[Phylobase-commits] r906 - pkg/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Apr 8 18:52:35 CEST 2014
Author: francois
Date: 2014-04-08 18:52:35 +0200 (Tue, 08 Apr 2014)
New Revision: 906
Removed:
pkg/R/subset.R
Log:
deleting old subset.R
Deleted: pkg/R/subset.R
===================================================================
--- pkg/R/subset.R 2014-04-08 16:18:16 UTC (rev 905)
+++ pkg/R/subset.R 2014-04-08 16:52:35 UTC (rev 906)
@@ -1,422 +0,0 @@
-################
-## subset phylo4
-################
-
-##' Methods for creating subsets of phylogenies
-##'
-##' Methods for creating subsets of phylogenies, based on pruning a
-##' tree to include or exclude a set of terminal taxa, to include all
-##' descendants of the MRCA of multiple taxa, or to return a subtree
-##' rooted at a given node.
-##'
-##' The \code{subset} methods must be called using no more than one of
-##' the four main subsetting criteria arguments (\code{tips.include},
-##' \code{tips.exclude}, \code{mrca}, or \code{node.subtree}). Each
-##' of these arguments can be either character or numeric. In the
-##' first case, they are treated as node labels; in the second case,
-##' they are treated as node numbers. For the first two arguments,
-##' any supplied tips not found in the tree (\code{tipLabels(x)}) will
-##' be ignored, with a warning. Similarly, for the \code{mrca}
-##' argument, any supplied tips or internal nodes not found in the
-##' tree will be ignored, with a warning. For the \code{node.subtree}
-##' argument, failure to provide a single, valid internal node will
-##' result in an error.
-##'
-##' Although \code{prune} is mainly intended as the workhorse function
-##' called by \code{subset}, it may also be called directly. In
-##' general it should be equivalent to the \code{tips.exclude} form of
-##' \code{subset} (although perhaps with less up-front error
-##' checking).
-##'
-##' The "[" operator, when used as \code{x[i]}, is similar to the
-##' \code{tips.include} form of \code{subset}. However, the indices
-##' used with this operator can also be logical, in which case the
-##' corresponding tips are assumed to be ordered as in \code{nodeId(x,
-##' "tip")}, and recycling rules will apply (just like with a vector
-##' or a matrix). With a \linkS4class{phylo4d} object 'x',
-##' \code{x[i,j]} creates a subset of \code{x} taking \code{i} for a
-##' tip index and \code{j} for the index of data variables in
-##' \code{tdata(geospiza, "all")}. Note that the second index is
-##' optional: \code{x[i, TRUE]}, \code{x[i,]}, and \code{x[i]} are all
-##' equivalent.
-##'
-##' Regardless of which approach to subsetting is used, the argument
-##' values must be such that at least two tips are retained.
-##'
-##' If the most recent common ancestor of the retained tips is not the
-##' original root node, then the root node of the subset tree will be
-##' a descendant of the original root. For rooted trees with non-NA
-##' root edge length, this has implications for the new root edge
-##' length. In particular, the new length will be the summed edge
-##' length from the new root node back to the original root (including
-##' the original root edge). As an alternative, see the examples for
-##' a way to determine the length of the edge that was immediately
-##' ancestral to the new root node in the original tree.
-##'
-##' Note that the correspondance between nodes and labels (and data in
-##' the case of \linkS4class{phylo4d}) will be retained after all
-##' forms of subsetting. Beware, however, that the node numbers (IDs)
-##' will likely be altered to reflect the new tree topology, and
-##' therefore cannot be compared directly between the original tree
-##' and the subset tree.
