simulateTree: Simulating a phylogenetic trees through the birth-death...

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Simulating a phylogenetic trees through the birth-death process

Description

simulateTree uses a birth-death process to simulate a phylogenetic tree, following the format of ape package's phylo object. The function is basically a wrapper for the diversitree's tree.bd function.

Usage

simulateTree(
  pars,
  max.taxa = Inf,
  max.t,
  min.taxa = 2,
  include.extinct = FALSE
)

Arguments

pars	numeric vector with the simulation parameters: speciation (first slot) and extinction (second slot) rates, respectively. Should follow any formats stated in the function tree.bd from the diversitree package.
max.taxa	Maximum number of taxa to include in the tree. If Inf, then the tree will be evolved until max.t time has passed.
max.t	Maximum length to evolve the phylogeny over. If equal to Inf, then the tree will evolve until max.taxa extant taxa are present.
min.taxa	Minimum number of taxa to include in the tree.
include.extinct	A logical indicating if extinct taxa should be included in the final phylogeny.

Details

see help page from diversitree::tree.bd

Value

A phylo object

Author(s)

Daniel Rabosky, Matheus Januario, Jennifer Auler

References

Paradis, E. (2012). Analysis of Phylogenetics and Evolution with R (Vol. 2). New York: Springer.

Popescu, A. A., Huber, K. T., & Paradis, E. (2012). ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics, 28(11), 1536-1537.

FitzJohn, R. G. (2010). Analysing diversification with diversitree. R Packag. ver, 9-2.

FitzJohn, R. G. (2012). Diversitree: comparative phylogenetic analyses of diversification in R. Methods in Ecology and Evolution, 3(6), 1084-1092.

Examples

S <- 1
E <- 0
set.seed(1)
phy <- simulateTree(pars = c(S, E), max.taxa = 6, max.t=Inf)
ape::plot.phylo(phy)
ape::axisPhylo()

# alternatively, we can stop the simulation using time:
set.seed(42)
phy2 <- simulateTree(pars = c(S, E), max.t=7)
ape::plot.phylo(phy2)
ape::axisPhylo()

evolved documentation built on April 3, 2025, 9:23 p.m.