Draw Confidences Intervals on Phylogenies

These are low-level plotting commands to draw the confidence intervals on the node of a tree as rectangles with coloured backgrounds or add boxplots to ultrametric or tipdated trees.

Usage

add_ci(tree, trees, col95 = "#FF00004D", col50 = "#0000FF4D",
  height = 0.7, legend = TRUE, ...)

add_boxplot(tree, trees, ...)

Arguments

tree: a phylogenetic tree to which the confidences should be added.
trees: phylogenetic trees, i.e. an object of class `multiPhylo`
col95: colour used for the 95 red.
col50: colour used for the 50 blue.
height: the height of the boxes.
legend: a logical value.
...: arguments passed to other functions, legend or bxp.

Value

Nothing. Function is called for adding to a plot.

Details

All trees should to be rooted, either ultrametric or tip dated.

Author

Emmanuel Paradis, Santiago Claramunt, Joseph Brown, Klaus Schliep

Examples

data("Laurasiatherian")
dm <- dist.hamming(Laurasiatherian)
tree <- upgma(dm)
set.seed(123)
trees <- bootstrap.phyDat(Laurasiatherian,
                          FUN=function(x)upgma(dist.hamming(x)), bs=100)
tree <- plotBS(tree, trees, "phylogram")
add_ci(tree, trees, bty="n")

plot(tree, direction="downwards")
add_boxplot(tree, trees, boxwex=.7)