-##'
-##' @name subset-methods
-##' @docType methods
-##' @param x an object of class \code{"phylo4"} or \code{"phylo4d"}
-##' @param tips.include A vector of tips to include in the subset tree
-##' @param tips.exclude A vector of tips to exclude from the subset
-##' tree
-##' @param mrca A vector of nodes for determining the most recent
-##' common ancestor, which is then used as the root of the subset tree
-##' @param node.subtree A single internal node specifying the root of
-##' the subset tree
-##' @param trim.internal A logical specifying whether to remove
-##' internal nodes that no longer have tip descendants in the subset
-##' tree
-##' @param i (\code{[} method) An index vector indicating tips to
-##' include
-##' @param j (\code{[} method, phylo4d only) An index vector
-##' indicating columns of node/tip data to include
-##' @param \dots additional arguments to be passed to other methods
-##' @return an object of class \code{"phylo4"} or \code{"phylo4d"}
-##' @section Methods: \describe{ \item{x = "phylo4"}{subset tree}
-##' \item{x = "phylo4d"}{subset tree and corresponding node and tip
-##' data} }
-##' @author Jim Regetz \email{regetz@@nceas.ucsb.edu}\cr Steven Kembel
-##' \email{skembel@@berkeley.edu}\cr Damien de Vienne
-##' \email{damien.de-vienne@@u-psud.fr}\cr Thibaut Jombart
-##' \email{jombart@@biomserv.univ-lyon1.fr}
-##' @keywords methods
-##' @export
-##' @rdname subset-methods
-##' @examples
-##' data(geospiza)
-##' nodeLabels(geospiza) <- paste("N", nodeId(geospiza, "internal"), sep="")
-##' geotree <- extractTree(geospiza)
-##'
-##' ## "subset" examples
-##' tips <- c("difficilis", "fortis", "fuliginosa", "fusca", "olivacea",
-##' "pallida", "parvulus", "scandens")
-##' plot(subset(geotree, tips.include=tips))
-##' plot(subset(geotree, tips.include=tips, trim.internal=FALSE))
-##' plot(subset(geotree, tips.exclude="scandens"))
-##' plot(subset(geotree, mrca=c("scandens","fortis","pauper")))
-##' plot(subset(geotree, node.subtree=18))
-##'
-##' ## "prune" examples (equivalent to subset using tips.exclude)
-##' plot(prune(geotree, tips))
-##'
-##' ## "[" examples (equivalent to subset using tips.include)
-##' plot(geotree[c(1:6,14)])
-##' plot(geospiza[c(1:6,14)])
-##'
-##' ## for phylo4d, subset both tips and data columns
-##' geospiza[c(1:6,14), c("wingL", "beakD")]
-##'
-##' ## note handling of root edge length:
-##' edgeLength(geotree)['0-15'] <- 0.1
-##' geotree2 <- geotree[1:2]
-##' ## in subset tree, edge of new root extends back to the original root
-##' edgeLength(geotree2)['0-3']
-##' ## edge length immediately ancestral to this node in the original tree
-##' edgeLength(geotree, MRCA(geotree, tipLabels(geotree2)))
-setGeneric("subset")
-
-##' @rdname subset-methods
-##' @aliases subset,phylo4-method
-setMethod("subset", "phylo4", function(x, tips.include=NULL,
- tips.exclude=NULL, mrca=NULL, node.subtree=NULL, ...) {
- ## FIXME: could eliminate NULL and make the test
- ## if (!missing) rather than if (!is.null)
- ## (might have to change next line?)
- if (sum(!sapply(list(tips.include, tips.exclude, mrca,
- node.subtree), is.null))>1) {
- stop("must specify at most one criterion for subsetting")
- }
- all.tips <- nodeId(x, "tip")
- if (!is.null(tips.include)) {
- nodes <- getNode(x, tips.include, missing="OK")
- is.valid.tip <- nodes %in% all.tips
- kept <- nodes[is.valid.tip]
- dropped <- setdiff(all.tips, kept)
- unknown <- tips.include[!is.valid.tip]
- } else if (!is.null(tips.exclude)) {
- nodes <- getNode(x, tips.exclude, missing="OK")
- is.valid.tip <- nodes %in% all.tips
- dropped <- nodes[is.valid.tip]
- kept <- setdiff(all.tips, dropped)
- unknown <- tips.exclude[!is.valid.tip]
- } else if (!is.null(mrca)) {
- nodes <- getNode(x, mrca, missing="OK")
- is.valid.node <- nodes %in% nodeId(x, "all")
- mnode <- MRCA(x, nodes[is.valid.node])
- if (length(mnode)!=1) {
- stop("mrca must include at least one valid node")
- }
- kept <- descendants(x, mnode)
- dropped <- setdiff(all.tips, kept)
- unknown <- mrca[!is.valid.node]
- } else if (!is.null(node.subtree)) {
- node <- getNode(x, node.subtree, missing="OK")
- if (length(node)!=1 || !(node %in% nodeId(x, "internal"))) {
- stop("node.subtree must be a single valid internal node")
- }
- kept <- descendants(x, node)
- dropped <- setdiff(all.tips, kept)
- unknown <- numeric(0)
- } else {
- kept <- getNode(x, nodeId(x, "tip"))
- dropped <- numeric(0)
- unknown <- numeric(0)
- }
- if (length(unknown)>0) {
- warning("invalid nodes ignored: ", paste(unknown,
- collapse=", "))
- }
- if (length(kept)<2) {
- stop("0 or 1 tips would remain after subsetting")
- }
- if (length(dropped)==0) return(x)
- return(prune(x, dropped, ...))
