simulate_yule: Ranked topology with Birth-death process depths
In apTreeshape: Analyses of Phylogenetic Treeshape

Description Usage Arguments Value Author(s) References Examples

Simulates the ranked topology with node depths simulated using the constant birth-death process

1 2	simulate_yule(epsilon, alpha, beta, N, b, d, tmax = Inf, equal.ab = TRUE, eta = 1, lambda = NULL)

`epsilon`	Minimum size of unsampled splits (see appendix 1)
`alpha`	Clade age-richness index
`beta`	Imbalance index
`N`	Tip number
`b`	Birth rate
`d`	Death rate
`tmax`	Maximal crown age
`equal.ab`	If set to TRUE, all species have the same probability to go extinct first (default to TRUE)
`eta`	Clade abundance-richness index (if equal.ab == FALSE)
`lambda`	Optional, vector of lambda_epsilon returned by the function lambda_N. If set to NULL (the default) it will be computed inside the function

A phylo object with ranked shape drawn from our model, with an additional tip.ab field containing a vector of tip abundances.

Odile Maliet, Fanny Gascuel & Amaury Lambert

Maliet O., Gascuel F., Lambert A. (2018) Ranked tree shapes, non-random extinctions and the loss of phylogenetic diversity, bioRxiv 224295, doi: https://doi.org/10.1101/224295

# Simulate a tree
set.seed(813)
tree=simulate_yule(epsilon=0.001,alpha=-1,beta=-1,
                    N=20,equal.ab=FALSE,eta=1.5, b=1, d=0.5)

# Plot the tree with dots at tips that have sizes scaling with log abundance
tree$tip.label = rep(".", length(tree$tip.label))
plot.phylo(tree, show.node.label=TRUE, 
          cex=(log(tree$tip.ab)-min(log(tree$tip.ab)-0.1))*6/diff(range(log(tree$tip.ab))), adj=0.1)