plotThresh | R Documentation |
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 |
burnin |
number of generations (not samples) to exclude as burn in; if |
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 ( |
legend |
logical value or text to be plotted in the legend. |
... |
other arguments to be passed to |
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.
Liam Revell liam.revell@umb.edu
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.
ancThresh
, plot.phylo
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