View source: R/is.monophyletic.R
is.monophyletic | 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 |
tips |
a vector of mode numeric or character specifying the tips to be tested. |
reroot |
a logical. If |
plot |
a logical. If |
... |
further arguments passed to |
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
which.edge
, drop.tip
, mrca
.
## 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"))
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