tess.sim.age: tess.sim.age: Simulate a reconstructed tree for a given age...

In hoehna/TESS: Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events

Description

tess.sim.age simulates a reconstructed phylogenetic tree under a global, time-dependent birth-death process conditioned on the age of the tree. The rates may be any positive function of time or a constant. The process starts at time 0 and goes forward in time, hence the rates and events should be interpreted in the time after the origin. Additionally, mass-extinction event can be provided and a uniform taxon sampling probability. It is possible to start either with the origin (1 species) or with the most recent common ancestor (2 species).

Usage

tess.sim.age(n, age, lambda, mu, massExtinctionTimes = c(), 
   massExtinctionSurvivalProbabilities = c(), samplingProbability = 1, 
   samplingStrategy = "uniform", maxTaxa = Inf, MRCA = TRUE)

Arguments

n	Number of simulations.
age	The age of the tree, i.e. the time to simulate.
lambda	The speciation rate function or constant.
mu	The extinction rate function or constant.
massExtinctionTimes	The set of mass-extinction times after the start of the process.
massExtinctionSurvivalProbabilities	The set of survival probabilities for each speciation event. The set must have the same length as the set of mass-extinction times.
samplingProbability	The probability for a species to be included in the sample.
samplingStrategy	The strategy how samples were obtained. Options are: uniform|diversified.
maxTaxa	The maximum number of possible taxa. If by chance a higher number is simulated, than simply ntaxa=maxTaxa. This is useful when too large trees should be simulated because this takes too much time and memory.
MRCA	Does the process start with the most recent common ancestor?

Value

Returns a set of trees in 'phylo' format.

Author(s)

Sebastian Hoehna

References

S. Hoehna: Fast simulation of reconstructed phylogenies under global, time-dependent birth-death processes. 2013, Bioinformatics, 29:1367-1374

Examples

l <- function(x) { if (x > 0.5 || x < 0.3) { return (1) } else { return (2) } }
e <- function(x) { if (x > 0.5 || x < 0.3) { return (0.95) } else { return (0.5) } }

tess.sim.age(n=1,age=1,l,e,MRCA=TRUE)

# simulation under constant rates
tess.sim.age(n=1,age=1,2.0,1.0,MRCA=TRUE)

hoehna/TESS documentation built on Feb. 3, 2022, 5:59 a.m.