[Adephylo-commits] r193 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon May 20 18:33:39 CEST 2013
Author: jombart
Date: 2013-05-20 18:33:39 +0200 (Mon, 20 May 2013)
New Revision: 193
Modified:
pkg/man/abouheif.Rd
pkg/man/adephylo.package.Rd
pkg/man/carni19.Rd
pkg/man/carni70.Rd
pkg/man/dibas.Rd
pkg/man/distRoot.Rd
pkg/man/distTips.Rd
pkg/man/lizards.Rd
pkg/man/maples.Rd
pkg/man/mjrochet.Rd
pkg/man/orthobasis.Rd
pkg/man/orthogram.Rd
pkg/man/palm.Rd
pkg/man/ppca.Rd
pkg/man/procella.Rd
pkg/man/proxTips.Rd
pkg/man/sp.tips.Rd
pkg/man/table.phylo4d.Rd
pkg/man/tithonia.Rd
pkg/man/treePart.Rd
pkg/man/ungulates.Rd
Log:
fixing manpage line length
Modified: pkg/man/abouheif.Rd
===================================================================
--- pkg/man/abouheif.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/abouheif.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -12,18 +12,20 @@
proximities as well.\cr
Note that the original Abouheif's proximity (Abouheif, 1999; Pavoine
- \emph{et al.} 2008) unifies Moran's I and Geary'c tests (Thioulouse \emph{et
- al.} 1995).\cr
+ \emph{et al.} 2008) unifies Moran's I and Geary'c tests (Thioulouse
+ \emph{et al.} 1995).\cr
\code{abouheif.moran} can be used in two ways:\cr
- providing a data.frame of traits (\code{x}) and a matrix of
- phylogenetic proximities (\code{W})\cr
- - providing a \linkS4class{phylo4d} object (\code{x}) and specifying the type of proximity to be
- used (\code{method}).
+ phylogenetic proximities (\code{W})\cr
+ - providing a \linkS4class{phylo4d} object (\code{x}) and specifying
+ the type of proximity to be used (\code{method}).
}
\usage{
-abouheif.moran(x, W=NULL, method=c("oriAbouheif","patristic","nNodes","Abouheif","sumDD"), a=1, nrepet = 999, alter=c("greater", "less", "two-sided"))
+abouheif.moran(x, W=NULL,
+ method=c("oriAbouheif","patristic","nNodes","Abouheif","sumDD"),
+ a=1, nrepet = 999, alter=c("greater", "less", "two-sided"))
}
\arguments{
\item{x}{a data frame with continuous variables, or a
@@ -56,10 +58,12 @@
}
\references{
-Thioulouse, J., Chessel, D. and Champely, S. (1995) Multivariate analysis of spatial patterns: a unified approach to local and global structures.
-\emph{Environmental and Ecological Statistics}, \bold{2}, 1--14.
+Thioulouse, J., Chessel, D. and Champely, S. (1995) Multivariate
+analysis of spatial patterns: a unified approach to local and global
+structures. \emph{Environmental and Ecological Statistics}, \bold{2}, 1--14.
}
-\author{Original code from ade4 (gearymoran function) by Sébastien Ollier\cr
+\author{
+ Original code from ade4 (gearymoran function) by Sébastien Ollier\cr
Adapted and maintained by Thibaut Jombart <tjombart at imperial.ac.uk>.
}
\seealso{
Modified: pkg/man/adephylo.package.Rd
===================================================================
--- pkg/man/adephylo.package.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/adephylo.package.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -60,20 +60,22 @@
Several procedures allow one to measure, and/or test phylogenetic
signal in biological traits:\cr
- - \code{\link{abouheif.moran}}: performs Abouheif's test, designed to detect phylogenetic
- autocorrelation in a quantitative trait. This implementation is not
- based on original heuristic procedure, but on the exact formulation
- proposed by Pavoine et al. (2008), showing that the test is in fact a
- Moran's index test. This implementation further extends the procedure
- by allowing any measure of phylogenetic proximity (5 are proposed).\cr
+ - \code{\link{abouheif.moran}}: performs Abouheif's test, designed to
+ detect phylogenetic autocorrelation in a quantitative trait. This
+ implementation is not based on original heuristic procedure, but on
+ the exact formulation proposed by Pavoine et al. (2008), showing that
+ the test is in fact a Moran's index test. This implementation further
+ extends the procedure by allowing any measure of phylogenetic
+ proximity (5 are proposed).\cr
- \code{\link{orthogram}}: performs the orthonormal decomposition of
variance of a quantitative variable on an orthonormal basis as in
Ollier et al. (2005). It also returns the results of five non
parametric tests associated to the variance decomposition.\cr
- - \code{\link{moran.idx}}: computes Moran's index of autocorrelation given a
- variable and a matrix of proximities among observations (no test).\cr
+ - \code{\link{moran.idx}}: computes Moran's index of autocorrelation
+ given a variable and a matrix of proximities among observations (no
+ test).\cr
=== MODELLING/INVESTIGATION OF PHYLOGENETIC SIGNAL ===\cr
@@ -142,7 +144,8 @@
\author{
Thibaut Jombart <tjombart at imperial.ac.uk>\cr
with contributions Stéphane Dray <dray at biomserv.univ-lyon1.fr>. \cr
- Parts of former code from \code{ade4} by Daniel Chessel and Sébastien Ollier.
