add_ci: Draw Confidences Intervals on Phylogenies

In phangorn: Phylogenetic Reconstruction and Analysis

Draw Confidences Intervals on Phylogenies

Description

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.

Details

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

Author(s)

Emmanuel Paradis, Santiago Claramunt, Joseph Brown, Klaus Schliep

See Also

plot.phylo, plotBS

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")
tree <- plotBS(tree, trees, "phylogram")
add_ci(tree, trees)
plot(tree, direction="downwards")
add_boxplot(tree, trees, boxwex=.7)

phangorn documentation built on Jan. 23, 2023, 5:37 p.m.