X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=R%2Fdist.topo.R;h=230f009e30d633935907327d2010f0846d2c9abd;hb=a2fc961dffe9f9b7994ed880e68c03b2334dc341;hp=04313b43a0a8ae0ad9f37e1e3bc6e8a85ad977d9;hpb=cc052f3adebcde0dbf4531719f84dfc349373f2c;p=ape.git

diff --git a/R/dist.topo.R b/R/dist.topo.R
index 04313b4..230f009 100644
--- a/R/dist.topo.R
+++ b/R/dist.topo.R
@@ -1,100 +1,118 @@
-## dist.topo.R (2008-02-27)
+## dist.topo.R (2012-12-12)
 
 ##      Topological Distances, Tree Bipartitions,
 ##   Consensus Trees, and Bootstrapping Phylogenies
 
-## Copyright 2005-2008 Emmanuel Paradis
+## Copyright 2005-2012 Emmanuel Paradis
 
 ## This file is part of the R-package `ape'.
 ## See the file ../COPYING for licensing issues.
 
 dist.topo <- function(x, y, method = "PH85")
 {
-    if (method == "BHV01" && (is.null(x$edge.length) || is.null(y$edge.length)))
-      stop("trees must have branch lengths for Billera et al.'s distance.")
-    n <- length(x$tip.label)
-    bp1 <- .Call("bipartition", x$edge, n, x$Nnode, PACKAGE = "ape")
+    if (method == "score" && (is.null(x$edge.length) || is.null(y$edge.length)))
+        stop("trees must have branch lengths for branch score distance.")
+    nx <- length(x$tip.label)
+    x <- unroot(x)
+    y <- unroot(y)
+    bp1 <- .Call("bipartition", x$edge, nx, x$Nnode, PACKAGE = "ape")
     bp1 <- lapply(bp1, function(xx) sort(x$tip.label[xx]))
-    bp2 <- .Call("bipartition", y$edge, n, y$Nnode, PACKAGE = "ape")
-    bp2 <- lapply(bp2, function(xx) sort(y$tip.label[xx]))
+    ny <- length(y$tip.label) # fix by Otto Cordero
+    ## fix by Tim Wallstrom:
+    bp2.tmp <- .Call("bipartition", y$edge, ny, y$Nnode, PACKAGE = "ape")
+    bp2 <- lapply(bp2.tmp, function(xx) sort(y$tip.label[xx]))
+    bp2.comp <- lapply(bp2.tmp, function(xx) setdiff(1:ny, xx))
+    bp2.comp <- lapply(bp2.comp, function(xx) sort(y$tip.label[xx]))
+    ## End
     q1 <- length(bp1)
     q2 <- length(bp2)
     if (method == "PH85") {
         p <- 0
         for (i in 1:q1) {
             for (j in 1:q2) {
-                if (identical(all.equal(bp1[[i]], bp2[[j]]), TRUE)) {
+                if (identical(bp1[[i]], bp2[[j]]) | identical(bp1[[i]], bp2.comp[[j]])) {
                     p <- p + 1
                     break
                 }
             }
         }
-        dT <- if (q1 == q2) 2*(q1 - p) else 2*(min(q1, q2) - p) + abs(q1 - q2)
+        dT <- q1 + q2 - 2 * p # same than:
+        ##dT <- if (q1 == q2) 2*(q1 - p) else 2*(min(q1, q2) - p) + abs(q1 - q2)
     }
-    if (method == "BHV01") {
+    if (method == "score") {
         dT <- 0
         found1 <- FALSE
         found2 <- logical(q2)
         found2[1] <- TRUE
         for (i in 2:q1) {
             for (j in 2:q2) {
-                if (identical(bp1[[i]], bp2[[j]])) {
-                    dT <- dT + abs(x$edge.length[which(x$edge[, 2] == n + i)] -
-                                   y$edge.length[which(y$edge[, 2] == n + j)])
+                if (identical(bp1[[i]], bp2[[j]]) | identical(bp1[[i]], bp2.comp[[j]])) {
+                    dT <- dT + (x$edge.length[which(x$edge[, 2] == nx + i)] -
+                                y$edge.length[which(y$edge[, 2] == ny + j)])^2
                     found1 <- found2[j] <- TRUE
                     break
                 }
             }
             if (found1) found1 <- FALSE
-            else dT <- dT + x$edge.length[which(x$edge[, 2] == n + i)]
+            else dT <- dT + (x$edge.length[which(x$edge[, 2] == nx + i)])^2
         }
         if (!all(found2))
-          dT <- dT + sum(y$edge.length[y$edge[, 2] %in% (n + which(!found2))])
+            dT <- dT + sum((y$edge.length[y$edge[, 2] %in% (ny + which(!found2))])^2)
+        dT <- sqrt(dT)
     }
     dT
 }
 
