1 ## dist.topo.R (2009-07-06)
3 ## Topological Distances, Tree Bipartitions,
4 ## Consensus Trees, and Bootstrapping Phylogenies
6 ## Copyright 2005-2009 Emmanuel Paradis
8 ## This file is part of the R-package `ape'.
9 ## See the file ../COPYING for licensing issues.
11 dist.topo <- function(x, y, method = "PH85")
13 if (method == "BHV01" && (is.null(x$edge.length) || is.null(y$edge.length)))
14 stop("trees must have branch lengths for Billera et al.'s distance.")
15 n <- length(x$tip.label)
16 bp1 <- .Call("bipartition", x$edge, n, x$Nnode, PACKAGE = "ape")
17 bp1 <- lapply(bp1, function(xx) sort(x$tip.label[xx]))
18 ## fix by Tim Wallstrom:
19 bp2.tmp <- .Call("bipartition", y$edge, n, y$Nnode, PACKAGE = "ape")
20 bp2 <- lapply(bp2.tmp, function(xx) sort(y$tip.label[xx]))
21 bp2.comp <- lapply(bp2.tmp, function(xx) setdiff(1:n, xx))
22 bp2.comp <- lapply(bp2.comp, function(xx) sort(y$tip.label[xx]))
26 if (method == "PH85") {
30 if (identical(bp1[[i]], bp2[[j]]) |
31 identical(bp1[[i]], bp2.comp[[j]])) {
37 dT <- q1 + q2 - 2 * p # same than:
38 ##dT <- if (q1 == q2) 2*(q1 - p) else 2*(min(q1, q2) - p) + abs(q1 - q2)
40 if (method == "BHV01") {
47 if (identical(bp1[[i]], bp2[[j]])) {
48 dT <- dT + abs(x$edge.length[which(x$edge[, 2] == n + i)] -
49 y$edge.length[which(y$edge[, 2] == n + j)])
50 found1 <- found2[j] <- TRUE
54 if (found1) found1 <- FALSE
55 else dT <- dT + x$edge.length[which(x$edge[, 2] == n + i)]
58 dT <- dT + sum(y$edge.length[y$edge[, 2] %in% (n + which(!found2))])
63 .compressTipLabel <- function(x)
65 ## 'x' is a list of objects of class "phylo" possibly with no class
66 if (!is.null(attr(x, "TipLabel"))) return(x)
67 ref <- x[[1]]$tip.label
68 if (any(table(ref) != 1))
69 stop("some tip labels are duplicated in tree no. 1")
71 for (i in 2:length(x)) {
72 if (identical(x[[i]]$tip.label, ref)) next
73 ilab <- match(x[[i]]$tip.label, ref)
74 ## can use tabulate here because 'ilab' contains integers
75 if (any(tabulate(ilab) > 1))
76 stop(paste("some tip labels are duplicated in tree no.", i))
78 stop(paste("tree no.", i, "has different tip labels"))
79 ie <- match(1:n, x[[i]]$edge[, 2])
80 x[[i]]$edge[ie, 2] <- ilab
82 for (i in 1:length(x)) x[[i]]$tip.label <- NULL
83 attr(x, "TipLabel") <- ref
87 prop.part <- function(..., check.labels = TRUE)
90 if (length(obj) == 1 && class(obj[[1]]) != "phylo")
93 ## class(obj) <- NULL # needed?
96 if (ntree == 1) check.labels <- FALSE
97 if (check.labels) obj <- .compressTipLabel(obj)
98 for (i in 1:ntree) storage.mode(obj[[i]]$Nnode) <- "integer"
100 ## The 1st must have tip labels
101 ## Maybe simply pass the number of tips to the C code??
102 if (!is.null(attr(obj, "TipLabel")))
103 for (i in 1:ntree) obj[[i]]$tip.label <- attr(obj, "TipLabel")
105 clades <- .Call("prop_part", obj, ntree, TRUE, PACKAGE = "ape")
106 attr(clades, "number") <- attr(clades, "number")[1:length(clades)]
107 attr(clades, "labels") <- obj[[1]]$tip.label
108 class(clades) <- "prop.part"
112 print.prop.part <- function(x, ...)
114 if (is.null(attr(x, "labels"))) {
115 for (i in 1:length(x)) {
116 cat("==>", attr(x, "number")[i], "time(s):")
117 print(x[[i]], quote = FALSE)
120 for (i in 1:length(attr(x, "labels")))
121 cat(i, ": ", attr(x, "labels")[i], "\n", sep = "")
123 for (i in 1:length(x)) {
124 cat("==>", attr(x, "number")[i], "time(s):")
125 print(x[[i]], quote = FALSE)
130 summary.prop.part <- function(object, ...) attr(object, "number")
132 plot.prop.part <- function(x, barcol = "blue", leftmar = 4, ...)