+ Parts of former code from \code{ade4} by Daniel Chessel and Sébastien
+ Ollier.
}
\keyword{manip}
\keyword{multivariate}
Modified: pkg/man/carni19.Rd
===================================================================
--- pkg/man/carni19.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/carni19.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -3,7 +3,9 @@
\docType{data}
\title{Phylogeny and quantative trait of carnivora}
\description{
-This data set describes the phylogeny of carnivora as reported by Diniz-Filho et al. (1998). It also gives the body mass of these 19 species.
+This data set describes the phylogeny of carnivora as reported by
+Diniz-Filho et al. (1998). It also gives the body mass of these 19
+species.
}
\usage{data(carni19)}
\format{
@@ -13,8 +15,9 @@
\item{bm}{is a numeric vector which values correspond to the body mass of the 19 species (log scale).}
}}
\source{
-Diniz-Filho, J. A. F., de Sant'Ana, C.E.R. and Bini, L.M. (1998)
-An eigenvector method for estimating phylogenetic inertia. \emph{Evolution}, \bold{52}, 1247--1262.
+Diniz-Filho, J. A. F., de Sant'Ana, C.E.R. and Bini, L.M. (1998) An
+eigenvector method for estimating phylogenetic
+inertia. \emph{Evolution}, \bold{52}, 1247--1262.
}
\note{
This dataset replaces the former version in ade4.
Modified: pkg/man/carni70.Rd
===================================================================
--- pkg/man/carni70.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/carni70.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -4,7 +4,9 @@
\docType{data}
\title{Phylogeny and quantitative traits of carnivora}
\description{
-This data set describes the phylogeny of 70 carnivora as reported by Diniz-Filho and Torres (2002). It also gives the geographic range size and body size corresponding to these 70 species.
+This data set describes the phylogeny of 70 carnivora as reported by
+Diniz-Filho and Torres (2002). It also gives the geographic range size
+and body size corresponding to these 70 species.
}
\usage{data(carni70)}
\format{
@@ -15,8 +17,10 @@
\item{tab}{is a data frame with 70 species and two traits: size (body size (kg)) ; range (geographic range size (km)).}
}}
\source{
-Diniz-Filho, J. A. F., and N. M. Tôrres. (2002) Phylogenetic comparative methods and the
-geographic range size-body size relationship in new world terrestrial carnivora. \emph{Evolutionary Ecology}, \bold{16}, 351--367.
+Diniz-Filho, J. A. F., and N. M. Tôrres. (2002) Phylogenetic comparative
+methods and the geographic range size-body size relationship in new
+world terrestrial carnivora. \emph{Evolutionary Ecology}, \bold{16},
+351--367.
}
\note{
This dataset replaces the former version in ade4.