-prop.part <- function(..., check.labels = FALSE)
+.compressTipLabel <- function(x)
+{
+    ## 'x' is a list of objects of class "phylo" possibly with no class
+    if (!is.null(attr(x, "TipLabel"))) return(x)
+    ref <- x[[1]]$tip.label
+    n <- length(ref)
+    if (length(unique(ref)) != n)
+        stop("some tip labels are duplicated in tree no. 1")
+
+    ## serious improvement by Joseph W. Brown!
+    relabel <- function (y) {
+        label <- y$tip.label
+        if (!identical(label, ref)) {
+            if (length(label) != length(ref))
+                stop(paste("tree ", y, "has a different number of tips"))
+            ilab <- match(label, ref)
+            if (any(is.na(ilab)))
+                stop(paste("tree ", y, "has different tip labels"))
+            ie <- match(1:n, y$edge[, 2])
+            y$edge[ie, 2] <- ilab
+        }
+        y$tip.label <- NULL
+        y
+    }
+    x <- lapply(x, relabel)
+    attr(x, "TipLabel") <- ref
+    class(x) <- "multiPhylo"
+    x
+}
+
+prop.part <- function(..., check.labels = TRUE)
 {
     obj <- list(...)
     if (length(obj) == 1 && class(obj[[1]]) != "phylo")
-      obj <- unlist(obj, recursive = FALSE)
+        obj <- obj[[1]]
+    ## <FIXME>
+    ## class(obj) <- NULL # needed? apparently not, see below (2010-11-18)
+    ## </FIXME>
     ntree <- length(obj)
-    if (!check.labels) {
-        for (i in 1:ntree) storage.mode(obj[[i]]$Nnode) <- "integer"
-        clades <- .Call("prop_part", obj, ntree, TRUE, PACKAGE = "ape")
-        attr(clades, "number") <- attr(clades, "number")[1:length(clades)]
-        attr(clades, "labels") <- obj[[1]]$tip.label
-    } else {
-        bp <- .Call("bipartition", obj[[1]]$edge, length(obj[[1]]$tip.label),
-                    obj[[1]]$Nnode, PACKAGE = "ape")
-        clades <- lapply(bp, function(xx) sort(obj[[1]]$tip.label[xx]))
-        no <- rep(1, length(clades))
-
-        if (ntree > 1) {
-            for (k in 2:ntree) {
-                bp <- .Call("bipartition", obj[[k]]$edge,
-                            length(obj[[k]]$tip.label), obj[[k]]$Nnode,
-                            PACKAGE = "ape")
-                bp <- lapply(bp, function(xx) sort(obj[[k]]$tip.label[xx]))
-                for (i in 1:length(bp)) {
-                    done <- FALSE
-                    for (j in 1:length(clades)) {
-                        if (identical(all.equal(bp[[i]], clades[[j]]), TRUE)) {
-                            no[j] <- no[j] + 1
-                            done <- TRUE
-                            break
-                        }
-                    }
-                    if (!done) {
-                        clades <- c(clades, bp[i])
-                        no <- c(no, 1)
-                    }
-                }
-            }
-        }
-        attr(clades, "number") <- no
-    }
+    if (ntree == 1) check.labels <- FALSE
+    if (check.labels) obj <- .compressTipLabel(obj) # fix by Klaus Schliep (2011-02-21)
+    for (i in 1:ntree) storage.mode(obj[[i]]$Nnode) <- "integer"
+    ## <FIXME>
+    ## The 1st must have tip labels
+    ## Maybe simply pass the number of tips to the C code??
+    obj <- .uncompressTipLabel(obj) # fix a bug (2010-11-18)
+    ## </FIXME>
+    clades <- .Call("prop_part", obj, ntree, TRUE, PACKAGE = "ape")
+    attr(clades, "number") <- attr(clades, "number")[1:length(clades)]
+    attr(clades, "labels") <- obj[[1]]$tip.label
     class(clades) <- "prop.part"
     clades
 }
@@ -128,31 +146,38 @@ plot.prop.part <- function(x, barcol = "blue", leftmar = 4, ...)
     layout(matrix(1:2, 2, 1), heights = c(1, 3))
     par(mar = c(0.1, leftmar, 0.1, 0.1))
     plot(1:L, attr(x, "number"), type = "h", col = barcol, xlim = c(1, L),
-         xlab = "", ylab = "Number", xaxt = "n", bty = "n")
+         xlab = "", ylab = "Frequency", xaxt = "n", bty = "n")
     plot(0, type = "n", xlim = c(1, L), ylim = c(1, n),
          xlab = "", ylab = "", xaxt = "n", yaxt = "n")
     for (i in 1:L) points(rep(i, length(x[[i]])), x[[i]], ...)
     mtext(attr(x, "labels"), side = 2, at = 1:n, las = 1)
 }
 