-})
-
-###############
-# '[' operator
-###############
-
-## Consider using some combination of these for stricter argument
-## checking? Not implementing now because extra arguments are just
-## ignored, which is fairly common S4 method behavior:
-## * in "[" methods for phylo4:
-## if (nargs()>2) stop("unused arguments")
-## * in "[" methods for both phylo4 and phylo4d:
-## if (!missing(...)) stop("unused argument(s)")
-
-##### -------- phylo4 '[' methods
-
-##' @rdname subset-methods
-##' @aliases [,phylo4,character,missing-method
-setMethod("[", signature(x="phylo4", i="character", j="missing",
- drop="missing"), function(x, i, j, ..., drop) {
- subset(x, tips.include=i)
-})
-
-##' @rdname subset-methods
-##' @aliases [,phylo4,numeric,missing-method
-setMethod("[", signature(x="phylo4", i="numeric", j="missing",
- drop="missing"), function(x, i, j, ..., drop) {
- subset(x, tips.include=i)
-})
-
-##' @rdname subset-methods
-##' @aliases [,phylo4,logical,missing-method
-setMethod("[", signature(x="phylo4", i="logical", j="missing",
- drop="missing"), function(x, i, j, ..., drop) {
- subset(x, tips.include=nodeId(x, "tip")[i])
-})
-
-##' @rdname subset-methods
-##' @aliases [,phylo4,missing,missing-method
-setMethod("[", signature(x="phylo4", i="missing", j="missing",
- drop="missing"), function(x, i, j, ..., drop) {
- x
-})
-
-##### -------- phylo4d '[' methods
-
-##' @rdname subset-methods
-##' @aliases [,phylo4d,ANY,character,missing-method
-setMethod("[", signature(x="phylo4d", i="ANY", j="character",
- drop="missing"), function(x, i, j, ..., drop) {
- if (!missing(i)) x <- x[i]
- tdata(x, type="all") <- tdata(x, type="all")[j]
- return(x)
-})
-
-##' @rdname subset-methods
-##' @aliases [,phylo4d,ANY,numeric,missing-method
-setMethod("[", signature(x="phylo4d", i="ANY", j="numeric",
- drop="missing"), function(x, i, j, ..., drop) {
- if (!missing(i)) x <- x[i]
- tdata(x, type="all") <- tdata(x, type="all")[j]
- return(x)
-})
-
-##' @rdname subset-methods
-##' @aliases [,phylo4d,ANY,logical,missing-method
-setMethod("[", signature(x="phylo4d", i="ANY", j="logical",
- drop="missing"), function(x, i, j, ..., drop) {
- if (!missing(i)) x <- x[i]
- tdata(x, type="all") <- tdata(x, type="all")[j]
- return(x)
-})
-
-## borrow from Matrix package approach of trapping invalid usage
-##' @rdname subset-methods
-##' @aliases [,phylo4,ANY,ANY,ANY-method
-setMethod("[", signature(x="phylo4", i="ANY", j="ANY", drop="ANY"),
- function(x, i, j, ..., drop) {
- stop("invalid argument(s)")
-})
-
-##### -------- prune
-
-##' @rdname subset-methods
-##' @aliases prune
-setGeneric("prune", function(x, ...) {
- standardGeneric("prune")
-})
-
-## return characters, sorted in NUMERIC order
-.chnumsort <- function(x) {
- as.character(sort(as.numeric(x)))
-}
-
-##' @rdname subset-methods
-##' @aliases prune,phylo4-method
-setMethod("prune", "phylo4",
- function(x, tips.exclude, trim.internal=TRUE) {
-
- makeEdgeNames <- function(edge) {
- paste(edge[,1], edge[,2], sep="-")
- }
-
- ## drop tips and obsolete internal nodes from edge matrix
- tip.drop <- getNode(x, tips.exclude, missing="fail")
- tip.keep <- setdiff(nodeId(x, "tip"), tip.drop)
- nodes <- nodeId(x, "all")
- node.keep <- rep(FALSE, length(nodes))
- node.keep[tip.keep] <- TRUE
- if (trim.internal) {
- if (edgeOrder(x) == "postorder") {
- edge.post <- edges(x)
- } else {
- edge.post <- edges(reorder(x, "postorder"))
- }
- for (i in seq_along(edge.post[,2])) {
- if (node.keep[edge.post[i,2]]) {
- node.keep[edge.post[i,1]] <- TRUE
- }
- }
- } else {
- node.keep[nodeId(x, "internal")] <- TRUE
- }
- edge.new <- edges(x)[edges(x)[,2] %in% nodes[node.keep], ]
-
- ## remove singletons
- edge.length.new <- edgeLength(x)
- edge.label.new <- edgeLabels(x)
- singletons <- which(tabulate(edge.new[edge.new[, 1] != 0, 1])==1)
