From 21eb56120c84786502f24ff9c27b39d5badfe1f7 Mon Sep 17 00:00:00 2001 From: paradis Date: Fri, 2 Apr 2010 15:36:35 +0000 Subject: [PATCH] various corrections git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@116 6e262413-ae40-0410-9e79-b911bd7a66b7 --- DESCRIPTION | 2 +- R/cophyloplot.R | 45 +++++++++++++++++---------- R/read.nexus.R | 2 +- R/read.tree.R | 2 +- R/reorder.phylo.R | 9 +++--- man/DNAbin.Rd | 2 +- man/GC.content.Rd | 2 +- man/MoranI.Rd | 2 +- man/ace.Rd | 3 +- man/add.scale.bar.Rd | 2 +- man/as.alignment.Rd | 2 +- man/as.matching.Rd | 2 +- man/as.phylo.Rd | 2 +- man/axisPhylo.Rd | 2 +- man/balance.Rd | 2 +- man/base.freq.Rd | 2 +- man/bd.ext.Rd | 2 +- man/birthdeath.Rd | 2 +- man/boot.phylo.Rd | 2 +- man/branching.times.Rd | 2 +- man/cherry.Rd | 2 +- man/chronoMPL.Rd | 2 +- man/chronopl.Rd | 2 +- man/compar.gee.Rd | 2 +- man/compute.brlen.Rd | 2 +- man/consensus.Rd | 2 +- man/cophenetic.phylo.Rd | 2 +- man/correlogram.formula.Rd | 2 +- man/del.gaps.Rd | 2 +- man/delta.plot.Rd | 3 +- man/dist.dna.Rd | 2 +- man/dist.gene.Rd | 2 +- man/dist.topo.Rd | 2 +- man/diversi.gof.Rd | 2 +- man/diversi.time.Rd | 2 +- man/drop.tip.Rd | 2 +- man/gammaStat.Rd | 2 +- man/howmanytrees.Rd | 2 +- man/identify.phylo.Rd | 2 +- man/is.ultrametric.Rd | 2 +- man/ladderize.Rd | 2 +- man/ltt.plot.Rd | 2 +- man/makeNodeLabel.Rd | 2 +- man/matexpo.Rd | 2 +- man/mrca.Rd | 2 +- man/mst.Rd | 2 +- man/multi2di.Rd | 2 +- man/nj.Rd | 2 +- man/node.depth.Rd | 2 +- man/nodelabels.Rd | 4 +-- man/phymltest.Rd | 2 +- man/pic.Rd | 2 +- man/plot.correlogram.Rd | 2 +- man/plot.phylo.Rd | 2 +- man/print.phylo.Rd | 3 +- man/read.GenBank.Rd | 2 +- man/read.dna.Rd | 2 +- man/read.nexus.Rd | 2 +- man/read.tree.Rd | 3 +- man/reorder.phylo.Rd | 2 +- man/root.Rd | 2 +- man/seg.sites.Rd | 2 +- man/summary.phylo.Rd | 2 +- man/weight.taxo.Rd | 2 +- man/which.edge.Rd | 2 +- man/write.dna.Rd | 2 +- man/write.nexus.Rd | 2 +- man/write.tree.Rd | 3 +- man/yule.Rd | 2 +- man/yule.cov.Rd | 2 +- man/yule.time.Rd | 2 +- man/zoom.Rd | 2 +- src/dist_dna.c | 63 +------------------------------------- 73 files changed, 106 insertions(+), 158 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 981ea9f..f452091 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ape Version: 2.5-1 -Date: 2010-03-19 +Date: 2010-03-29 Title: Analyses of Phylogenetics and Evolution Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne Maintainer: Emmanuel Paradis diff --git a/R/cophyloplot.R b/R/cophyloplot.R index 04425c6..faf9e34 100644 --- a/R/cophyloplot.R +++ b/R/cophyloplot.R @@ -53,7 +53,7 @@ plotCophylo2 <- font = font, ...) { res <- list() -###choice of the minimum space between the trees### +###choice of the minimum space between the trees left <- max(nchar(x$tip.label, type = "width")) + length.line right <- max(nchar(y$tip.label, type = "width")) + length.line space.min <- left + right + gap * 2 @@ -66,8 +66,8 @@ plotCophylo2 <- res$a <- a b <- plotPhyloCoor(y, use.edge.length = use.edge.length, direction = "leftwards", type = type) - ###for the two trees to have the extreme leaves at the same ordinate. - a[, 2] <- a[, 2] - min(a[, 2]) +###for the two trees to have the extreme leaves at the same ordinate. + a[, 2] <- a[, 2] - min(a[, 2]) b[, 2] <- b[, 2] - min(b[, 2]) res$b <- b b2 <- b @@ -122,9 +122,10 @@ plotCophylo2 <- } } if (show.tip.label) { - text(a[1:N.tip.x, ], cex = 0, font = font, pos = 4, labels = x$tip.label) + text(a[1:N.tip.x, ], cex = 0, font = font, pos = 4, + labels = x$tip.label) text(b2[1:N.tip.y, ], cex = 1, font = font, pos = 2, - labels = y$tip.label) + labels = y$tip.label) } ###links between associated taxa. Takes into account the size of the character strings of the taxa names. lsa <- 1:N.tip.x @@ -142,26 +143,36 @@ plotCophylo2 <- else if (length(lwd)>=nrow(assoc)) lwidths<-lwd else lwidths<-c(rep(lwd, as.integer(nrow(assoc)/length(lwd))+1)) - #lty + #lty if (length(lty) == 1) ltype <- c(rep(lty, nrow(assoc))) else if (length(lty) >= nrow(assoc)) ltype <- lty else ltype <- c(rep(lty, as.integer(nrow(assoc)/length(lty))+1)) for (i in 1:nrow(assoc)) { - - if (show.tip.label) { - decx[i] <- strwidth(x$tip.label[lsa[x$tip.label == - assoc[i, 1]]]) - decy[i] <- strwidth(y$tip.label[lsb[y$tip.label == - assoc[i, 2]]]) - } - else { + if (show.tip.label) { + decx[i] <- strwidth(x$tip.label[lsa[x$tip.label == assoc[i, 1]]]) + decy[i] <- strwidth(y$tip.label[lsb[y$tip.label == assoc[i, 2]]]) + } else { decx[i] <- decy[i] <- 0 } - segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + decx[i] + gap, a[lsa[x$tip.label == assoc[i, 1]], 2], a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left, a[lsa[x$tip.label == assoc[i, 1]], 2], col = colors[i], lwd=lwidths[i], lty=ltype[i]) - segments(b2[lsb[y$tip.label == assoc[i, 2]], 1] - (decy[i] + gap), b2[lsb[y$tip.label == assoc[i, 2]], 2], b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right), b2[lsb[y$tip.label == assoc[i, 2]], 2], col = colors[i], lwd=lwidths[i], lty=ltype[i]) - segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left, a[lsa[x$tip.label == assoc[i, 1]], 2], b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right), b2[lsb[y$tip.label == assoc[i, 2]], 2], col = colors[i], lwd=lwidths[i], lty=ltype[i]) + segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + decx[i] + gap, + a[lsa[x$tip.label == assoc[i, 1]], 2], + a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left, + a[lsa[x$tip.label == assoc[i, 1]], 2], + col = colors[i], lwd = lwidths[i], lty = ltype[i]) + + segments(b2[lsb[y$tip.label == assoc[i, 2]], 1] - (decy[i] + gap), + b2[lsb[y$tip.label == assoc[i, 2]], 2], + b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right), + b2[lsb[y$tip.label == assoc[i, 2]], 2], + col = colors[i], lwd = lwidths[i], lty = ltype[i]) + + segments(a[lsa[x$tip.label == assoc[i, 1]], 1] + gap + left, + a[lsa[x$tip.label == assoc[i, 1]], 2], + b2[lsb[y$tip.label == assoc[i, 2]], 1] - (gap + right), + b2[lsb[y$tip.label == assoc[i, 2]], 2], + col = colors[i], lwd = lwidths[i], lty = ltype[i]) } if (return == TRUE) return(res) } diff --git a/R/read.nexus.R b/R/read.nexus.R index 969d42c..abcd131 100644 --- a/R/read.nexus.R +++ b/R/read.nexus.R @@ -53,7 +53,7 @@ clado.build <- function(tp) obj <- list(edge = matrix(c(2, 1), 1, 2), Nnode = 1) tp <- unlist(strsplit(tp, "[\\(\\);]")) obj$tip.label <- tp[2] - if (length(tp) == 3) obj$node.label <- tp[3] + if (tp[3] != "") obj$node.label <- tp[3] class(obj) <- "phylo" return(obj) } diff --git a/R/read.tree.R b/R/read.tree.R index d19acae..efb3117 100644 --- a/R/read.tree.R +++ b/R/read.tree.R @@ -38,7 +38,7 @@ tree.build <- function(tp) obj$edge.length <- as.numeric(tp[3]) obj$Nnode <- 1L obj$tip.label <- tp[2] - if (length(tp) == 4) obj$node.label <- tp[4] + if (tp[4] != "") obj$node.label <- tp[4] class(obj) <- "phylo" return(obj) } diff --git a/R/reorder.phylo.R b/R/reorder.phylo.R index 38a7da2..e06b26b 100644 --- a/R/reorder.phylo.R +++ b/R/reorder.phylo.R @@ -1,8 +1,8 @@ -## reorder.phylo.R (2007-06-16) +## reorder.phylo.R (2010-04-02) ## Internal Reordering of Trees -## Copyright 2006-2007 Emmanuel Paradis +## Copyright 2006-2010 Emmanuel Paradis ## This file is part of the R-package `ape'. ## See the file ../COPYING for licensing issues. @@ -11,9 +11,10 @@ reorder.phylo <- function(x, order = "cladewise", ...) { order <- match.arg(order, c("cladewise", "pruningwise")) if (!is.null(attr(x, "order"))) - if (attr(x, "order") == order) return(x) - nb.tip <- length(x$tip.label) + if (attr(x, "order") == order) return(x) nb.node <- x$Nnode + if (nb.node == 1) return(x) + nb.tip <- length(x$tip.label) nb.edge <- dim(x$edge)[1] neworder <- if (order == "cladewise") .C("neworder_cladewise", as.integer(nb.tip), diff --git a/man/DNAbin.Rd b/man/DNAbin.Rd index b08446f..701fab6 100644 --- a/man/DNAbin.Rd +++ b/man/DNAbin.Rd @@ -78,7 +78,7 @@ Paradis, E. (2007) A Bit-Level Coding Scheme for Nucleotides. \url{http://ape.mpl.ird.fr/misc/BitLevelCodingScheme_20April2007.pdf} } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{as.DNAbin}}, \code{\link{read.dna}}, \code{\link{read.GenBank}}, \code{\link{write.dna}} diff --git a/man/GC.content.Rd b/man/GC.content.Rd index 667e0c7..dc59d07 100644 --- a/man/GC.content.Rd +++ b/man/GC.content.Rd @@ -20,7 +20,7 @@ GC.content(x) \value{ A single numeric value is returned. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{base.freq}}, \code{\link{seg.sites}}, \code{\link{nuc.div}} diff --git a/man/MoranI.Rd b/man/MoranI.Rd index 50eb63b..fd7b28e 100644 --- a/man/MoranI.Rd +++ b/man/MoranI.Rd @@ -59,7 +59,7 @@ \bold{39}, 227--241. } \author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr} and - Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} + Emmanuel Paradis} \seealso{ \code{\link{weight.taxo}} } diff --git a/man/ace.Rd b/man/ace.Rd index 73934df..1e711fd 100644 --- a/man/ace.Rd +++ b/man/ace.Rd @@ -130,8 +130,7 @@ ace(x, phy, type = "continuous", method = "ML", CI = TRUE, Likelihood of ancestor states in adaptive radiation. \emph{Evolution}, \bold{51}, 1699--1711. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}, Ben Bolker -\email{bolker@zoo.ufl.edu}} +\author{Emmanuel Paradis, Ben Bolker \email{bolker@zoo.ufl.edu}} \seealso{ \code{\link{corBrownian}}, \code{\link{corGrafen}}, \code{\link{corMartins}}, \code{\link{compar.ou}}, diff --git a/man/add.scale.bar.Rd b/man/add.scale.bar.Rd index 41dca60..ecef307 100644 --- a/man/add.scale.bar.Rd +++ b/man/add.scale.bar.Rd @@ -30,7 +30,7 @@ add.scale.bar(x, y, length = NULL, ask = FALSE, ...) The function \code{\link[graphics]{locator}} may be used to determine the \code{x} and \code{y} arguments. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{plot.phylo}}, \code{\link{axisPhylo}}, \code{\link[graphics]{locator}} diff --git a/man/as.alignment.Rd b/man/as.alignment.Rd index 47de1d2..276d68d 100644 --- a/man/as.alignment.Rd +++ b/man/as.alignment.Rd @@ -48,7 +48,7 @@ as.DNAbin(x, ...) of \code{"as.DNAbin"}; a matrix of mode character or a list containing vectors of mode character in the case of \code{"as.character"}. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{DNAbin}}, \code{\link{read.dna}}, \code{\link{read.GenBank}}, \code{\link{write.dna}} diff --git a/man/as.matching.Rd b/man/as.matching.Rd index 9595688..8a156c6 100644 --- a/man/as.matching.Rd +++ b/man/as.matching.Rd @@ -49,7 +49,7 @@ as.matching(x, ...) \note{ Branch lengths are not supported in the present version. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \references{ Diaconis, P. W. and Holmes, S. P. (1998) Matchings and phylogenetic trees. \emph{Proceedings of the National Academy of Sciences USA}, diff --git a/man/as.phylo.Rd b/man/as.phylo.Rd index 4b757ac..eb34dc3 100644 --- a/man/as.phylo.Rd +++ b/man/as.phylo.Rd @@ -37,7 +37,7 @@ new2old.phylo(phy) \value{ An object of class \code{"hclust"} or \code{"phylo"}. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link[stats]{hclust}}, \code{\link[stats]{as.hclust}}, \code{\link[stats]{dendrogram}}, \code{\link[ade4]{phylog}}, diff --git a/man/axisPhylo.Rd b/man/axisPhylo.Rd index b96c831..42caaff 100644 --- a/man/axisPhylo.Rd +++ b/man/axisPhylo.Rd @@ -18,7 +18,7 @@ axisPhylo(side = 1, ...) the help pages on \code{\link[graphics]{axis}} and \code{\link[graphics]{par}}). } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{plot.phylo}}, \code{\link{add.scale.bar}}, \code{\link[graphics]{axis}}, \code{\link[graphics]{par}} diff --git a/man/balance.Rd b/man/balance.Rd index bee8d25..35f037b 100644 --- a/man/balance.Rd +++ b/man/balance.Rd @@ -25,5 +25,5 @@ balance(phy) phylogenetic trees, from Yule to today. \emph{Statistical Science}, \bold{16}, 23--34. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \keyword{manip} diff --git a/man/base.freq.Rd b/man/base.freq.Rd index 96414a5..dcb564e 100644 --- a/man/base.freq.Rd +++ b/man/base.freq.Rd @@ -24,7 +24,7 @@ base.freq(x, freq = FALSE) A numeric vector storing the relative frequencies with names \code{c("a", "c", "g", "t")}. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{GC.content}}, \code{\link{seg.sites}}, \code{\link{nuc.div}}, \code{\link{DNAbin}} diff --git a/man/bd.ext.Rd b/man/bd.ext.Rd index e7e0fa0..b26776f 100644 --- a/man/bd.ext.Rd +++ b/man/bd.ext.Rd @@ -39,7 +39,7 @@ bd.ext(phy, S) and taxonomic data. \emph{Proceedings of the Royal Society of London. Series B. Biological Sciences}, \bold{270}, 2499--2505. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{birthdeath}}, \code{\link{branching.times}}, \code{\link{diversi.gof}}, \code{\link{diversi.time}}, diff --git a/man/birthdeath.Rd b/man/birthdeath.Rd index b91d562..3bb5d4f 100644 --- a/man/birthdeath.Rd +++ b/man/birthdeath.Rd @@ -56,7 +56,7 @@ birthdeath(phy) extinctions from molecular phylogenies. in \emph{Extinction Rates}, eds. Lawton, J. H. and May, R. M., pp. 164--182, Oxford University Press. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{branching.times}}, \code{\link{diversi.gof}}, \code{\link{diversi.time}}, \code{\link{ltt.plot}}, diff --git a/man/boot.phylo.Rd b/man/boot.phylo.Rd index d46e095..f0a650b 100644 --- a/man/boot.phylo.Rd +++ b/man/boot.phylo.Rd @@ -111,7 +111,7 @@ prop.clades(phy, ..., part = NULL) Felsenstein, J. (1985) Confidence limits on phylogenies: an approach using the bootstrap. \emph{Evolution}, \bold{39}, 783--791. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{dist.topo}}, \code{\link{consensus}}, \code{\link{nodelabels}} } diff --git a/man/branching.times.Rd b/man/branching.times.Rd index 77639f5..9bb5329 100644 --- a/man/branching.times.Rd +++ b/man/branching.times.Rd @@ -20,7 +20,7 @@ branching.times(phy) returned vector; otherwise the numbers (of mode character) of the matrix \code{edge} of \code{phy} are used as names. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{is.ultrametric}} } diff --git a/man/cherry.Rd b/man/cherry.Rd index 3ba41ad..e57f275 100644 --- a/man/cherry.Rd +++ b/man/cherry.Rd @@ -40,7 +40,7 @@ cherry(phy) McKenzie, A. and Steel, M. (2000) Distributions of cherries for two models of trees. \emph{Mathematical Biosciences}, \bold{164}, 81--92. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{gammaStat}} } diff --git a/man/chronoMPL.Rd b/man/chronoMPL.Rd index 6122699..4c2f850 100644 --- a/man/chronoMPL.Rd +++ b/man/chronoMPL.Rd @@ -51,7 +51,7 @@ chronoMPL(phy, se = TRUE, test = TRUE) lengths. \emph{Molecular Phylogenetics and Evolution}, \bold{24}, 58--65. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{chronogram}}, \code{\link{ratogram}}, \code{\link{NPRS.criterion}}, \code{\link{chronopl}} diff --git a/man/chronopl.Rd b/man/chronopl.Rd index 7d79179..728195b 100644 --- a/man/chronopl.Rd +++ b/man/chronopl.Rd @@ -98,7 +98,7 @@ chronopl(phy, lambda, age.min = 1, age.max = NULL, approach. \emph{Molecular Biology and Evolution}, \bold{19}, 101--109. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{chronogram}}, \code{\link{ratogram}}, \code{\link{NPRS.criterion}}, \code{\link{chronoMPL}} diff --git a/man/compar.gee.Rd b/man/compar.gee.Rd index 28ceb8b..eec81f1 100644 --- a/man/compar.gee.Rd +++ b/man/compar.gee.Rd @@ -72,7 +72,7 @@ compar.gee(formula, data = NULL, family = "gaussian", phy, Biology}, \bold{218}, 175--185. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.tree}}, \code{\link{pic}}, diff --git a/man/compute.brlen.Rd b/man/compute.brlen.Rd index fa0fbd0..780655c 100644 --- a/man/compute.brlen.Rd +++ b/man/compute.brlen.Rd @@ -36,7 +36,7 @@ compute.brlen(phy, method = "Grafen", power = 1, ...) An object of class \code{phylo} with branch lengths. } \author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr} and - Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} + Emmanuel Paradis} \references{ Grafen, A. (1989) The phylogenetic regression. \emph{Philosophical Transactions of the Royal society of London. Series B. Biological diff --git a/man/consensus.Rd b/man/consensus.Rd index bbedf37..2f7bdeb 100644 --- a/man/consensus.Rd +++ b/man/consensus.Rd @@ -31,7 +31,7 @@ consensus(..., p = 1, check.labels = TRUE) \value{ an object of class \code{"phylo"}. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{prop.part}}, \code{\link{dist.topo}} } diff --git a/man/cophenetic.phylo.Rd b/man/cophenetic.phylo.Rd index 18c1dc7..78913eb 100644 --- a/man/cophenetic.phylo.Rd +++ b/man/cophenetic.phylo.Rd @@ -22,7 +22,7 @@ dist.nodes(x) \code{phy}), or, in the case of \code{dist.nodes}, the numbers of the tips and the nodes (as given by the element \code{edge}). } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.tree}} to read tree files in Newick format, \code{\link[stats]{cophenetic}} for the generic function diff --git a/man/correlogram.formula.Rd b/man/correlogram.formula.Rd index a04ecd5..6522ea9 100644 --- a/man/correlogram.formula.Rd +++ b/man/correlogram.formula.Rd @@ -38,7 +38,7 @@ response in \code{formula}. } \author{Julien Dutheil \email{julien.dutheil@univ-montp2.fr} and - Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} + Emmanuel Paradis} \seealso{ \code{\link{plot.correlogram}, \link{Moran.I}} } diff --git a/man/del.gaps.Rd b/man/del.gaps.Rd index 3a22424..d25d7ba 100644 --- a/man/del.gaps.Rd +++ b/man/del.gaps.Rd @@ -23,7 +23,7 @@ del.gaps(x) A vector (if there is only one input sequence) or a list of class \code{"DNAbin"}. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{base.freq}}, \code{\link{GC.content}}, \code{\link{theta.s}}, \code{\link{nuc.div}}, \code{\link{seg.sites}} diff --git a/man/delta.plot.Rd b/man/delta.plot.Rd index 0a24cfe..59877a0 100644 --- a/man/delta.plot.Rd +++ b/man/delta.plot.Rd @@ -26,7 +26,7 @@ delta.plot(X, k = 20, plot = TRUE, which = 1:2) may be very long with only a slight increase in sample size. } \value{ - This function returns invisibly a named list with two componente: + This function returns invisibly a named list with two components: \itemize{ \item{counts}{the counts for the histogram of @@ -48,6 +48,7 @@ delta.plot(X, k = 20, plot = TRUE, which = 1:2) data(woodmouse) d <- dist.dna(woodmouse) delta.plot(d) +layout(1) delta.plot(d, 40, which = 1) } \keyword{hplot} diff --git a/man/dist.dna.Rd b/man/dist.dna.Rd index b2c270a..394baf5 100644 --- a/man/dist.dna.Rd +++ b/man/dist.dna.Rd @@ -176,7 +176,7 @@ dist.dna(x, model = "K80", variance = FALSE, substitutions in the control region of mitochondrial DNA in humans and chimpanzees. \emph{Molecular Biology and Evolution}, \bold{10}, 512--526. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.GenBank}}, \code{\link{read.dna}}, \code{\link{write.dna}}, \code{\link{DNAbin}}, diff --git a/man/dist.gene.Rd b/man/dist.gene.Rd index bf9cc3b..11d6d2e 100644 --- a/man/dist.gene.Rd +++ b/man/dist.gene.Rd @@ -43,7 +43,7 @@ dist.gene(x, method = "pairwise", pairwise.deletion = FALSE, an object of class \code{dist}. If \code{variance = TRUE} an attribute called \code{"variance"} is given to the returned object. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{dist.dna}}, \code{\link{cophenetic.phylo}}, \code{\link[stats]{dist}} diff --git a/man/dist.topo.Rd b/man/dist.topo.Rd index 2c2a285..2017246 100644 --- a/man/dist.topo.Rd +++ b/man/dist.topo.Rd @@ -55,7 +55,7 @@ dist.topo(x, y, method = "PH85") testing minimum-evolution trees. \emph{Molecular Biology and Evolution}, \bold{9}, 945--967. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.tree}} to read tree files in Newick format, \code{\link{cophenetic.phylo}}, \code{\link{prop.part}} diff --git a/man/diversi.gof.Rd b/man/diversi.gof.Rd index 1a8e128..202082c 100644 --- a/man/diversi.gof.Rd +++ b/man/diversi.gof.Rd @@ -52,7 +52,7 @@ diversi.gof(x, null = "exponential", z = NULL) comparisons. \emph{Journal of the American Statistical Association}, \bold{69}, 730--737. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{branching.times}}, \code{\link{diversi.time}} \code{\link{ltt.plot}}, \code{\link{birthdeath}}, \code{\link{yule}}, diff --git a/man/diversi.time.Rd b/man/diversi.time.Rd index cbb16c6..24d6856 100644 --- a/man/diversi.time.Rd +++ b/man/diversi.time.Rd @@ -49,7 +49,7 @@ diversi.time(x, census = NULL, censoring.codes = c(1, 0), Tc = NULL) testing. \emph{Proceedings of the Royal Society of London. Series B. Biological Sciences}, \bold{264}, 1141--1147. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{branching.times}}, \code{\link{diversi.gof}} \code{\link{ltt.plot}}, \code{\link{birthdeath}}, diff --git a/man/drop.tip.Rd b/man/drop.tip.Rd index 9317977..4b4b60e 100644 --- a/man/drop.tip.Rd +++ b/man/drop.tip.Rd @@ -60,7 +60,7 @@ extract.clade(phy, node, root.edge = 0, interactive = FALSE) \value{ an object of class \code{"phylo"}. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{bind.tree}}, \code{\link{root}} } diff --git a/man/gammaStat.Rd b/man/gammaStat.Rd index 4df8a76..c4b3b80 100644 --- a/man/gammaStat.Rd +++ b/man/gammaStat.Rd @@ -34,7 +34,7 @@ gammaStat(phy) the Royal Society of London. Series B. Biological Sciences}, \bold{267}, 2267--2272. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{branching.times}}, \code{\link{ltt.plot}}, \code{\link{skyline}} } diff --git a/man/howmanytrees.Rd b/man/howmanytrees.Rd index cd98f7c..a576551 100644 --- a/man/howmanytrees.Rd +++ b/man/howmanytrees.Rd @@ -54,7 +54,7 @@ howmanytrees(n, rooted = TRUE, binary = TRUE, Felsenstein, J. (2004) \emph{Inferring phylogenies}. Sunderland: Sinauer Associates. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \examples{ ### Table 3.1 in Felsenstein 2004: for (i in c(1:20, 30, 40, 50)) diff --git a/man/identify.phylo.Rd b/man/identify.phylo.Rd index 7e05425..166653a 100644 --- a/man/identify.phylo.Rd +++ b/man/identify.phylo.Rd @@ -40,7 +40,7 @@ \code{"nodes"} with the identification of the tips and/or of the nodes. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{plot.phylo}}, \code{\link{nodelabels}}, \code{\link[graphics]{identify}} for the generic function diff --git a/man/is.ultrametric.Rd b/man/is.ultrametric.Rd index 51bd573..767cde9 100644 --- a/man/is.ultrametric.Rd +++ b/man/is.ultrametric.Rd @@ -22,7 +22,7 @@ is.ultrametric(phy, tol = .Machine$double.eps^0.5) The default value for \code{tol} is based on the numerical characteristics of the machine R is running on. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{is.binary.tree}}, \code{\link[base]{.Machine}} } diff --git a/man/ladderize.Rd b/man/ladderize.Rd index 1d7ac45..8855837 100644 --- a/man/ladderize.Rd +++ b/man/ladderize.Rd @@ -14,7 +14,7 @@ ladderize(phy, right = TRUE) This function reorganizes the internal structure of the tree to get the ladderized effect when plotted. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{plot.phylo}}, \code{\link{reorder.phylo}} } diff --git a/man/ltt.plot.Rd b/man/ltt.plot.Rd index a36ec22..922fcfe 100644 --- a/man/ltt.plot.Rd +++ b/man/ltt.plot.Rd @@ -69,7 +69,7 @@ mltt.plot(phy, ..., dcol = TRUE, dlty = FALSE, legend = TRUE, Transactions of the Royal Society of London. Series B. Biological Sciences}, \bold{349}, 25--31. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{skyline}}, \code{\link{branching.times}}, \code{\link{birthdeath}}, \code{\link{bd.ext}}, \code{\link{yule.cov}} diff --git a/man/makeNodeLabel.Rd b/man/makeNodeLabel.Rd index e7e920a..062b7c8 100644 --- a/man/makeNodeLabel.Rd +++ b/man/makeNodeLabel.Rd @@ -54,7 +54,7 @@ makeNodeLabel(phy, method = "number", prefix = "Node", nodeList = list(), ...) } \examples{ tr <- -"((Pan_paniscus,Pan_troglodytes),((Homo_sapiens,Hom_erectus),Homo_abilis));" +"((Pan_paniscus,Pan_troglodytes),((Homo_sapiens,Homo_erectus),Homo_abilis));" tr <- read.tree(text = tr) tr <- makeNodeLabel(tr, "u", nodeList = list(Pan = "Pan", Homo = "Homo")) plot(tr, show.node.label = TRUE) diff --git a/man/matexpo.Rd b/man/matexpo.Rd index a38b581..9172a96 100644 --- a/man/matexpo.Rd +++ b/man/matexpo.Rd @@ -14,7 +14,7 @@ matexpo(x) \value{ a numeric matrix of the same dimensions than `x'. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \examples{ ### a simple rate matrix: m <- matrix(0.1, 4, 4) diff --git a/man/mrca.Rd b/man/mrca.Rd index df0805e..d36ef34 100644 --- a/man/mrca.Rd +++ b/man/mrca.Rd @@ -24,5 +24,5 @@ mrca(phy, full = FALSE) \value{ a matrix of mode numeric. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \keyword{manip} diff --git a/man/mst.Rd b/man/mst.Rd index 06c9dfa..936b2b9 100644 --- a/man/mst.Rd +++ b/man/mst.Rd @@ -54,7 +54,7 @@ mst(X) \author{ Yvonnick Noel \email{noel@univ-lille3.fr}, Julien Claude \email{claude@isem.univ-montp2.fr} and - Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr} + Emmanuel Paradis } \seealso{ \code{\link{dist.dna}}, \code{\link{dist.gene}}, diff --git a/man/multi2di.Rd b/man/multi2di.Rd index ddb0f3c..2dd5f03 100644 --- a/man/multi2di.Rd +++ b/man/multi2di.Rd @@ -28,7 +28,7 @@ di2multi(phy, tol = 1e-08) \seealso{ \code{\link{is.binary.tree}} } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \value{ Both functions return an object of class \code{"phylo"}. } diff --git a/man/nj.Rd b/man/nj.Rd index 7789a03..5198358 100644 --- a/man/nj.Rd +++ b/man/nj.Rd @@ -19,7 +19,7 @@ nj(X) method for reconstructing phylogenetic trees. \emph{Molecular Biology and Evolution}, \bold{4}, 406--425. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{write.tree}}, \code{\link{read.tree}}, \code{\link{dist.dna}}, \code{\link{bionj}}, diff --git a/man/node.depth.Rd b/man/node.depth.Rd index ee1d457..aced56a 100644 --- a/man/node.depth.Rd +++ b/man/node.depth.Rd @@ -19,7 +19,7 @@ node.depth(phy) A numeric vector indexed with the node numbers of the matrix `edge' of \code{phy}. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{plot.phylo}} } diff --git a/man/nodelabels.Rd b/man/nodelabels.Rd index 292dc13..82a3acb 100644 --- a/man/nodelabels.Rd +++ b/man/nodelabels.Rd @@ -80,8 +80,8 @@ edgelabels(text, edge, adj = c(0.5, 0.5), frame = "rect", \code{show.tip.label}) of \code{plot.phylo} in most cases (see the examples). } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}, Ben Bolker - \email{bolker@zoo.ufl.edu}, and Jim Lemon} +\author{Emmanuel Paradis, Ben Bolker \email{bolker@zoo.ufl.edu}, and Jim + Lemon} \seealso{ \code{\link{plot.phylo}}, \code{\link{edges}} } diff --git a/man/phymltest.Rd b/man/phymltest.Rd index 762aee1..6a1cd74 100644 --- a/man/phymltest.Rd +++ b/man/phymltest.Rd @@ -117,7 +117,7 @@ phymltest(seqfile, format = "interleaved", itree = NULL, \emph{Systematic Biology}, \bold{52}, 696--704. \url{http://www.atgc-montpellier.fr/phyml/} } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.tree}}, \code{\link{write.tree}}, \code{\link{dist.dna}} diff --git a/man/pic.Rd b/man/pic.Rd index b34a753..0c9de0b 100644 --- a/man/pic.Rd +++ b/man/pic.Rd @@ -37,7 +37,7 @@ pic(x, phy, scaled = TRUE, var.contrasts = FALSE) Felsenstein, J. (1985) Phylogenies and the comparative method. \emph{American Naturalist}, \bold{125}, 1--15. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.tree}}, \code{\link{compar.gee}}, \code{\link{compar.lynch}} } diff --git a/man/plot.correlogram.Rd b/man/plot.correlogram.Rd index 58540d8..bf38608 100644 --- a/man/plot.correlogram.Rd +++ b/man/plot.correlogram.Rd @@ -48,7 +48,7 @@ the points. To keep black lines, it is better to leave \code{pch} between 21 and 25. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{correlogram.formula}}, \code{\link{Moran.I}} } diff --git a/man/plot.phylo.Rd b/man/plot.phylo.Rd index fa2658f..614ce62 100644 --- a/man/plot.phylo.Rd +++ b/man/plot.phylo.Rd @@ -160,7 +160,7 @@ \item{Ntip}{} \item{Nnode}{} } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.tree}}, \code{\link{add.scale.bar}}, \code{\link{axisPhylo}}, \code{\link{nodelabels}}, diff --git a/man/print.phylo.Rd b/man/print.phylo.Rd index 779f3f1..466fe87 100644 --- a/man/print.phylo.Rd +++ b/man/print.phylo.Rd @@ -36,8 +36,7 @@ An object of class \code{"phylo"} (\code{[[}, \code{$}) or of class \code{"multiPhylo"} (\code{[}), or NULL. } -\author{Ben Bolker \email{bolker@zoo.ufl.edu} and Emmanuel Paradis - \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Ben