-prop.clades <- function(phy, ..., part = NULL)
+prop.clades <- function(phy, ..., part = NULL, rooted = FALSE)
 {
     if (is.null(part)) {
+        ## <FIXME>
+        ## Are we going to keep the '...' way of passing trees?
         obj <- list(...)
         if (length(obj) == 1 && class(obj[[1]]) != "phylo")
-          obj <- unlist(obj, recursive = FALSE)
+            obj <- unlist(obj, recursive = FALSE)
+        ## </FIXME>
         part <- prop.part(obj, check.labels = TRUE)
     }
-    bp <- .Call("bipartition", phy$edge, length(phy$tip.label),
-                phy$Nnode, PACKAGE = "ape")
-    if (!is.null(attr(part, "labels")))
-      for (i in 1:length(part))
-        part[[i]] <- sort(attr(part, "labels")[part[[i]]])
-    bp <- lapply(bp, function(xx) sort(phy$tip.label[xx]))
+
+    bp <- prop.part(phy)
+    if (!rooted) {
+        bp <- postprocess.prop.part(bp)
+        part <- postprocess.prop.part(part) # fix by Klaus Schliep
+        ## actually the above line in not needed if called from boot.phylo()
+    }
+
     n <- numeric(phy$Nnode)
-    for (i in 1:phy$Nnode) {
-        for (j in 1:length(part)) {
-            if (identical(all.equal(bp[[i]], part[[j]]), TRUE)) {
+    for (i in seq_along(bp)) {
+        for (j in seq_along(part)) {
+            ## we rely on the fact the values returned by prop.part are
+            ## sorted and without attributes, so identical can be used:
+            if (identical(bp[[i]], part[[j]])) {
                 n[i] <- attr(part, "number")[j]
                 done <-  TRUE
                 break
@@ -162,10 +187,11 @@ prop.clades <- function(phy, ..., part = NULL)
     n
 }
 
