lagtime {PhySim}R Documentation

Correction for lag-time to speciation along a phylogeny

Description

Each node is classified as an interspecific or intraspecific phylogenetic split by drawing a lag-time to speciaton randomly from a exponential distribution of lag-times. Beginning from the root, once a node is classified as a intraspecific split all of its daughter lineages keep the same classification in order to maintain species as monophyletic. All nodes classified as intra-specific splits are pruned.

Usage

lagtime(phy, rate)

Arguments

phy a phylogenetic tree of class phylo
rate the average lag-time to speciation. 1 / rate is the rate parameter of the exponential distribution used to model speciation along a phylogenetic tree.

Value

returns a phylogenetic tree of class phylo, possessing only inter-specific splits.

Author(s)

Jason T. Weir

References

Weir, J. T. and Schluter, D. 2007. Science in press

See Also

lagtime.batch, to model a lag-time to speciation for a batch of phylogenetic trees

Examples

 #Apply an average lag-time of 1
 tree <- birthdeath.tree(b=0.3, d=0, T=10)
 tree2 <- lagtime(phy=tree, rate = 1)

[Package PhySim version 1.0 Index]