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Last data update: 2014.03.03

R: Plot lineages through time.

plotLTT

R Documentation

Plot lineages through time.

Description

Creates a (or adds to an existing) plot of the lineages-through-time of a list of phylogenetic trees.

Usage

plotLTT(trees,col=rgb(.5,.5,.5,.5),xlab="Time", ylab="Lineages",log="y",add=FALSE,
        plot=TRUE,plot.tree=NA,type="s",...)

Arguments

`trees`	A list of trees in two-column format. Column 1 is the branching/sampling time and column two is the event type (1 = branching, 0 = sampling)
`col`	Color of the lineages.
`xlab`	x-axis label.
`ylab`	y-axis label.
`log`	Use logarithmic axis (defaults to logarithmic y-axis).
`add`	Add the lineages to the current plotting device.
`plot`	If set to FALSE, only the number of lineages at each time point are returned.
`plot.tree`	Plot the phylogenetic tree in the background. Only works for one tree.
`type`	Line type. Defaults to steps 's'.
`...`	Other parameters to pass to 'plot()'.

Author(s)

Gabriel E Leventhal

References

Leventhal, Bonhoeffer, Guenthard & Stadler, 2012

Examples

  N <- 100
  beta <- 1
  mu <- 0.1
  psi <- 0.4
  nsamp <- 100

  epis <- lapply(1:10,function(i) sim.epi(N,beta,mu,psi,nsamp))
  trees <- lapply(epis,function(x) cbind(x$times,x$ttypes))
  plotLTT(trees)