various corrections

git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@116 6e262413-ae40-0410-9e79-b911bd7a66b7

diff --git a/DESCRIPTION b/DESCRIPTION
index 981ea9f2ad76306c69db48c8eb7182fdfcdc6973..f452091b78cae92ae5061fe83c343a2a3519e0ea 100644 (file)
--- 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 <Emmanuel.Paradis@ird.fr>

diff --git a/R/cophyloplot.R b/R/cophyloplot.R
index 04425c64360aa171f399fb78b790c5d444bfce06..faf9e34ae792f5571dc4b80910e4514c27b3b719 100644 (file)
--- 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 969d42c0e403c23c28bb459ecdc41dc1d2a3305c..abcd1314b8d3b7b91c7449a580446f453577c7b7 100644 (file)
--- 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 d19acaef73edfa15054bb30a1158d647eaa5b06f..efb311709460535abef52f0503d5c8e63360f9df 100644 (file)
--- 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 38a7da2e3158a6e516869941ef877a5ff64705ee..e06b26bb44e6a7e9439819d03544c52f4c4971a7 100644 (file)
--- 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 b08446f6005a67dae11e2b9503a3f76bb14112e7..701fab66d213e039827b15171452ba03361382a8 100644 (file)
--- 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 667e0c72082d9978bceaaf2855e912aa952d76a7..dc59d07b5f18640ff3ba57bc3ec9bd48f9c954f5 100644 (file)
--- 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 50eb63b2ebd17ca8e54c12afda8d420749f6fe95..fd7b28ef42e612aa5847571a24de842ddefc9103 100644 (file)
--- 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 73934dfb303498aacbdcaf7a2fe78bc536f7b532..1e711fdaece40483ea439729a76dc2022026ea73 100644 (file)
--- 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 41dca6061d72f75a50fcacb0b161757e744da7cb..ecef307ea0274a167bb8f74eede9fad2297c580b 100644 (file)
--- 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 47de1d2d9526f0cbc5960b7ffaeb8993ae44a4ec..276d68dc274613f65437ad5a5d697f0d157c16c8 100644 (file)
--- 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 9595688353647a0629d88058de5c5b2a84f6fc4e..8a156c64507e5799ac729223da620687149a007d 100644 (file)
--- 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 4b757ac08960f10cad988410766009abd197827a..eb34dc36583bfc6c50efa3459312ec88d5fbb866 100644 (file)
--- 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 b96c83172ae34628189de64d02053cbc20ca33dc..42caaff6a6cd4a217b52b94d5c5845795f13c0f1 100644 (file)
--- 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 bee8d256803f8cfebc4f68406950ee38ad2f64f6..35f037b8ab138aa318a79f84c9c2054ebd9a22d0 100644 (file)
--- 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 96414a5f2e6234c32dfbc1cfbb493f4f28960e1d..dcb564e6329f6263eb9d1ca4f69f7708b48c7e46 100644 (file)
--- 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 e7e0fa002073ad02d7aaccde495e02c092cd69b6..b26776f886be0786656c71b0b1146f7f4f1b4f4d 100644 (file)
--- 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 b91d5628a3fd9d3e373085ed690c460f4dc37c1b..3bb5d4f38be5cee82a9eb2f7b54530c29035a5c3 100644 (file)
--- 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 d46e0959a2ce8abe8d131766ae361cbed4e380fb..f0a650b44caa434854050f6b2cf900211dde7e76 100644 (file)
--- 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 77639f5e8274d2ddf83d321939dd8334b410564c..9bb5329e0a42883d02b411bf731f84d3cfed998e 100644 (file)
--- 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 3ba41ad84ba7cccb7dd2a964b027bb904ba0382d..e57f275278b3728e9a40d8efc0005e5916b4e849 100644 (file)
--- 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 6122699a56e5d053dbe8f117e61fca0248c7ca96..4c2f85040b6a66a17e76169bb794e656e5772296 100644 (file)
--- 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 7d7917971a44b7ca20109643be9fd672702c822b..728195b7ec37143bd0455356bdd06d119aa99c74 100644 (file)
--- 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 28ceb8bbc54ebad78c94e99db15103202a711e5d..eec81f1b3ffe6a6dfd03577b7bd1756163ff5214 100644 (file)