Modified: pkg/man/dibas.Rd
===================================================================
--- pkg/man/dibas.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/dibas.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -58,7 +58,8 @@
## make a tree
tre <- nj(dist(dat$dat))
-plot(tre,type="unr", tip.col=c("blue","red")[as.integer(dat$grp)],main="simulated data - tree")
+plot(tre,type="unr", tip.col=c("blue","red")[as.integer(dat$grp)],
+ main="simulated data - tree")
## use dibas method
res <- dibas(tre, dat$grp, metric="nNodes")
@@ -70,11 +71,13 @@
#### NON-PARAMETRIC TEST BASED ON MEAN SUCCESSFUL ASSIGNMENT ####
## use dibas method
-distHo <- replicate(100, dibas(tre, sample(dat$grp), metric="patristic")$mean.ok)
+distHo <- replicate(100,
+ dibas(tre, sample(dat$grp), metric="patristic")$mean.ok)
pval <- mean(res$mean.ok<=c(distHo,res$mean.ok))
pval
-hist(c(distHo,res$mean.ok), col="grey", main="Mean successful assignement - permuted values")
+hist(c(distHo,res$mean.ok), col="grey",
+ main="Mean successful assignement - permuted values")
abline(v=res$mean.ok, col="red")
mtext(side=3, text="Observed value in red")
@@ -87,7 +90,8 @@
## make a tree
tre <- nj(dist(dat$dat))
-plot(tre,type="unr", tip.col=c("blue","red")[as.integer(dat$grp)],main="simulated data - tree")
+plot(tre,type="unr", tip.col=c("blue","red")[as.integer(dat$grp)],
+ main="simulated data - tree")
mtext(side=3, text="hand-fan syndrome")
## use dibas method
@@ -105,7 +109,8 @@
#### MORE COMPLEX DATASET ####
if(require(adegenet)){
-dat <- simDatGroups(k=5, p=50, n=c(5,10,10,30,60), mu=sample(1:5, 5, replace=TRUE), sigma=sample(1:5)/2)
+dat <- simDatGroups(k=5, p=50, n=c(5,10,10,30,60), mu=sample(1:5, 5,
+ replace=TRUE), sigma=sample(1:5)/2)
names(dat)
## make a tree
Modified: pkg/man/distRoot.Rd
===================================================================
--- pkg/man/distRoot.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/distRoot.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -2,8 +2,9 @@
\alias{distRoot}
\title{Compute the distance of tips to the root}
\description{
- The function \code{distRoot} computes the distance of a set of tips to the
- root. Several distances can be used, defaulting to the sum of branch lengths.
+ The function \code{distRoot} computes the distance of a set of tips to
+ the root. Several distances can be used, defaulting to the sum of
+ branch lengths.
}
\usage{
distRoot(x, tips, method=c("patristic","nNodes","Abouheif","sumDD"))
Modified: pkg/man/distTips.Rd
===================================================================
--- pkg/man/distTips.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/distTips.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -77,9 +77,12 @@
## compare C and pure R code outputs
x <- rtree(10)
all.equal(as.matrix(distTips(x)), as.matrix(distTips(x, useC=FALSE)))
-all.equal(as.matrix(distTips(x, meth="nNode")), as.matrix(distTips(x, meth="nNode", useC=FALSE)))
-all.equal(as.matrix(distTips(x, meth="Abou")), as.matrix(distTips(x, meth="Abou", useC=FALSE)))
-all.equal(as.matrix(distTips(x, meth="sumDD")), as.matrix(distTips(x, meth="sumDD", useC=FALSE)))
+all.equal(as.matrix(distTips(x, meth="nNode")),
+ as.matrix(distTips(x, meth="nNode", useC=FALSE)))
+all.equal(as.matrix(distTips(x, meth="Abou")),
+ as.matrix(distTips(x, meth="Abou", useC=FALSE)))
+all.equal(as.matrix(distTips(x, meth="sumDD")),
+ as.matrix(distTips(x, meth="sumDD", useC=FALSE)))
## compare speed
x <- rtree(50)
Modified: pkg/man/lizards.Rd
===================================================================
--- pkg/man/lizards.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/lizards.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -3,13 +3,14 @@
\docType{data}
\title{Phylogeny and quantitative traits of lizards}
\description{
-This data set describes the phylogeny of 18 lizards as reported by Bauwens and D\'iaz-Uriarte (1997).
-It also gives life-history traits corresponding to these 18 species.
+This data set describes the phylogeny of 18 lizards as reported by
+Bauwens and D\'iaz-Uriarte (1997). It also gives life-history traits
+corresponding to these 18 species.
}
\usage{data(lizards)}
\format{
\code{lizards} is a list containing the 3 following objects :
-\describe{
+\describe{
\item{traits}{is a data frame with 18 species and 8 traits.}
\item{hprA}{is a character string giving the phylogenetic tree (hypothesized phylogenetic relationships based on immunological distances) in Newick format.}
\item{hprB}{is a character string giving the phylogenetic tree (hypothesized phylogenetic relationships based on morphological characteristics) in Newick format.}
@@ -40,7 +41,8 @@
## compute and plot principal components
if(require(ade4)){
-liz.pca1 <- dudi.pca(lizards$traits, cent=TRUE, scale=TRUE, scannf=FALSE, nf=2) # PCA of traits
+liz.pca1 <- dudi.pca(lizards$traits, cent=TRUE,
+ scale=TRUE, scannf=FALSE, nf=2) # PCA of traits
myPC <- phylo4d(liz.tr, liz.pca1$li) # store PC in a phylo4d object
varlab <- paste("Principal \ncomponent", 1:2) # make labels for PCs
table.phylo4d(myPC, ratio=.8, var.lab=varlab) # plot the PCs
Modified: pkg/man/maples.Rd
===================================================================
--- pkg/man/maples.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/maples.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -3,20 +3,24 @@
\docType{data}
\title{Phylogeny and quantitative traits of flowers}
\description{
-This data set describes the phylogeny of 17 flowers as reported by Ackerly and Donoghue (1998). It also gives 31 traits corresponding to these 17 species.
