plotSimmap.mcmc: Plot a phylogenetic tree with posterior probabilities from a...
In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Description Usage Arguments

Plot a phylogenetic tree with posterior probabilities from a bayouMCMC chain (function adapted from phytools' plotSimmap)

plotSimmap.mcmc(chain, burnin = NULL, lwd = 1, edge.type = c("regimes",
  "theta", "none", "pp"), pal = rainbow, pp.cutoff = 0.3, circles = TRUE,
  circle.cex.max = 3, circle.col = "red", circle.pch = 21,
  circle.lwd = 0.75, circle.alpha = 100, pp.labels = FALSE, pp.col = 1,
  pp.alpha = 255, pp.cex = 0.75, edge.color = 1,
  parameter.sample = 1000, ...)

`chain`	A bayouMCMC chain
`burnin`	The proportion of runs to be discarded, if NULL, then the value stored in the bayouMCMC chain's attributes is used
`lwd`	The width of the edges
`edge.type`	Either "theta" (branches will be colored according to their median value of theta), "regimes" (clades will be assigned to distinct regimes if the posterior probability of a shift on that branch is > pp.cutoff), or "pp" (branches will be colored according to the probability of a shift on that branch). If "none" then edge.color will be assigned to all branches.
`pal`	A color palette function used to paint the branches (unless edge.type="none")
`pp.cutoff`	If edge.type=="regimes", the posterior probability above which a shift should be reconstructed on the tree.
`circles`	a logical value indicating whether or not a circle should be plotted at the base of the node with values that correspond to the posterior probability of having a shift.
`circle.cex.max`	The cex value of a circle with a posterior probability of 1
`circle.col`	The color used to fill the circles
`circle.pch`	the type of symbol used to plot at the node to indicate posterior probability
`circle.lwd`	the line width of the points plotted at the nodes
`circle.alpha`	a value between 0 and 255 that indicates the transparency of the circles (255 is completely opaque).
`pp.labels`	a logical indicating whether the posterior probability for each branch should be printed above the branch
`pp.col`	The color used for the posterior probability labels
`pp.alpha`	a logical or numeric value indicating transparency of posterior probability labels. If TRUE, then transparency is ramped from invisible (pp=0), to black (pp=1). If numeric, all labels are given the same transparency. If NULL, then no transparency is given.
`pp.cex`	the size of the posterior probability labels
`edge.color`	The color of edges if edge.type="none"
`parameter.sample`	When edge.type=="theta", the number of samples used to estimate the median "theta" value from each branch. Since this is computationally intensive, this enables you to downsample the chain.
`...`	Additional arguments passed to ape's plot.phylo