-boot.phylo <- function(phy, x, FUN, B = 100, block = 1)
+boot.phylo <- function(phy, x, FUN, B = 100, block = 1,
+                       trees = FALSE, quiet = FALSE, rooted = FALSE)
 {
-    if (is.list(x)) {
-        if (class(x) == "DNAbin") x <- as.matrix(x)
+    if (is.list(x) && !is.data.frame(x)) {
+        if (inherits(x, "DNAbin")) x <- as.matrix(x)
         else {
             nm <- names(x)
             n <- length(x)
@@ -176,6 +202,8 @@ boot.phylo <- function(phy, x, FUN, B = 100, block = 1)
         }
     }
     boot.tree <- vector("list", B)
+    if (!quiet) # suggestion by Alastair Potts
+        progbar <- utils::txtProgressBar(style = 3)
     for (i in 1:B) {
         if (block > 1) {
             y <- seq(block, ncol(x), block)
@@ -183,48 +211,143 @@ boot.phylo <- function(phy, x, FUN, B = 100, block = 1)
             boot.samp <- numeric(ncol(x))
             boot.samp[y] <- boot.i
             for (j in 1:(block - 1))
-              boot.samp[y - j] <- boot.i - j
+                boot.samp[y - j] <- boot.i - j
         } else boot.samp <- sample(ncol(x), replace = TRUE)
         boot.tree[[i]] <- FUN(x[, boot.samp])
+        if (!quiet) utils::setTxtProgressBar(progbar, i/B)
     }
+    if (!quiet) close(progbar)
     for (i in 1:B) storage.mode(boot.tree[[i]]$Nnode) <- "integer"
     storage.mode(phy$Nnode) <- "integer"
-    attr(.Call("prop_part", c(list(phy), boot.tree), B + 1, FALSE,
-               PACKAGE = "ape"), "number") - 1
+
+    pp <- prop.part(boot.tree)
+    if (!rooted) pp <- postprocess.prop.part(pp)
+    ans <- prop.clades(phy, part = pp, rooted = rooted)
+
+    ##ans <- attr(.Call("prop_part", c(list(phy), boot.tree),
+    ##                  B + 1, FALSE, PACKAGE = "ape"), "number") - 1
+    if (trees) {
+        class(boot.tree) <- "multiPhylo"
+        ans <- list(BP = ans, trees = boot.tree)
+    }
+    ans
 }
 