+This data set describes the phylogeny of 17 flowers as reported by
+Ackerly and Donoghue (1998). It also gives 31 traits corresponding to
+these 17 species.
}
\usage{data(maples)}
\format{
-\code{tithonia} is a list containing the 2 following objects :
- - tre: a character string giving the phylogenetic tree in Newick format.\cr
- - tab: a data frame with 17 species and 31 traits.\cr
+ \code{tithonia} is a list containing the 2 following objects :
+ - tre: a character string giving the phylogenetic tree in Newick
+ format.\cr
+ - tab: a data frame with 17 species and 31 traits.\cr
}
\source{
Data were obtained from the URL
\url{http://www.stanford.edu/~dackerly/acerdata.html} (no longer maintained).
}
\references{
-Ackerly, D. D. and Donoghue, M.J. (1998) Leaf size, sappling allometry, and Corner's rules: phylogeny and correlated evolution in Maples (Acer).
+Ackerly, D. D. and Donoghue, M.J. (1998) Leaf size, sappling allometry,
+and Corner's rules: phylogeny and correlated evolution in Maples (Acer).
\emph{American Naturalist}, \bold{152}, 767--791.
}
\note{
Modified: pkg/man/mjrochet.Rd
===================================================================
--- pkg/man/mjrochet.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/mjrochet.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -4,7 +4,9 @@
\docType{data}
\title{Phylogeny and quantitative traits of teleos fishes}
\description{
-This data set describes the phylogeny of 49 teleos fishes as reported by Rochet et al. (2000). It also gives life-history traits corresponding to these 49 species.
+This data set describes the phylogeny of 49 teleos fishes as reported by
+Rochet et al. (2000). It also gives life-history traits corresponding to
+these 49 species.
}
\usage{data(mjrochet)}
\format{
@@ -14,10 +16,11 @@
\item{tab}{is a data frame with 49 rows and 7 traits.}
}}
\details{
- Variables of \code{mjrochet$tab} are the following ones : tm (age at maturity (years)),
- lm (length at maturity (cm)), l05 (length at 5 per cent survival (cm)),
- t05 (time to 5 per cent survival (years)), fb (slope of the log-log fecundity-length relationship),
- fm (fecundity the year of maturity), egg (volume of eggs (\eqn{mm^{3}}{mm^3})).
+ Variables of \code{mjrochet$tab} are the following ones : tm (age at
+ maturity (years)), lm (length at maturity (cm)), l05 (length at 5 per
+ cent survival (cm)), t05 (time to 5 per cent survival (years)), fb
+ (slope of the log-log fecundity-length relationship), fm (fecundity the
+ year of maturity), egg (volume of eggs (\eqn{mm^{3}}{mm^3})).
}
\source{
Data taken from: \cr
@@ -33,9 +36,9 @@
Phylogenetic tree : \url{http://www.ifremer.fr/maerha/life_history.html}
}
\references{
-Rochet, M. J., Cornillon, P-A., Sabatier, R. and Pontier, D. (2000)
-Comparative analysis of phylogenic and fishing effects in life history patterns of teleos fishes.
-\emph{Oïkos}, \bold{91}, 255--270.
+Rochet, M. J., Cornillon, P-A., Sabatier, R. and Pontier, D. (2000)
+Comparative analysis of phylogenic and fishing effects in life history
+patterns of teleos fishes. \emph{Oïkos}, \bold{91}, 255--270.
}
\note{
This dataset replaces the former version in ade4.
Modified: pkg/man/orthobasis.Rd
===================================================================
--- pkg/man/orthobasis.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/orthobasis.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -21,8 +21,10 @@
\code{\link{proxTips}}.
