Skip to contents

Simulating a phylogenetic trees through the birth-death process

Source: R/simulateTree.R
simulateTree.Rd

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.

Value

A phylo object

Details

see help page from diversitree::tree.bd

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.

See also

Other macroevolution: calcFossilDivTT(), checkAndFixUltrametric(), countSeqDiffs(), estimateSpeciation(), fitCRBD(), lttPlot(), plotPaintedWhales(), plotProteinSeq(), plotRawFossilOccs(), simulateBirthDeathRich()

Author

Daniel Rabosky, Matheus Januario, Jennifer Auler

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()