--- 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 fa0fbd0509f34c637d95f88ecad0b19057991bfb..780655c6475e1ce001c749c15659c3a7f9b124c2 100644 (file)
--- 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 bbedf3706d11cf6f30b63e57c227db3527bedbf5..2f7bdeb282018b18821a66d0958c90f8b1d59f37 100644 (file)
--- 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 18c1dc7fabd13c44a5f3d43e1a44c8597e9bdcff..78913ebbffef8dec65007250559d65fb5516d38d 100644 (file)
--- 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 a04ecd528f962a1c205681caf7d2eb339faec788..6522ea933ee5e7e4b416f3e456d9e5a5739bad7c 100644 (file)
--- 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 3a22424a75a08160b79327be0d83578e651d53c6..d25d7ba53e3873cf3a7e706cc2062193a99c6a15 100644 (file)
--- 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 0a24cfedebd0a362a51779684bf1aa9e5cf1409a..59877a0b0e4ca745f177ffdb5838f3e92e011d01 100644 (file)
--- 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 b2c270a3bf8dfa8845a304f9b924f98912389cdd..394baf57ba2ec75423650b190c66d505033c2341 100644 (file)
--- 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 bf9cc3bec2a3b5ada6b227874ba1f3772937ff69..11d6d2e79a123e46e150fd677dedf6ebe7359136 100644 (file)
--- 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 2c2a28525aa026c6ec5583cf0206b9eb3ccc5496..2017246d41cee719e9fe27e391175866f7ee57dc 100644 (file)
--- 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 1a8e128de7bb351095bb3014b12e182b732f000a..202082c7c481c10c257bce6a8f63ce5f5b67deb3 100644 (file)
--- 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 cbb16c69c0685156daa14054c65a2e1346d1e5a4..24d68564ed380a25189b90ad796c3a9b18e7e6e2 100644 (file)
--- 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 9317977fa7cb8383bdcf23c84d8c25b127458dbf..4b4b60e3e496f3c8a9bdf7c2a8b985a69b9b0d52 100644 (file)
--- 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 4df8a76e11759958030de407c055853873fdd8ae..c4b3b80f0ed64cb5762b33c902b476892505560a 100644 (file)
--- 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 cd98f7cec3a941b15f4cbabd897d7efb7acd76cc..a576551a517e00d11567bdbd276b26e83697f058 100644 (file)
--- 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 7e05425b114efffdcf6bfb1d26ed160f6a975d1d..166653aac4f9ac96031b5356af4d866dcc46fbd8 100644 (file)
--- 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 51bd573c35e84b5f7218bac93416df883145f033..767cde9dc9b2b1b8397ecbf8e152ffb893733e1a 100644 (file)
--- 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 1d7ac45b91aad0d47100e84ec448bfde6b0cfc6e..88558373f8d0f6f25f224f74f286152e4437b4e9 100644 (file)
--- 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 a36ec22c52a8ccaa6af622b5edda8c3b342d7917..922fcfe56c699065874c40f7247ed0b255b2e96e 100644 (file)
--- 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 e7e920a9de9b2a57b17bcbf8905f04eb56b6582e..062b7c88682f97a76a910517d738043a4130aae3 100644 (file)
--- 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 a38b58135dd46c91666001cb78a7e05cce63f589..9172a9698960502793ca890d8987c00aa0d0a9e1 100644 (file)
--- 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 df0805ed9863ef4792f56f45e1bf63ea31ca46ae..d36ef348aebc89f2102659faa07bfcfd2bea448a 100644 (file)
--- 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 06c9dfabdde237303e3da709fcef6b4746ff7522..936b2b9a8dcb0d5f0e822597e126af9d4e8ebc58 100644 (file)
--- 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 ddb0f3c20745fb0965408d1c408fc8bf38914279..2dd5f03e63bdbdc5865ddb219c4c042b684aa657 100644 (file)
--- 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 7789a03cdddc6c0f40401945345acef45709e7b9..51983589a8ad4238a578c374181ae71176f8b6e0 100644 (file)
--- 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 ee1d4570dcfd60bbc5a4e24af319fc2a96b6e30b..aced56a8c4952757ddc07958b0546ee4dab8fbdb 100644 (file)