134 if (is.null(attr(x, "labels")))
135 stop("cannot plot this partition object; see ?prop.part for details.")
137 n <- length(attr(x, "labels"))
138 layout(matrix(1:2, 2, 1), heights = c(1, 3))
139 par(mar = c(0.1, leftmar, 0.1, 0.1))
140 plot(1:L, attr(x, "number"), type = "h", col = barcol, xlim = c(1, L),
141 xlab = "", ylab = "Frequency", xaxt = "n", bty = "n")
142 plot(0, type = "n", xlim = c(1, L), ylim = c(1, n),
143 xlab = "", ylab = "", xaxt = "n", yaxt = "n")
144 for (i in 1:L) points(rep(i, length(x[[i]])), x[[i]], ...)
145 mtext(attr(x, "labels"), side = 2, at = 1:n, las = 1)
148 prop.clades <- function(phy, ..., part = NULL)
152 if (length(obj) == 1 && class(obj[[1]]) != "phylo")
153 obj <- unlist(obj, recursive = FALSE)
154 part <- prop.part(obj, check.labels = TRUE)
156 bp <- .Call("bipartition", phy$edge, length(phy$tip.label),
157 phy$Nnode, PACKAGE = "ape")
158 if (!is.null(attr(part, "labels")))
159 for (i in 1:length(part))
160 part[[i]] <- sort(attr(part, "labels")[part[[i]]])
161 bp <- lapply(bp, function(xx) sort(phy$tip.label[xx]))
162 n <- numeric(phy$Nnode)
163 for (i in 1:phy$Nnode) {
164 for (j in 1:length(part)) {
165 if (identical(all.equal(bp[[i]], part[[j]]), TRUE)) {
166 n[i] <- attr(part, "number")[j]
175 boot.phylo <- function(phy, x, FUN, B = 100, block = 1, trees = FALSE)
177 if (is.list(x) && !is.data.frame(x)) {
178 if (inherits(x, "DNAbin")) x <- as.matrix(x)
184 x <- matrix(x, n, nL/n, byrow = TRUE)
188 boot.tree <- vector("list", B)
191 y <- seq(block, ncol(x), block)
192 boot.i <- sample(y, replace = TRUE)
193 boot.samp <- numeric(ncol(x))
194 boot.samp[y] <- boot.i
195 for (j in 1:(block - 1))
196 boot.samp[y - j] <- boot.i - j
197 } else boot.samp <- sample(ncol(x), replace = TRUE)
198 boot.tree[[i]] <- FUN(x[, boot.samp])
200 for (i in 1:B) storage.mode(boot.tree[[i]]$Nnode) <- "integer"
201 storage.mode(phy$Nnode) <- "integer"
202 ans <- attr(.Call("prop_part", c(list(phy), boot.tree),
203 B + 1, FALSE, PACKAGE = "ape"), "number") - 1
204 if (trees) ans <- list(BP = ans, trees = boot.tree)
208 consensus <- function(..., p = 1, check.labels = TRUE)
210 foo <- function(ic, node) {
212 ## node: node number in the final tree
215 for (j in (ic + 1):m) {
216 wh <- match(pp[[j]], pool)
217 if (!any(is.na(wh))) {
218 edge[pos, 1] <<- node
220 edge[pos, 2] <<- nextnode <<- nextnode + 1L
228 ind <- pos:(pos + size - 1)
229 edge[ind, 1] <<- node
230 edge[ind, 2] <<- pool
235 if (length(obj) == 1) {
236 ## better than unlist(obj, recursive = FALSE)
237 ## because "[[" keeps the class of 'obj':
239 if (class(obj) == "phylo") return(obj)
241 if (!is.null(attr(obj, "TipLabel")))
242 labels <- attr(obj, "TipLabel")
244 labels <- obj[[1]]$tip.label
245 if (check.labels) obj <- .compressTipLabel(obj)
248 ## Get all observed partitions and their frequencies:
249 pp <- prop.part(obj, check.labels = FALSE)
250 ## Drop the partitions whose frequency is less than 'p':
251 pp <- pp[attr(pp, "number") >= p * ntree]
252 ## Get the order of the remaining partitions by decreasing size:
253 ind <- sort(unlist(lapply(pp, length)), decreasing = TRUE,
254 index.return = TRUE)$ix
258 edge <- matrix(0L, n + m - 1, 2)
267 structure(list(edge = edge, tip.label = labels,
268 Nnode = m), class = "phylo")