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 = NULL, col95 = "#FF00004D", col50 = "#0000FF4D",
  height = 0.7, legend = TRUE, ...)

add_boxplot(tree, trees = NULL, boxwex = 0.7, ...)

Arguments

tree: either an object of class phylo to which the confidences should be added or an object of class pml. In case of the later the tree is extracted from the object.
trees: phylogenetic trees, i.e. an object of class multiPhylo. Can be empty if tree is an object of class pml.
col95: colour used for the 95% intervals; by default: transparent red.
col50: colour used for the 50% intervals; by default: transparent blue.
height: the height of the boxes.
legend: a logical value.
...: arguments passed to other functions, legend or bxp.
boxwex: a scale factor to be applied to all boxes, see bxp.

Value

add_ci and add_boxplot return silently the tree object.

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)