define.clade {PCPS} | R Documentation |
Define clade
Description
Function to define groups (clades) in a phylogenetic tree.
Usage
define.clade(tree, threshold, time, method = c("threshold", "time"))
Arguments
tree |
Phylogenetic tree. |
threshold |
A threshold value to form the groups. |
time |
A cutting height (age) to form the groups. |
method |
Method to define the clades, "threshold" or "time". |
Details
In the method threshold the total length of phylogenetic tree is used as cutting factor. If threshold is near to zero the cutting is near the root, if threshold near to one cutting is near the tips.
The phylogenetic tree must contain the node labels for the function work. Use the
makeNodeLabel
for defining node labels in a flexible way.
Value
clades |
Tips and their clades. |
height |
The cutting height (age). |
Author(s)
Vanderlei Julio Debastiani <vanderleidebastiani@yahoo.com.br>
See Also
Examples
require(ape)
tree<-makeNodeLabel(rcoal(10))
clades<-define.clade(tree, threshold = 0.8, method = "threshold")
clades
plot.phylo(tree, show.node.label = TRUE)
abline(v = clades$height)
[Package PCPS version 1.0.7 Index]