simulate_tree: Simulates ranked topology

In bcm-uga/apTreeshape: Analyses of Phylogenetic Treeshape

Description

Simulates a ranked topology with tip abundance data from the beta alpha eta model

Usage

simulate_tree(epsilon, alpha, beta, N, equal.ab = TRUE, eta = 1, lambda = NULL)

Arguments

epsilon	Minimum size of unsampled splits (see appendix 1)
alpha	Clade age-richness index
beta	Imbalance index
N	Tip number
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

Value

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

Branch lengths are so that node depths are in 1:(n-1)

Author(s)

Odile Maliet, Fanny Gascuel & Amaury Lambert

References

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

Examples

# Simulate a tree
set.seed(813)
tree=simulate_tree(epsilon=0.001,alpha=2,beta=-1,N=20,equal.ab=FALSE,eta=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)

bcm-uga/apTreeshape documentation built on Sept. 26, 2019, 4:56 p.m.