}
\usage{
-me.phylo(x=NULL, prox=NULL, method=c("patristic","nNodes","oriAbouheif","Abouheif","sumDD"), a=1)
-orthobasis.phylo(x=NULL, prox=NULL, method=c("patristic","nNodes","oriAbouheif","Abouheif","sumDD"), a=1)
+me.phylo(x=NULL, prox=NULL, method=c("patristic","nNodes",
+ "oriAbouheif","Abouheif","sumDD"), a=1)
+orthobasis.phylo(x=NULL, prox=NULL, method=c("patristic","nNodes",
+ "oriAbouheif","Abouheif","sumDD"), a=1)
}
\arguments{
\item{x}{A tree of class \code{\link[ape:read.tree]{phylo}},
@@ -96,7 +98,7 @@
myME <- me.phylo(tre, method="Abou")
lm2 <- lm(neonatw ~ myME[,1] + afbw) # use for ME as covariable
resid2 <- residuals(lm2)
-orthogram(resid2, tre) # there is no longer phylogenetic autocorrelation
+orthogram(resid2, tre) # there is no longer phylogenetic autocorrelation
## see the difference
table.phylo4d(phylo4d(tre, cbind.data.frame(resid1, resid2)))
Modified: pkg/man/orthogram.Rd
===================================================================
--- pkg/man/orthogram.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/orthogram.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -3,10 +3,12 @@
\alias{orthogram}
\title{Orthonormal decomposition of variance}
\description{
-This function performs the orthonormal decomposition of variance of a quantitative variable on an orthonormal basis. It also returns the results of five non parametric tests associated to the variance decomposition.
-It thus provides tools (graphical displays and test) for analysing
-phylogenetic, pattern in one quantitative trait. This implementation
-replace the (deprecated) version from the \code{ade4} package.\cr
+This function performs the orthonormal decomposition of variance of a
+quantitative variable on an orthonormal basis. It also returns the
+results of five non parametric tests associated to the variance
+decomposition. It thus provides tools (graphical displays and test) for
+analysing phylogenetic, pattern in one quantitative trait. This
+implementation replace the (deprecated) version from the \code{ade4} package.\cr
Several orthonormal bases can be used. By default, basis is constructed
from a partition of tips according to tree topology (as returned by
@@ -43,23 +45,47 @@
must be one of "greater" (default), "less" or "two-sided"}
}
\details{
-The function computes the variance decomposition of a quantitative vector x on an orthonormal basis B. The variable is normalized given the uniform weight to eliminate problem of scales.
-It plots the squared correlations \eqn{R^{2}}{R^2} between x and vectors of B (variance decomposition) and the cumulated squared correlations \eqn{SR^{2}}{SR^2} (cumulative decomposition).
-The function also provides five non parametric tests to test the existence of autocorrelation. The tests derive from the five following statistics :
- - R2Max=\eqn{\max(R^{2})}{max(R^2)}. It takes high value when a high part of the variability is explained by one score.\cr
- - SkR2k=\eqn{\sum_{i=1}^{n-1}(iR^{2}_i)}{sum_i^(n-1) i*(R^2)_i}. It compares the part of variance explained by internal nodes to the one explained by end nodes.\cr
- - Dmax=\eqn{\max_{m=1,...,n-1}(\sum_{j=1}^{m}R^{2}_j - \frac{m}{n-1})}{max_(m=1,...,n-1)(sum_(j=1)^m(R^2_j) - (m/n-1))}. It examines the accumulation of variance for a sequence of scores.\cr
- - SCE=\eqn{\sum_{m=1}^{n-1} (\sum_{j=1}^{m}R^{2}_j - \frac{m}{n-1})^{2}}{sum_(m=1)^(n-1)(sum_(j=1)^m(R^2_j) - (m/n-1))^2}. It examines also the accumulation of variance for a sequence of scores.\cr
- - ratio: depends of the parameter posinega. If posinega > 0, the statistic ratio exists and equals \eqn{\sum_{i=1}^{posinega}R^{2}_i}{sum_i (R^2)_i with i < posinega + 1}. It compares the part of variance explained by internal nodes to the one explained by end nodes when we can define how many vectors correspond to internal nodes.
