From 2741f6e9f61e33c7b499f27c47604606d08f4bea Mon Sep 17 00:00:00 2001 From: paradis Date: Mon, 1 Nov 2010 17:33:56 +0000 Subject: [PATCH] final version for ape 2.6-1 git-svn-id: https://svn.mpl.ird.fr/ape/dev/ape@134 6e262413-ae40-0410-9e79-b911bd7a66b7 --- ChangeLog | 8 +++++--- DESCRIPTION | 2 +- R/birthdeath.R | 4 ++-- man/dist.dna.Rd | 36 ++++++++++++++++++++---------------- man/mixedFontLabel.Rd | 3 ++- 5 files changed, 30 insertions(+), 23 deletions(-) diff --git a/ChangeLog b/ChangeLog index 16201fb..50d75d7 100644 --- a/ChangeLog +++ b/ChangeLog @@ -4,12 +4,14 @@ NEW FEATURES o The new speciesTree calculates the species tree from a set of gene - trees. Two methods are currently available: maximum tree and + trees. Several methods are available including maximum tree and shallowest divergence tree. BUG FIXES + o A bug introduced in write.tree() with ape 2.6 has been fixed. + o as.list.DNAbin() did not work correctly with vectors. o as.hclust.phylo() failed with trees with node labels (thanks to @@ -76,8 +78,8 @@ OTHER CHANGES o pic() now returns a vector with the node labels of the tree (if available) as names. - o write.tree() and read.tree() have been substantially thanks to - contributions by Klaus Schliep. + o write.tree() and read.tree() have been substantially improved thanks + to contributions by Klaus Schliep. diff --git a/DESCRIPTION b/DESCRIPTION index 27ce5f3..e38fc9f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: ape Version: 2.6-1 -Date: 2010-10-20 +Date: 2010-11-01 Title: Analyses of Phylogenetics and Evolution Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong, Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel, Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer Opgen-Rhein, Klaus Schliep, Korbinian Strimmer, Damien de Vienne Maintainer: Emmanuel Paradis diff --git a/R/birthdeath.R b/R/birthdeath.R index 4c65ecd..b4a25e1 100644 --- a/R/birthdeath.R +++ b/R/birthdeath.R @@ -84,8 +84,8 @@ bd.ext <- function(phy, S) if (!inherits(phy, "phylo")) stop('object "phy" is not of class "phylo"') if (!is.null(names(S))) { if (all(names(S) %in% phy$tip.label)) S <- S[phy$tip.label] - else warning('the names of argument "S" and the names of the tip labels -did not match: the former were ignored in the analysis.') + else warning('the names of argument "S" and the tip labels +did not match: the former were ignored.') } N <- length(S) x <- branching.times(phy) diff --git a/man/dist.dna.Rd b/man/dist.dna.Rd index 3a5e3e0..83211d0 100644 --- a/man/dist.dna.Rd +++ b/man/dist.dna.Rd @@ -11,10 +11,11 @@ dist.dna(x, model = "K80", variance = FALSE, of class \code{"DNAbin"} (use \code{\link{as.DNAbin}} is they are stored as character).} \item{model}{a character string specifying the evlutionary model to be - used; must be one of \code{"raw"}, \code{"N"}, \code{"JC69"}, - \code{"K80"} (the default), \code{"F81"}, \code{"K81"}, - \code{"F84"}, \code{"BH87"}, \code{"T92"}, \code{"TN93"}, - \code{"GG95"}, \code{"logdet"}, or \code{"paralin"}.} + used; must be one of \code{"raw"}, \code{"N"}, \code{"TS"}, + \code{"TV"}, \code{"JC69"}, \code{"K80"} (the default), + \code{"F81"}, \code{"K81"}, \code{"F84"}, \code{"BH87"}, + \code{"T92"}, \code{"TN93"}, \code{"GG95"}, \code{"logdet"}, or + \code{"paralin"}.} \item{variance}{a logical indicating whether to compute the variances of the distances; defaults to \code{FALSE} so the variances are not computed.} @@ -43,12 +44,15 @@ dist.dna(x, model = "K80", variance = FALSE, References. \itemize{ - \item{``raw'', ``N''}{This is simply the proportion or the number of + \item{\code{raw}, \code{N}: }{This is simply the proportion or the number of sites that differ between each pair of sequences. This may be useful to draw ``saturation plots''. The options \code{variance} and \code{gamma} have no effect, but \code{pairwise.deletion} can.} - \item{``JC69''}{This model was developed by Jukes and Cantor (1969). It + \item{\code{TS}, \code{TV}: }{These are the numbers of transitions and + transversions, respectively.