runExpoTree: Density-dependent likelihood caluculation

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/runExpoTree.R

Description

Calculates the density dependent likelihood of a phylogenetic tree. It takes branching and sampling times as an argument and integrates the likelihoood function over the whole tree.

Usage

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runExpoTree(pars,times,ttypes,survival=TRUE,shifts=NULL,vflag=0,
                        return.full=FALSE,rescale=TRUE,root.lineages=0)

Arguments

pars

Matrix of parameters. If the number of columns is larger than 5, only the first 5 columns are used. Each row is of the form c(N,beta,mu,psi,rho). The rows correspond to rate shifts.

times

Vector of event times.

ttypes

Vector of event types.

survival

Condition on the likelihood of observing the tree.

shifts

Times of rate shifts.

vflag

Verbosity level.

return.full

Return full probability vector rather than just the entry for I=1.

rescale

Rescale probability vector in the calculation. Avoids some numerical issues.

root.lineages

Number of lineages that are extant at the 'root' of the tree.

Details

Parameter matrix:

N = Total population size. Must be at least the maximal number of extant lineages at any given time.

beta = Branching rate. For epidemic trees, this is the infection rate. For species trees, this is the speciation rate.

mu = Extinction rate. For epidemic trees, this is the death/recovery rate. For species trees, this is the extinction rate.

psi = Sampling rate.

rho = Initial sampling rate.

Value

Log-Likelihood or vector of log-likelihoods.

Author(s)

Gabriel E Leventhal

References

Leventhal, Guenthard, Bonhoeffer & Stadler, 2013

See Also

expoTree

Examples

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times <- cumsum(runif(10))
ttypes <- rep(1,10)

N <- 15
beta <- 1
mu <- 0.1
psi <- 0
rho <- 1
pars <- matrix(c(N,beta,mu,psi,rho),nrow=1)
lik <- runExpoTree(pars,times,ttypes)

expoTree documentation built on May 29, 2017, 3:49 p.m.