Bolker \email{bolker@zoo.ufl.edu} and Emmanuel Paradis} \seealso{ \code{\link{read.tree}}, \code{\link{summary.phylo}}, \code{\link[base]{print}} for the generic R function diff --git a/man/read.GenBank.Rd b/man/read.GenBank.Rd index e323b44..9783e12 100644 --- a/man/read.GenBank.Rd +++ b/man/read.GenBank.Rd @@ -34,7 +34,7 @@ read.GenBank(access.nb, seq.names = access.nb, \code{\link{read.dna}}, \code{\link{write.dna}}, \code{\link{dist.dna}}, \code{\link{DNAbin}} } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \examples{ ### This won't work if your computer is not connected ### to the Internet!!! diff --git a/man/read.dna.Rd b/man/read.dna.Rd index 3d4d33b..4c02232 100644 --- a/man/read.dna.Rd +++ b/man/read.dna.Rd @@ -95,7 +95,7 @@ read.dna(file, format = "interleaved", skip = 0, \code{\link{read.GenBank}}, \code{\link{write.dna}}, \code{\link{DNAbin}}, \code{\link{dist.dna}}, \code{\link{woodmouse}} } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \examples{ ### a small extract from `data(woddmouse)' cat("3 40", diff --git a/man/read.nexus.Rd b/man/read.nexus.Rd index a517e89..3c8d9c1 100644 --- a/man/read.nexus.Rd +++ b/man/read.nexus.Rd @@ -72,7 +72,7 @@ read.nexus(file, tree.names = NULL) extensible file format for systematic information. \emph{Systematic Biology}, \bold{46}, 590--621. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.tree}}, \code{\link{write.nexus}}, \code{\link{write.tree}}, \code{\link{read.nexus.data}}, diff --git a/man/read.tree.Rd b/man/read.tree.Rd index 8ad6ed4..1bf915c 100644 --- a/man/read.tree.Rd +++ b/man/read.tree.Rd @@ -84,8 +84,7 @@ read.tree(file = "", text = NULL, tree.names = NULL, skip = 0, in R. \url{http://ape.mpl.ird.fr/misc/FormatTreeR_28July2008.pdf} } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr} and Daniel - Lawson \email{dan.lawson@bristol.ac.uk}} +\author{Emmanuel Paradis and Daniel Lawson \email{dan.lawson@bristol.ac.uk}} \seealso{ \code{\link{write.tree}}, \code{\link{read.nexus}}, \code{\link{write.nexus}}, \code{\link[base]{scan}} for the basic R diff --git a/man/reorder.phylo.Rd b/man/reorder.phylo.Rd index f63dda5..6a002fa 100644 --- a/man/reorder.phylo.Rd +++ b/man/reorder.phylo.Rd @@ -31,7 +31,7 @@ \value{ an object of class \code{"phylo"}. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.tree}} to read tree files in Newick format, \code{\link[stats]{reorder}} for the generic function diff --git a/man/root.Rd b/man/root.Rd index f721c04..6559a69 100644 --- a/man/root.Rd +++ b/man/root.Rd @@ -54,7 +54,7 @@ is.rooted(phy) an object of class \code{"phylo"} for \code{root} and \code{unroot}; a single logical value for \code{is.rooted}. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{bind.tree}}, \code{\link{drop.tip}}, \code{\link{nodelabels}}, \code{\link{identify.phylo}} diff --git a/man/seg.sites.Rd b/man/seg.sites.Rd index 8f97c52..d03b56a 100644 --- a/man/seg.sites.Rd +++ b/man/seg.sites.Rd @@ -21,7 +21,7 @@ seg.sites(x) A numeric (integer) vector giving the indices of the segregating sites. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \note{ The present version looks for the sites which are ``variable'' in the data in terms of different \emph{letters}. This may give unexpected diff --git a/man/summary.phylo.Rd b/man/summary.phylo.Rd index 3904a4b..6278760 100644 --- a/man/summary.phylo.Rd +++ b/man/summary.phylo.Rd @@ -38,7 +38,7 @@ Nedge(phy) A NULL value in the case of \code{summary}, a single numeric value for the three other functions. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.tree}}, \code{\link[base]{summary}} for the generic R function diff --git a/man/weight.taxo.Rd b/man/weight.taxo.Rd index b6bc15c..5d47407 100644 --- a/man/weight.taxo.Rd +++ b/man/weight.taxo.Rd @@ -27,7 +27,7 @@ \value{ a square numeric matrix. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{Moran.I}}, \code{\link{correlogram.formula}} } diff --git a/man/which.edge.Rd b/man/which.edge.Rd index d8cbbf5..c2a782e 100644 --- a/man/which.edge.Rd +++ b/man/which.edge.Rd @@ -24,7 +24,7 @@ which.edge(phy, group) \value{ a numeric vector. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{bind.tree}}, \code{\link{drop.tip}}, \code{\link{root}} } diff --git a/man/write.dna.Rd b/man/write.dna.Rd index 318a341..fb87ae7 100644 --- a/man/write.dna.Rd +++ b/man/write.dna.Rd @@ -76,7 +76,7 @@ write.dna(x, file, format = "interleaved", append = FALSE, \value{ None (invisible `NULL'). } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \references{ Anonymous. FASTA format description. \url{http://www.ncbi.nlm.nih.gov/BLAST/fasta.html} diff --git a/man/write.nexus.Rd b/man/write.nexus.Rd index fb5d653..a3e66aa 100644 --- a/man/write.nexus.Rd +++ b/man/write.nexus.Rd @@ -40,7 +40,7 @@ write.nexus(..., file = "", translate = TRUE, original.data = TRUE) Biology}, \bold{46}, 590--621. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{read.nexus}}, \code{\link{read.tree}}, \code{\link{write.tree}}, \code{\link{read.nexus.data}}, diff --git a/man/write.tree.Rd b/man/write.tree.Rd index a90f4c5..64e0c70 100644 --- a/man/write.tree.Rd +++ b/man/write.tree.Rd @@ -44,8 +44,7 @@ write.tree(phy, file = "", append = FALSE, \url{http://evolution.genetics.washington.edu/phylip/newick_doc.html} } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr} and Daniel - Lawson \email{dan.lawson@bristol.ac.uk}} +\author{Emmanuel Paradis and Daniel Lawson \email{dan.lawson@bristol.ac.uk}} \seealso{ \code{\link{read.tree}}, \code{\link{read.nexus}}, \code{\link{write.nexus}} diff --git a/man/yule.Rd b/man/yule.Rd index 8b3d406..c5d8012 100644 --- a/man/yule.Rd +++ b/man/yule.Rd @@ -40,7 +40,7 @@ yule(phy, use.root.edge = FALSE) \item{se}{the standard-error of lambda.} \item{loglik}{the log-likelihood at its maximum.} } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{branching.times}}, \code{\link{diversi.gof}}, \code{\link{diversi.time}}, \code{\link{ltt.plot}}, diff --git a/man/yule.cov.Rd b/man/yule.cov.Rd index 7e3b1a2..10313c8 100644 --- a/man/yule.cov.Rd +++ b/man/yule.cov.Rd @@ -78,7 +78,7 @@ method. This can be done with the function \code{\link{ace}}. Paradis, E. (2005) Statistical analysis of diversification with species traits. \emph{Evolution}, \bold{59}, 1--12. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{branching.times}}, \code{\link{diversi.gof}}, \code{\link{diversi.time}}, \code{\link{ltt.plot}}, diff --git a/man/yule.time.Rd b/man/yule.time.Rd index f67642b..e5904e2 100644 --- a/man/yule.time.Rd +++ b/man/yule.time.Rd @@ -46,7 +46,7 @@ yule.time(phy, birth, BIRTH = NULL, root.time = 0, opti = "nlm", start = 0.01) \value{ An object of class "yule" (see \code{\link{yule}}). } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{branching.times}}, \code{\link{ltt.plot}}, \code{\link{birthdeath}}, \code{\link{yule}}, \code{\link{yule.cov}} diff --git a/man/zoom.Rd b/man/zoom.Rd index 314f3a3..7c02013 100644 --- a/man/zoom.Rd +++ b/man/zoom.Rd @@ -37,7 +37,7 @@ zoom(phy, focus, subtree = FALSE, col = rainbow, ...) subtrees: see \code{\link[grDevices]{rainbow}} for some possibilities with colours. } -\author{Emmanuel Paradis \email{Emmanuel.Paradis@mpl.ird.fr}} +\author{Emmanuel Paradis} \seealso{ \code{\link{plot.phylo}}, \code{\link{drop.tip}}, \code{\link[graphics]{layout}}, \code{\link[grDevices]{rainbow}}, diff --git a/src/dist_dna.c b/src/dist_dna.c index 9057b9b..2cabb7d 100644 --- a/src/dist_dna.c +++ b/src/dist_dna.c @@ -1,4 +1,4 @@ -/* dist_dna.c 2010-03-16 */ +/* dist_dna.c 2010-03-29 */ /* Copyright 2005-2010 Emmanuel Paradis @@ -800,67 +800,6 @@ void distDNA_BH87(unsigned char *x, int *n, int *s, double *d, for (i2 = i1 + 1; i2 <= *n; i2++) { for (k = 0; k < 16; k++) Ntab[k] = 0; for (s1 = i1 - 1, s2 = i2 - 1; s1 < i1 + *n*(*s - 1); s1+= *n, s2 += *n) { -#define PREPARE_BF_F84\ - A = (BF[0]*BF[2])/(BF[0] + BF[2]) + (BF[1]*BF[3])/(BF[1] + BF[3]);\ - B = BF[0]*BF[2] + BF[1]*BF[3];\ - C = (BF[0] + BF[2])*(BF[1] + BF[3]); - -#define COMPUTE_DIST_F84\ - P = ((double) Ns/L);\ - Q = ((double) (Nd - Ns)/L);\ - d[target] = -2*A*log(1 - P/(2*A) - (A - B)*Q/(2*A*C)) + 2*(A - B - C)*log(1 - Q/(2*C));\ - if (*variance) {\ - t1 = A*C;\ - t2 = C*P/2;\ - t3 = (A - B)*Q/2;\ - a = t1/(t1 - t2 - t3);\ - b = A*(A - B)/(t1 - t2 - t3) - (A - B - C)/(C - Q/2);\ - var[target] = (a*a*P + b*b*Q - pow(a*P + b*Q, 2))/2;\ - } - -void distDNA_F84(unsigned char *x, int *n, int *s, double *d, - double *BF, int *variance, double *var) -{ - int i1, i2, Nd, Ns, L, target, s1, s2; - double P, Q, A, B, C, a, b, t1, t2, t3; - - PREPARE_BF_F84 - L = *s; - - target = 0; - for (i1 = 1; i1 < *n; i1++) { - for (i2 = i1 + 1; i2 <= *n; i2++) { - Nd = Ns = 0; - for (s1 = i1 - 1, s2 = i2 - 1; s1 < i1 + *n*(*s - 1); s1+= *n, s2 += *n) { - COUNT_TS_TV - } - COMPUTE_DIST_F84 - target++; - } - } -} - -void distDNA_F84_pairdel(unsigned char *x, int *n, int *s, double *d, - double *BF, int *variance, double *var) -{ - int i1, i2, Nd, Ns, L, target, s1, s2; - double P, Q, A, B, C, a, b, t1, t2, t3; - - PREPARE_BF_F84 - - target = 0; - for (i1 = 1; i1 < *n; i1++) { - for (i2 = i1 + 1; i2 <= *n; i2++) { - Nd = Ns = L = 0; - for (s1 = i1 - 1, s2 = i2 - 1; s1 < i1 + *n*(*s - 1); s1+= *n, s2 += *n) { - CHECK_PAIRWISE_DELETION - COUNT_TS_TV - } - COMPUTE_DIST_F84 - target++; - } - } -} DO_CONTINGENCY_NUCLEOTIDES } -- 2.39.2