slower than the transition 1 → 0 (0.05 and 0.1, respectively).

library(diversitree) pars <- c(0.1, 0.1, 0.05, 0.01, 0.05, 0.1) res <- tree.bisse(pars, max.taxa = 100) res

## ## Phylogenetic tree with 100 tips and 99 internal nodes. ## ## Tip labels: ## sp5, sp8, sp9, sp10, sp16, sp17, ... ## Node labels: ## nd1, nd2, nd3, nd6, nd7, nd9, ... ## ## Rooted; includes branch lengths.

The output is a tree which can be plotted or further examined with the
usual functions in `ape`

. Furthermore, this tree has additional
elements specific to the simulations. For instance, we can see that
most species are in state 0 at the end of the simulation:

table(res$tip.state)

## ## 0 1 ## 65 35

Thus, even though species in state 0 go extinct faster than those in state 1, they are more abundant because state 1 is more unstable.

- FitzJohn RG (2012) Diversitree: comparative phylogenetic analyses of diversification in R. Methods in Ecology and Evolution 3:1084-1092