R: Tree plotting with posterior probabilities of ancestral...

plotThresh {phytools}

R Documentation

Tree plotting with posterior probabilities of ancestral states from the threshold model

Plots estimated posterior probabilities at nodes under the threshold model.

plotThresh(tree, x, mcmc, burnin=NULL, piecol, tipcol="input", legend=TRUE, 
   ...)

`tree`	phylogenetic tree.
`x`	a named vector containing discrete character states; or a matrix containing the tip species, in rows, and probabilities of being in each state, in columns.
`mcmc`	list object returned by `ancThresh`.
`burnin`	number of generations (not samples) to exclude as burn in; if `NULL` then 20% of generations are excluded as burn-in.
`piecol`	a named vector containing the colors for the posterior probabilities plotted as pie charts at internal nodes.
`tipcol`	a string indicating whether the tip colors should be based on the input data (`"input"`) or sampled tip liabilities (`"estimated"`). These will only differ if there is uncertainty in the tip states.
`legend`	logical value or text to be plotted in the legend.
`...`	other arguments to be passed to `plot.phylo` - `label.offset` should be >0 so that tip labels and species names do not overlap.

This function uses the object returned by ancThresh to plot the posterior probabilities of ancestral states under the threshold model.

It is also called internally by ancThresh.

Plots a tree.

Revell, L. J. (2014) Ancestral character estimation under the threshold model from quantitative genetics. Evolution, 68, 743-759.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.