is.monophyletic: Is Group Monophyletic
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Author(s) See Also Examples

This function tests whether a list of tip labels is monophyletic on a given tree.

1	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

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"))

gjuggler/ape documentation built on May 17, 2019, 6:03 a.m.