} + + \item{\code{JC69}: }{This model was developed by Jukes and Cantor (1969). It assumes that all substitutions (i.e. a change of a base by another one) have the same probability. This probability is the same for all sites along the DNA sequence. This last assumption can be relaxed by @@ -57,7 +61,7 @@ dist.dna(x, model = "K80", variance = FALSE, default, no gamma correction is applied. Another assumption is that the base frequencies are balanced and thus equal to 0.25.} - \item{``K80''}{The distance derived by Kimura (1980), sometimes referred + \item{\code{K80}: }{The distance derived by Kimura (1980), sometimes referred to as ``Kimura's 2-parameters distance'', has the same underlying assumptions than the Jukes--Cantor distance except that two kinds of substitutions are considered: transitions (A <-> G, C <-> T), and @@ -72,50 +76,50 @@ dist.dna(x, model = "K80", variance = FALSE, Jukes--Cantor model, the gamma parameter must be given by the user. By default, no gamma correction is applied.} - \item{``F81''}{Felsenstein (1981) generalized the Jukes--Cantor model + \item{\code{F81}: }{Felsenstein (1981) generalized the Jukes--Cantor model by relaxing the assumption of equal base frequencies. The formulae used in this function were taken from McGuire et al. (1999)}. - \item{``K81''}{Kimura (1981) generalized his model (Kimura 1980) by + \item{\code{K81}: }{Kimura (1981) generalized his model (Kimura 1980) by assuming different rates for two kinds of transversions: A <-> C and G <-> T on one side, and A <-> T and C <-> G on the other. This is what Kimura called his ``three substitution types model'' (3ST), and is sometimes referred to as ``Kimura's 3-parameters distance''}. - \item{``F84''}{This model generalizes K80 by relaxing the assumption + \item{\code{F84}: }{This model generalizes K80 by relaxing the assumption of equal base frequencies. It was first introduced by Felsenstein in 1984 in Phylip, and is fully described by Felsenstein and Churchill (1996). The formulae used in this function were taken from McGuire et al. (1999)}. - \item{``BH87''}{Barry and Hartigan (1987) developed a distance based + \item{\code{BH87}: }{Barry and Hartigan (1987) developed a distance based on the observed proportions of changes among the four bases. This distance is not symmetric.} - \item{``T92''}{Tamura (1992) generalized the Kimura model by relaxing + \item{\code{T92}: }{Tamura (1992) generalized the Kimura model by relaxing the assumption of equal base frequencies. This is done by taking into account the bias in G+C content in the sequences. The substitution rates are assumed to be the same for all sites along the DNA sequence.} - \item{``TN93''}{Tamura and Nei (1993) developed a model which assumes + \item{\code{TN93}: }{Tamura and Nei (1993) developed a model which assumes distinct rates for both kinds of transition (A <-> G versus C <-> T), and transversions. The base frequencies are not assumed to be equal and are estimated from the data. A gamma correction of the inter-site variation in substitution rates is possible.} - \item{``GG95''}{Galtier and Gouy (1995) introduced a model where the + \item{\code{GG95}: }{Galtier and Gouy (1995) introduced a model where the G+C content may change through time. Different rates are assumed for transitons and transversions.} - \item{``logdet''}{The Log-Det distance, developed by Lockhart et + \item{\code{logdet}: }{The Log-Det distance, developed by Lockhart et al. (1994), is related to BH87. However, this distance is symmetric. Formulae from Gu and Li (1996) are used. \code{dist.logdet} in \pkg{phangorn} uses a different implementation that gives substantially different distances for low-diverging sequences.} - \item{``paralin''}{Lake (1994) developed the paralinear distance which + \item{\code{paralin}: }{Lake (1994) developed the paralinear distance which can be viewed as another variant of the Barry--Hartigan distance.} }} \value{ diff --git a/man/mixedFontLabel.Rd b/man/mixedFontLabel.Rd index 1736627..03b9a2a 100644 --- a/man/mixedFontLabel.Rd +++ b/man/mixedFontLabel.Rd @@ -44,7 +44,8 @@ mixedFontLabel(..., sep = " ", italic = NULL, bold = NULL, } \author{Emmanuel Paradis} \seealso{ - \code{\link{makeLabel}}, \code{\link{makeNodeLabel}} + \code{\link{makeLabel}}, \code{\link{makeNodeLabel}}, + \code{taxo.fonts} in package \pkg{phyloch} for fancy alignments } \examples{ tr <- read.tree(text = "((a,(b,c)),d);") -- 2.39.2