-consensus <- function(..., p = 1)
+### The next function transforms an object of class "prop.part" so
+### that the vectors which are identical in terms of split are aggregated.
+### For instance if n = 5 tips, 1:2 and 3:5 actually represent the same
+### split though they are different clades. The aggregation is done
+### arbitrarily. The call to ONEwise() insures that all splits include
+### the first tip.
+postprocess.prop.part <- function(x)
 {
+    n <- length(x[[1]])
+    N <- length(x)
+    w <- attr(x, "number")
+
+    drop <- logical(N)
+    V <- numeric(n)
+    for (i in 2:(N - 1)) {
+        if (drop[i]) next
+        A <- x[[i]]
+        for (j in (i + 1):N) {
+            if (drop[j]) next
+            B <- x[[j]]
+            if (length(A) + length(B) != n) next
+            V[] <- 0L
+            V[A] <- 1L
+            V[B] <- 1L
+            if (all(V == 1L)) {
+                drop[j] <- TRUE
+                w[i] <- w[i] + w[j]
+            }
+        }
+    }
+    if (any(drop)) {
+        labels <- attr(x, "labels")
+        x <- x[!drop]
+        w <- w[!drop]
+        attr(x, "number") <- w
+        attr(x, "labels") <- labels
+        class(x) <- "prop.part"
+    }
+    ONEwise(x)
+}
+
+### This function changes an object of class "prop.part" so that they
+### all include the first tip. For instance if n = 5 tips, 3:5 is
+### changed to 1:2.
+ONEwise <- function(x)
+{
+    n <- length(x[[1L]])
+    v <- 1:n
+    for (i in 2:length(x)) {
+        y <- x[[i]]
+        if (y[1] != 1) x[[i]] <- v[-y]
+    }
+    x
+}
+
+consensus <- function(..., p = 1, check.labels = TRUE)
+{
+    foo <- function(ic, node) {
+        ## ic: index of 'pp'
+        ## node: node number in the final tree
+        pool <- pp[[ic]]
+        if (ic < m) {
+            for (j in (ic + 1):m) {
+                wh <- match(pp[[j]], pool)
+                if (!any(is.na(wh))) {
+                    edge[pos, 1] <<- node
+                    pool <- pool[-wh]
+                    edge[pos, 2] <<- nextnode <<- nextnode + 1L
+                    pos <<- pos + 1L
+                    foo(j, nextnode)
+                }
+            }
+        }
+        size <- length(pool)
+        if (size) {
+            ind <- pos:(pos + size - 1)
+            edge[ind, 1] <<- node
+            edge[ind, 2] <<- pool
+            pos <<- pos + size
+        }
+    }
     obj <- list(...)
-    if (length(obj) == 1 && class(obj[[1]]) != "phylo")
-      obj <- unlist(obj, recursive = FALSE)
+    if (length(obj) == 1) {
+        ## better than unlist(obj, recursive = FALSE)
+        ## because "[[" keeps the class of 'obj':
+        obj <- obj[[1]]
+        if (class(obj) == "phylo") return(obj)
+    }
+    if (!is.null(attr(obj, "TipLabel")))
+        labels <- attr(obj, "TipLabel")
+    else {
+        labels <- obj[[1]]$tip.label
+        if (check.labels) obj <- .compressTipLabel(obj)
+    }
     ntree <- length(obj)
     ## Get all observed partitions and their frequencies:
-    pp <- prop.part(obj, check.labels = TRUE)
+    pp <- prop.part(obj, check.labels = FALSE)
     ## Drop the partitions whose frequency is less than 'p':
+    if (p == 0.5) p <- 0.5000001 # avoid incompatible splits
     pp <- pp[attr(pp, "number") >= p * ntree]
     ## Get the order of the remaining partitions by decreasing size:
-    ind <- rev(sort(unlist(lapply(pp, length)),
-                    index.return = TRUE)$ix)
-    pp <- lapply(pp, function(xx) paste("IMPROBABLE_PREFIX", xx,
-                                        "IMPROBABLE_SUFFIX", sep = "_"))
-    STRING <- paste(pp[[1]], collapse = ",")
-    STRING <- paste("(", STRING, ");", sep = "")
-    for (i in ind[-1]) {
-        ## 1. Delete all tips in the focus partition:
-        STRING <- unlist(strsplit(STRING, paste(pp[[i]], collapse = "|")))
-        ## 2. Put the partition in any of the created gaps:
-        STRING <- c(STRING[1],
-                    paste("(", paste(pp[[i]], collapse = ","), ")", sep = ""),
-                    STRING[-1])
-        ## 3. Stick back the Newick string:
-        STRING <- paste(STRING, collapse = "")
-    }
-    ## Remove the extra commas:
-    STRING <- gsub(",{2,}", ",", STRING)
-    STRING <- gsub("\\(,", "\\(", STRING)
-    STRING <- gsub(",\\)", "\\)", STRING)
-    STRING <- gsub("IMPROBABLE_PREFIX_", "", STRING)
-    STRING <- gsub("_IMPROBABLE_SUFFIX", "", STRING)
-    read.tree(text = STRING)
+    ind <- sort(unlist(lapply(pp, length)), decreasing = TRUE,
+                index.return = TRUE)$ix
+    pp <- pp[ind]
+    n <- length(labels)
+    m <- length(pp)
+    edge <- matrix(0L, n + m - 1, 2)
+    if (m == 1) {
+        edge[, 1] <- n + 1L
+        edge[, 2] <- 1:n
+    } else {
+        nextnode <- n + 1L
+        pos <- 1L
+        foo(1, nextnode)
+    }
+    structure(list(edge = edge, tip.label = labels,
+              Nnode = m), class = "phylo")
 }