+The function computes the variance decomposition of a quantitative
+vector x on an orthonormal basis B. The variable is normalized given the
+uniform weight to eliminate problem of scales. It plots the squared
+correlations \eqn{R^{2}}{R^2} between x and vectors of B (variance
+decomposition) and the cumulated squared correlations \eqn{SR^{2}}{SR^2}
+(cumulative decomposition). The function also provides five non
+parametric tests to test the existence of autocorrelation. The tests
+derive from the five following statistics :
+
+ - R2Max=\eqn{\max(R^{2})}{max(R^2)}. It takes high value when a high
+ part of the variability is explained by one score.\cr
+ - SkR2k=\eqn{\sum_{i=1}^{n-1}(iR^{2}_i)}{sum_i^(n-1) i*(R^2)_i}. It
+ compares the part of variance explained by internal nodes to the
+ one explained by end nodes.\cr
+ - Dmax=\eqn{\max_{m=1,...,n-1}(\sum_{j=1}^{m}R^{2}_j -
+ \frac{m}{n-1})}{max_(m=1,...,n-1)(sum_(j=1)^m(R^2_j) -
+ (m/n-1))}. It examines the accumulation of variance for a sequence
+ of scores.\cr
+ - SCE=\eqn{\sum_{m=1}^{n-1} (\sum_{j=1}^{m}R^{2}_j -
+ \frac{m}{n-1})^{2}}{sum_(m=1)^(n-1)(sum_(j=1)^m(R^2_j) -
+ (m/n-1))^2}. It examines also the accumulation of variance for a
+ sequence of scores.\cr
+ - ratio: depends of the parameter posinega. If posinega > 0, the
+ statistic ratio exists and equals
+ \eqn{\sum_{i=1}^{posinega}R^{2}_i}{sum_i (R^2)_i with i < posinega
+ + 1}. It compares the part of variance explained by internal nodes
+ to the one explained by end nodes when we can define how many
+ vectors correspond to internal nodes.
}
\value{
-If (high.scores = 0), returns an object of class \code{'krandtest'} (randomization tests) corresponding to the five non parametric tests. \cr \cr
-If (high.scores > 0), returns a list containg :
+If (high.scores = 0), returns an object of class \code{'krandtest'}
+(randomization tests) corresponding to the five non parametric
+tests. \cr \cr
+If (high.scores > 0), returns a list containg :
\item{w}{: an object of class \code{'krandtest'} (randomization tests)}
\item{scores.order}{: a vector which terms give labels of vectors that explain the larger part of variance}
}
\references{
-Ollier, S., Chessel, D. and Couteron, P. (2005) Orthonormal Transform to Decompose the Variance of a Life-History Trait across a Phylogenetic Tree. \emph{Biometrics}, \bold{62}, 471--477.
+Ollier, S., Chessel, D. and Couteron, P. (2005) Orthonormal Transform to
+Decompose the Variance of a Life-History Trait across a Phylogenetic
+Tree. \emph{Biometrics}, \bold{62}, 471--477.
}
\author{
Original code: Sébastien Ollier and Daniel Chessel.\cr
Modified: pkg/man/palm.Rd
===================================================================
--- pkg/man/palm.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/palm.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -4,7 +4,8 @@
\docType{data}
\title{Phylogenetic and quantitative traits of amazonian palm trees}
\description{
-This data set describes the phylogeny of 66 amazonian palm trees. It also gives 7 traits corresponding to these 66 species.
+This data set describes the phylogeny of 66 amazonian palm trees. It
+also gives 7 traits corresponding to these 66 species.
}
\usage{data(palm)}
\format{
@@ -17,7 +18,9 @@
Variables of \code{palm$traits} are the following ones: \cr
- rord: specific richness with five ordered levels\cr
- h: height in meter (squared transform)\cr
-- dqual: diameter at breast height in centimeter with five levels \code{sout : subterranean}, \code{ d1(0, 5 cm)}, \code{ d2(5, 15 cm)}, \code{ d3(15, 30 cm)} and \code{ d4(30, 100 cm)}\cr
+- dqual: diameter at breast height in centimeter with five levels
+ \code{sout : subterranean}, \code{ d1(0, 5 cm)}, \code{ d2(5, 15 cm)},
+ \code{ d3(15, 30 cm)} and \code{ d4(30, 100 cm)}\cr
- vfruit: fruit volume in \eqn{mm^{3}}{mm^3} (logged transform)\cr
- vgrain: seed volume in \eqn{mm^{3}}{mm^3} (logged transform)\cr
- aire: spatial distribution area (\eqn{km^{2}}{km^2})\cr
Modified: pkg/man/ppca.Rd
===================================================================
--- pkg/man/ppca.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/ppca.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -7,7 +7,8 @@
\alias{screeplot.ppca}
\alias{plot.ppca}
\title{Phylogenetic principal component analysis}
-\description{These functions are designed to perform a phylogenetic principal
+\description{
+ These functions are designed to perform a phylogenetic principal
component analysis (pPCA, Jombart et al. 2010) and to display the
results.
