4 \title{Remove Tips in a Phylogenetic Tree}
6 \code{drop.tip} removes the terminal branches of a phylogenetic tree,
7 possibly removing the corresponding internal branches.
9 \code{extract.clade} does the inverse operation: it keeps all the tips
10 from a given node, and deletes all the other tips.
13 drop.tip(phy, tip, trim.internal = TRUE, subtree = FALSE,
14 root.edge = 0, rooted = is.rooted(phy), interactive = FALSE)
15 extract.clade(phy, node, root.edge = 0, interactive = FALSE)
18 \item{phy}{an object of class \code{"phylo"}.}
19 \item{tip}{a vector of mode numeric or character specifying the tips
21 \item{trim.internal}{a logical specifying whether to delete the
22 corresponding internal branches.}
23 \item{subtree}{a logical specifying whether to output in the tree how
24 many tips have been deleted and where.}
25 \item{root.edge}{an integer giving the number of internal branches to
26 be used to build the new root edge. This has no effect if
27 \code{trim.internal = FALSE}.}
28 \item{rooted}{a logical indicating whether the tree must be treated as
29 rooted or not. This allows to force the tree to be considered as
30 unrooted (see examples).}
31 \item{node}{a node number or label.}
32 \item{interactive}{if \code{TRUE} the user is asked to select the tips
33 or the node by clicking on the tree which must be plotted.}
36 The argument \code{tip} can be either character or numeric. In the
37 first case, it gives the labels of the tips to be deleted; in the
38 second case the numbers of these labels in the vector
39 \code{phy$tip.label} are given.
41 This also applies to \code{node}, but if this argument is character
42 and the tree has no node label, this results in an error. If more than
43 one value is given with \code{node} (i.e., a vector of length two or
44 more), only the first one is used with a warning.
46 If \code{trim.internal = FALSE}, the new tips are given \code{"NA"} as
47 labels, unless there are node labels in the tree in which case they
50 If \code{subtree = TRUE}, the returned tree has one or several
51 terminal branches indicating how many tips have been removed (with a
52 label \code{"[x_tips]"}). This is done for as many monophyletic groups
53 that have been deleted.
55 Note that \code{subtree = TRUE} implies \code{trim.internal = TRUE}.
57 To undestand how the option \code{root.edge} works, see the examples
61 an object of class \code{"phylo"}.
63 \author{Emmanuel Paradis}
65 \code{\link{bind.tree}}, \code{\link{root}}
70 "Eopsaltriidae", "Acanthisittidae", "Pittidae", "Eurylaimidae",
71 "Philepittidae", "Tyrannidae", "Thamnophilidae", "Furnariidae",
72 "Formicariidae", "Conopophagidae", "Rhinocryptidae", "Climacteridae",
73 "Menuridae", "Ptilonorhynchidae", "Maluridae", "Meliphagidae",
74 "Pardalotidae", "Petroicidae", "Irenidae", "Orthonychidae",
75 "Pomatostomidae", "Laniidae", "Vireonidae", "Corvidae",
76 "Callaeatidae", "Picathartidae", "Bombycillidae", "Cinclidae",
77 "Muscicapidae", "Sturnidae", "Sittidae", "Certhiidae",
78 "Paridae", "Aegithalidae", "Hirundinidae", "Regulidae",
79 "Pycnonotidae", "Hypocoliidae", "Cisticolidae", "Zosteropidae",
80 "Sylviidae", "Alaudidae", "Nectariniidae", "Melanocharitidae",
81 "Paramythiidae","Passeridae", "Fringillidae")
82 plot(drop.tip(bird.families, tip))
83 plot(drop.tip(bird.families, tip, trim.internal = FALSE))
85 plot(drop.tip(bird.orders, 6:23, subtree = TRUE))
86 plot(drop.tip(bird.orders, c(1:5, 20:23), subtree = TRUE))
87 plot(drop.tip(bird.orders, c(1:20, 23), subtree = TRUE))
88 plot(drop.tip(bird.orders, c(1:20, 23), subtree = TRUE, rooted = FALSE))
89 ### Examples of the use of `root.edge'
90 tr <- read.tree(text = "(A:1,(B:1,(C:1,(D:1,E:1):1):1):1):1;")
91 drop.tip(tr, c("A", "B"), root.edge = 0) # = (C:1,(D:1,E:1):1);
92 drop.tip(tr, c("A", "B"), root.edge = 1) # = (C:1,(D:1,E:1):1):1;
93 drop.tip(tr, c("A", "B"), root.edge = 2) # = (C:1,(D:1,E:1):1):2;
94 drop.tip(tr, c("A", "B"), root.edge = 3) # = (C:1,(D:1,E:1):1):3;