- while (length(singletons)>0) {
- sing.node <- singletons[1]
-
- ## update edge matrix
- edges.drop <- which(edge.new==sing.node, arr.ind=TRUE)[,"row"]
- sing.edges <- edge.new[edges.drop,]
- edge.new[edges.drop[2], ] <- c(sing.edges[2,1], sing.edges[1,2])
- edge.new <- edge.new[-edges.drop[1], ]
-
- ## update edge lengths and edge labels
- edge.names.drop <- makeEdgeNames(sing.edges)
- edge.name.new <- paste(sing.edges[2,1], sing.edges[1,2], sep="-")
- edge.length.new[edge.name.new] <-
- sum(edge.length.new[edge.names.drop])
- edge.length.new <- edge.length.new[-match(edge.names.drop,
- names(edge.length.new))]
- edge.label.new[edge.name.new] <- NA
- edge.label.new <- edge.label.new[-match(edge.names.drop,
- names(edge.label.new))]
-
- singletons <- which(tabulate(edge.new[edge.new[, 1] != 0, 1])==1)
- }
-
- ## remove dropped elements from labels
- label.new <- labels(x)[names(labels(x)) %in% edge.new]
-
- ## subset and order edge.length and edge.label with respect to edge
- edge.names <- makeEdgeNames(edge.new)
- edge.length.new <- edge.length.new[edge.names]
- edge.label.new <- edge.label.new[edge.names]
-
- if (!trim.internal) {
- ## make sure now-terminal internal nodes are treated as tips
- tip.now <- setdiff(edge.new[,2], edge.new[,1])
- tip.add <- tip.now[tip.now>nTips(x)]
- if (length(tip.add)>0) {
- ind <- match(tip.add, names(label.new))
-
- ## node renumbering workaround to satisfy plot method
- newid <- sapply(tip.add, function(tip) descendants(x, tip)[1])
- names(label.new)[ind] <- newid
- edge.new[match(tip.add, edge.new)] <- newid
- tip.now[match(tip.add, tip.now)] <- newid
-
- isTip <- edge.new %in% tip.now
- edge.new[isTip] <- match(edge.new[isTip],
- sort(unique.default(edge.new[isTip])))
- }
- }
-
- ## renumber nodes in the edge matrix
- edge.new[] <- match(edge.new, sort(unique.default(edge.new))) - 1L
-
- ## update corresponding element names in the other slots
- edge.names <- makeEdgeNames(edge.new)
- names(edge.length.new) <- edge.names
- names(edge.label.new) <- edge.names
- label.new <- label.new[order(as.numeric(names(label.new)))]
- names(label.new) <- seq_along(label.new)
-
- ## update, check, then return the pruned phylo4 object
- x at edge <- edge.new
- ##TODO would prefer to leave out NA from edge.length slot, but can't
- x at edge.length <- edge.length.new
- x at edge.label <- edge.label.new[!is.na(edge.label.new)]
- x at label <- label.new[!is.na(label.new)]
- if(is.character(checkval <- checkPhylo4(x))) {
- stop(checkval)
- } else {
- return(x)
- }
-
-})
-
-##' @rdname subset-methods
-##' @aliases prune,phylo4d-method
-setMethod("prune", "phylo4d",
- function(x, tips.exclude, trim.internal=TRUE) {
-
- tree <- extractTree(x)
- phytr <- prune(tree, tips.exclude, trim.internal)
-
- ## create temporary phylo4 object with complete and unique labels
- tmpLbl <- .genlab("n", nTips(x)+nNodes(x))
- tmpPhy <- tree
- labels(tmpPhy, "all") <- tmpLbl
- tmpPhytr <- prune(tmpPhy, getNode(x, tips.exclude), trim.internal)
-
- ## get node numbers to keep
- oldLbl <- labels(tmpPhy, "all")
- newLbl <- labels(tmpPhytr, "all")
- wasKept <- oldLbl %in% newLbl
- nodesToKeep <- as.numeric(names(oldLbl[wasKept]))
-
- ## subset original data, and update names
- allDt <- x at data[match(nodesToKeep, rownames(x at data)), , drop=FALSE]
- rownames(allDt) <- match(newLbl, oldLbl[wasKept])
-
- phytr <- phylo4d(phytr, all.data=allDt, match.data=TRUE)
-
- phytr
-})
-
-## setMethod("prune","ANY",
-## function(phy, tip, trim.internal = TRUE, subtree = FALSE,
-## ,...) {
-## if (class(phy)=="phylo") {
-## ape::prune(phy, tip, trim.internal, subtree)
-## } else stop("no prune method available for",
-## deparse(substitute(phy)),
-## "(class",class(phy),")")
-## })
-
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