@@ -138,7 +139,8 @@
liz.tre <- read.tree(tex=lizards$hprA)
liz.4d <- phylo4d(liz.tre, lizards$traits)
par(mar=rep(.1,4))
-table.phylo4d(liz.4d,var.lab=c(names(lizards$traits),"ACP 1\n(\"size effect\")"),show.node=FALSE, cex.lab=1.2)
+table.phylo4d(liz.4d,var.lab=c(names(lizards$traits),
+ "ACP 1\n(\"size effect\")"),show.node=FALSE, cex.lab=1.2)
## REMOVE DUPLICATED POPULATIONS
@@ -147,7 +149,8 @@
## CORRECT LABELS
-lab <- c("Pa", "Ph", "Ll", "Lmca", "Lmcy", "Phha", "Pha", "Pb", "Pm", "Ae", "Tt", "Ts", "Lviv", "La", "Ls", "Lvir")
+lab <- c("Pa", "Ph", "Ll", "Lmca", "Lmcy", "Phha", "Pha",
+ "Pb", "Pm", "Ae", "Tt", "Ts", "Lviv", "La", "Ls", "Lvir")
tipLabels(liz.4d) <- lab
@@ -187,7 +190,8 @@
## FIGURE 1
par(mar=c(.1,2.4,2.1,1))
-table.phylo4d(obj.ppca, ratio=.7, var.lab=c("1st global PC", "1st local PC"), tip.label=myLab, box=FALSE,cex.lab=1.4, cex.sym=1.2, show.node.label=TRUE)
+table.phylo4d(obj.ppca, ratio=.7, var.lab=c("1st global PC", "1st local
+ PC"), tip.label=myLab,box=FALSE,cex.lab=1.4, cex.sym=1.2, show.node.label=TRUE)
add.scatter.eig(liz.ppca$eig,1,1,1,csub=1.2, posi="topleft", ratio=.23)
Modified: pkg/man/procella.Rd
===================================================================
--- pkg/man/procella.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/procella.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -3,7 +3,8 @@
\docType{data}
\title{Phylogeny and quantitative traits of birds}
\description{
-This data set describes the phylogeny of 19 birds as reported by Bried et al. (2002). It also gives 6 traits corresponding to these 19 species.
+This data set describes the phylogeny of 19 birds as reported by Bried
+et al. (2002). It also gives 6 traits corresponding to these 19 species.
}
\usage{data(procella)}
\format{
@@ -22,10 +23,12 @@
- col.size: an integer vector that describes the colony size (no nests monitored)
}
\references{
-Bried, J., Pontier, D. and Jouventin, P. (2002) Mate fidelity in monogamus birds: a re-examination of the Procellariiformes.
+Bried, J., Pontier, D. and Jouventin, P. (2002) Mate fidelity in
+monogamus birds: a re-examination of the Procellariiformes.
\emph{Animal Behaviour}, \bold{65}, 235--246.
-See a data description at \url{http://pbil.univ-lyon1.fr/R/pps/pps037.pdf} (in French).
+See a data description at
+\url{http://pbil.univ-lyon1.fr/R/pps/pps037.pdf} (in French).
}
\note{
This dataset replaces the former version in ade4.
Modified: pkg/man/proxTips.Rd
===================================================================
--- pkg/man/proxTips.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/proxTips.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -94,9 +94,10 @@
\code{sumDD} refers to a phylogenetic proximity quite similar to that
of Abouheif. We consider the same sets P and DDP. But instead of
- taking the inverse of the product of all terms in DDP, this proximity computes the
- inverse of the sum of all terms in DDP. This matrix was denoted 'M' in
- Pavoine \emph{et al.} (2008), who reported that it is related to May's index (May, 1990).
+ taking the inverse of the product of all terms in DDP, this proximity
+ computes the inverse of the sum of all terms in DDP. This matrix was
+ denoted 'M' in Pavoine \emph{et al.} (2008), who reported that it is
+ related to May's index (May, 1990).
}
\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\seealso{\code{\link{distTips}} which computes several phylogenetic
Modified: pkg/man/sp.tips.Rd
===================================================================
--- pkg/man/sp.tips.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/sp.tips.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -3,9 +3,9 @@
\title{Find the shortest path between tips of a tree}
\description{
The function \code{sp.tips} finds the shortest path between tips of a
- tree, identified as \code{tip1} and \code{tip2}.
- This function applies to trees with the class \code{\link[ape:read.tree]{phylo}}, \linkS4class{phylo4} or
- \linkS4class{phylo4d}. Several tips can be provided at a time.
+ tree, identified as \code{tip1} and \code{tip2}. This function
+ applies to trees with the class \code{\link[ape:read.tree]{phylo}},
+ \linkS4class{phylo4} or \linkS4class{phylo4d}. Several tips can be provided at a time.
