| is.monophyletic {ape} | R Documentation |
This function tests whether a list of tip labels is monophyletic on a given tree.
is.monophyletic(phy, tips, reroot = !is.rooted(phy), plot = FALSE, ...)
phy |
a phylogenetic tree description of class "phylo".
|
tips |
a vector of mode numeric or character specifying the tips to be tested. |
reroot |
a logical. If FALSE, then the input tree is not unrooted before the test.
|
plot |
a logical. If TRUE, then the tree is plotted with the specified group tips highlighted.
|
... |
further arguments passed to plot.
|
If phy is rooted, the test is done on the rooted tree, otherwise
the tree is first unrooted, then arbitrarily rerooted, in order to be
independent on the current position of the root. That is, the test
asks if tips could be monophyletic given any favourably rooting
of phy.
If phy is unrooted the test is done on an unrooted tree, unless
reroot = FALSE is specified.
If tip labels in the list tips are given as characters, they need
to be spelled as in the object phy.
TRUE or FALSE.
Johan Nylander jnylander@users.sourceforge.net
## Test one monophyletic and one paraphyletic group on the bird.orders tree
## Not run: data("bird.orders")
## Not run: is.monophyletic(phy = bird.orders, tips = c("Ciconiiformes", "Gruiformes"))
## Not run: is.monophyletic(bird.orders, c("Passeriformes", "Ciconiiformes", "Gruiformes"))