--- 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 292dc1389f06248583b42aef9b40918c1528c2cf..82a3acbc28ccdc14fe79f88df440090d78a567b8 100644 (file)
--- 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 762aee18016b2d48a8c21118eb847bce6897bea4..6a1cd74affb2bb14ffe47b8f369b544d6adf21c2 100644 (file)
--- 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 b34a7532475eaff7e026497ce03f9f72e80fb147..0c9de0ba5ce040f424a512dc1f1625f664942eb5 100644 (file)
--- 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 58540d882bba9319638059a7c24d275d3ecfefab..bf386089356cd481e7fd6475353505d0d4ff82b8 100644 (file)
--- 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 fa2658f71f5b64fe0275ea744903ada8a9f8dd71..614ce6285a24f8f5b28209d737ddfc65c016b014 100644 (file)
--- 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 779f3f13f9e051f3eb85e5cea9c7312a857fab56..466fe87de08fa5c8477139b317ea2e838179ef29 100644 (file)
--- 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 e323b44f6149841afaa6429493b043de3115b6c3..9783e1232f763d0788331f14bbd445664406f2bb 100644 (file)
--- 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 3d4d33b9cc250f1872a18d91e34e4e9d673ad2d5..4c02232ba8d332708162c35d257fdac66066415b 100644 (file)
--- 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 a517e8991ab156510612f5c80fd6d86cde105ee9..3c8d9c13d475c7f2b8cdf00d3aa3a6e3d8011de1 100644 (file)
--- 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 8ad6ed4db3ac76a88eadf748c420c9de192283d5..1bf915cd8656ae2862457f8865806b473ff17f83 100644 (file)
--- 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 f63dda597a920513036b686f60646249cd302ec2..6a002faee528f536db02578c939b6c75408d84cf 100644 (file)
--- 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 f721c04f7b3fc8326cabc50c6e65d5e7c762d4d3..6559a690eaab39e7fd713c96886e8945a0969b84 100644 (file)
--- 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 8f97c52ec16e6b98c70da739059b1f9d29748d5f..d03b56aa15e81f2014b3af1240465faa4932b2da 100644 (file)
--- 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 3904a4b882f025dfe15456e64586166c95696bc8..6278760b5e0398d289a0469741976f55916a4e34 100644 (file)
--- 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 b6bc15c977de75082b77db0c60b936a6ad3dba95..5d4740726424c03b8e59815578b4a85d8e3083f3 100644 (file)
--- 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 d8cbbf5346719ff51c87c75f4404852b64930962..c2a782ed846e3f1f7c724a0d2dba8ff3f7b81cdb 100644 (file)
--- 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 318a341378175137e6f2497835b84969a7180c36..fb87ae71e8f5b2be5f63dbff78cf1fba013e1a1d 100644 (file)
--- 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 fb5d653c834c4c252666856ab6263983e03ec5f1..a3e66aac2658c5fc79e6a6c981c38b269bc49597 100644 (file)
--- 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 a90f4c5816a14c8e318b51f7e6bf093686ca8e6e..64e0c70fa118c09596cb440b8402cfbf8d3bf6f5 100644 (file)
--- 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 8b3d406ddb8192e2869bb998d2c54bddb0f4ddba..c5d801208dd2a880c464a7545d37b6803f07573d 100644 (file)
--- 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 7e3b1a2fb395989daf87661fa8feed9d04864da2..10313c8d8c0e9bdb66a6af45a13d610851a3f863 100644 (file)
--- 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 f67642b1db52f6e0d51f3c46d7d64ee8b1c7256e..e5904e215420e391f4c13b2e7e9d409ec1ba5abf 100644 (file)
--- 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 314f3a3fe4b4028833d6b677a2ef258d83273ac1..7c0201325f0c647267631ad37391bcdd9706e831 100644 (file)
--- 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 9057b9be5bfe8190c41d08063496728e910fccb6..2cabb7de56bd3a5a05719623f40a93ff4d44ca9c 100644 (file)
--- 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
            }