}
\usage{
sp.tips(x, tip1, tip2, useTipNames=FALSE, quiet=FALSE, include.mrca=TRUE)
Modified: pkg/man/table.phylo4d.Rd
===================================================================
--- pkg/man/table.phylo4d.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/table.phylo4d.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -2,27 +2,31 @@
\alias{table.phylo4d}
\title{Graphical display of phylogeny and traits}
\description{
- This function represents traits onto the tips of
- a phylogeny. Plotted objects must be valid \linkS4class{phylo4d}
- objects (implemented by the \code{phylobase} package). Current version
- allows plotting of a tree and one or more quantitative traits
- (possibly containing missing data, represented by an 'x').\cr
+ This function represents traits onto the tips of a phylogeny. Plotted
+ objects must be valid \linkS4class{phylo4d} objects (implemented by
+ the \code{phylobase} package). Current version allows plotting of a
+ tree and one or more quantitative traits (possibly containing missing
+ data, represented by an 'x').\cr
- The plot of phylogenies is performed by a call to \code{\link[ape]{plot.phylo}}
- from the \code{ape} package. Hence, many of the arguments of
- \code{\link[ape]{plot.phylo}} can be passed to \code{table.phylo4d},
- through the \dots argument, but their names must be complete.
+ The plot of phylogenies is performed by a call to
+ \code{\link[ape]{plot.phylo}} from the \code{ape} package. Hence, many
+ of the arguments of \code{\link[ape]{plot.phylo}} can be passed to
+ \code{table.phylo4d}, through the \dots argument, but their names must
+ be complete.
For large trees, consider using \code{\link{bullseye}}.
}
\usage{
-table.phylo4d(x, treetype=c("phylogram","cladogram"), symbol=c("circles", "squares","colors"),
- repVar=1:ncol(tdata(x, type="tip")), center=TRUE, scale=TRUE, legend=TRUE, grid=TRUE, box=TRUE,
- show.tip.label=TRUE, show.node.label=TRUE, show.var.label=TRUE,
- ratio.tree=1/3, font=3,
- tip.label=tipLabels(x), var.label=colnames(tdata(x,type="tip")),
- cex.symbol=1, cex.label=1, cex.legend=1, pch=20, col=heat.colors(100),
- coord.legend=NULL, \dots)
+table.phylo4d(x, treetype=c("phylogram","cladogram"),
+ symbol=c("circles", "squares","colors"),
+ repVar=1:ncol(tdata(x, type="tip")), center=TRUE,
+ scale=TRUE, legend=TRUE, grid=TRUE, box=TRUE,
+ show.tip.label=TRUE, show.node.label=TRUE,
+ show.var.label=TRUE, ratio.tree=1/3, font=3,
+ tip.label=tipLabels(x),
+ var.label=colnames(tdata(x,type="tip")), cex.symbol=1,
+ cex.label=1, cex.legend=1, pch=20, col=heat.colors(100),
+ coord.legend=NULL, \dots)
}
\arguments{
\item{x}{a \linkS4class{phylo4d} object}
Modified: pkg/man/tithonia.Rd
===================================================================
--- pkg/man/tithonia.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/tithonia.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -3,7 +3,9 @@
\docType{data}
\title{Phylogeny and quantitative traits of flowers}
\description{
-This data set describes the phylogeny of 11 flowers as reported by Morales (2000). It also gives morphologic and demographic traits corresponding to these 11 species.
+This data set describes the phylogeny of 11 flowers as reported by
+Morales (2000). It also gives morphologic and demographic traits
+corresponding to these 11 species.
}
\usage{data(tithonia)}
\format{
Modified: pkg/man/treePart.Rd
===================================================================
--- pkg/man/treePart.Rd 2013-05-16 13:48:51 UTC (rev 192)
+++ pkg/man/treePart.Rd 2013-05-20 16:33:39 UTC (rev 193)
@@ -27,7 +27,9 @@
}
\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
\references{
-Ollier, S., Chessel, D. and Couteron, P. (2005) Orthonormal Transform to Decompose the Variance of a Life-History Trait across a Phylogenetic Tree. \emph{Biometrics}, \bold{62}, 471--477.
+Ollier, S., Chessel, D. and Couteron, P. (2005) Orthonormal Transform to
+Decompose the Variance of a Life-History Trait across a Phylogenetic
+Tree. \emph{Biometrics}, \bold{62}, 471--477.
}
\seealso{
@@ -62,7 +64,8 @@
ung.orthobas <- treePart(ung, res="orthobasis")
## comparison of the first 3 vectors
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/adephylo -r 193
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