lagtime.batch {PhySim}R Documentation

Correct for lag-time to speciation along a series of phylogenetic trees

Description

Each node in a series of phylogenetic trees is classified as an interspecific or intraspecific phylogenetic split by drawing a lag-time to speciation randomly from a exponential distribution of lag-times. Beginning from the root of each tree, 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 intras-specific splits are pruned.

Usage

lagtime.batch(b, d, n, T, rate)

Arguments

b birth (speciation) rate under which trees are simulated
d death (extinction) rate under which trees are simulated
n number of trees in simulation
T time units trees simulated for
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.

Details

Reads in a file of trees simulated with parameters b, d, n and T using the command 'birthdeath.simulation'. If b and d are a list, then multiple files will be read.

Value

write a series of phylogenetic trees of class phylo, possessing only inter-specific splits, to a file with '.tree\_no\_extinct' extension.

Author(s)

Jason T. Weir

References

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

See Also

lagtime, to model a lag-time to speciation along a single phylogenetic tree.


[Package PhySim version 1.0 Index]