[Adephylo-commits] r194 - in pkg: . R man vignettes vignettes/figs

[noreply at r-forge.r-project.org]

Author: jombart
Date: 2013-08-09 16:35:59 +0200 (Fri, 09 Aug 2013)
New Revision: 194

Modified:
   pkg/DESCRIPTION
   pkg/NAMESPACE
   pkg/R/abouheif.R
   pkg/R/bullseye.R
   pkg/R/dibas.R
   pkg/R/distances.R
   pkg/R/orthobasis.R
   pkg/R/orthogram.R
   pkg/R/partition.R
   pkg/R/ppca.R
   pkg/R/proximities.R
   pkg/R/table.phylo4d.R
   pkg/R/utils.R
   pkg/man/abouheif.Rd
   pkg/man/bullseye.Rd
   pkg/man/carni19.Rd
   pkg/man/carni70.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/tithonia.Rd
   pkg/man/ungulates.Rd
   pkg/vignettes/adephylo.Rnw
   pkg/vignettes/adephylo.pdf
   pkg/vignettes/figs/adephylo-012.pdf
   pkg/vignettes/figs/adephylo-016.pdf
   pkg/vignettes/figs/adephylo-018.pdf
   pkg/vignettes/figs/adephylo-aboutest.pdf
   pkg/vignettes/figs/adephylo-figFourBas.pdf
   pkg/vignettes/figs/adephylo-lm1.pdf
   pkg/vignettes/figs/adephylo-loadings.pdf
   pkg/vignettes/figs/adephylo-orthobas1.pdf
   pkg/vignettes/figs/adephylo-pca1.pdf
   pkg/vignettes/figs/adephylo-pca2.pdf
   pkg/vignettes/figs/adephylo-phylo4d.pdf
   pkg/vignettes/figs/adephylo-resid.pdf
Log:
trying to fix the package for the new urgent release.

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/DESCRIPTION	2013-08-09 14:35:59 UTC (rev 194)
@@ -1,11 +1,12 @@
 Package: adephylo
-Version: 1.1-4
-Date: 2013/05/15
+Version: 1.1-5
+Date: 2013/08/09
 Title: adephylo: exploratory analyses for the phylogenetic comparative method.
 Author: Thibaut Jombart <t.jombart at imperial.ac.uk>, Stephane Dray <stephane.dray at univ-lyon1.fr>
 Maintainer: Thibaut Jombart <t.jombart at imperial.ac.uk>
 Suggests:
-Depends: methods, phylobase, ape, ade4, adegenet
+Depends: methods
+Imports: phylobase, ape, ade4, adegenet
 Description: Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.
 License: GPL (>=2)
 LazyLoad: yes

Modified: pkg/NAMESPACE
===================================================================
--- pkg/NAMESPACE	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/NAMESPACE	2013-08-09 14:35:59 UTC (rev 194)
@@ -5,13 +5,18 @@
 exportPattern(".")
 
 # Import all packages listed as Imports or Depends
-import(
-  methods,
-  phylobase,
-  ape,
-  ade4
-)
+import(methods,phylobase)
 
+importFrom(ape, "as.character.DNAbin", "as.DNAbin", "as.DNAbin.alignment", "as.DNAbin.character",
+           "as.DNAbin.list", "as.list.DNAbin", "as.matrix.DNAbin", "cbind.DNAbin", "c.DNAbin",
+           "[.DNAbin", "labels.DNAbin", "print.DNAbin", "rbind.DNAbin", "dist.dna",
+           "plot.phylo", "root", "nj", "bionj", "read.tree", ".PlotPhyloEnv")
 
+importFrom(ade4, "as.krandtest", "as.dudi", "as.randtest", "orthobasis.mat", "dudi.acm", "redo.dudi",
+           "plot.randtest", "s.arrow", "s.label", "scatter", "scalewt", "dudi.pca")
+
+importFrom(adegenet, "bluepal", "redpal", "greenpal", "seasun", "spectral", "funky",
+           "num2col", "fac2col", "any2col", "transp")
+
 # Load DLL
 useDynLib(adephylo)

Modified: pkg/R/abouheif.R
===================================================================
--- pkg/R/abouheif.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/abouheif.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -3,7 +3,7 @@
                             a=1, nrepet=999,alter=c("greater", "less", "two-sided")) {
 
     ## some checks
-    if(!require(ade4)) stop("The ade4 package is not installed.")
+    ## if(!require(ade4)) stop("The ade4 package is not installed.")
     alter <- match.arg(alter)
     method <- match.arg(method)
 

Modified: pkg/R/bullseye.R
===================================================================
--- pkg/R/bullseye.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/bullseye.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -9,7 +9,7 @@
 ############
 ## bullseye
 ############
-bullseye <- function(phy, traits=NULL, col.tips.by=NULL, col.pal=seasun,
+bullseye <- function(phy, traits=NULL, col.tips.by=NULL, col.pal=spectral,
                      circ.n=6, circ.bg=transp("royalblue",.1), circ.unit=NULL,
                      legend=TRUE, leg.posi="bottomleft", leg.title="", leg.bg="white",
                      traits.inset=1.1, traits.space=0.05, traits.pch=19, traits.cex=1,

Modified: pkg/R/dibas.R
===================================================================
--- pkg/R/dibas.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/dibas.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -238,7 +238,7 @@
 ###############
 dibas.phylo <- function(x, grp, method=c("default","leaveOneOut"), fromRoot=FALSE, metric=c("Abouheif", "nNodes", "patristic", "sumDD"),
                         n.items=NULL, ...){
-    if(!require(ape)) stop("ape package is required")
+    ## if(!require(ape)) stop("ape package is required")
     if(!inherits(x,"phylo")) stop("x is not a phylo object")
 
     metric <- match.arg(metric)

Modified: pkg/R/distances.R
===================================================================
--- pkg/R/distances.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/distances.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -4,7 +4,7 @@
 distTips <- function(x, tips="all",
                       method=c("patristic","nNodes","Abouheif","sumDD"), useC=TRUE){
 
-    if(!require(phylobase)) stop("phylobase package is not installed")
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
 
     if(useC){
         tre <- as(x, "phylo")
@@ -126,7 +126,7 @@
 # distRoot
 ###########
 distRoot <- function(x, tips="all", method=c("patristic","nNodes","Abouheif","sumDD") ){
-    if(!require(phylobase)) stop("phylobase package is not installed")
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
 
     ## handle arguments
     x <- as(x, "phylo4")

Modified: pkg/R/orthobasis.R
===================================================================
--- pkg/R/orthobasis.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/orthobasis.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -3,8 +3,8 @@
 ###################
 orthobasis.phylo <- function(x=NULL, prox=NULL,
                              method=c("patristic","nNodes","oriAbouheif","Abouheif","sumDD"), a=1){
-    if(!require(phylobase)) stop("phylobase package is not installed")
-    if(!require(ade4)) stop("ade4 package is not installed")
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
+    ## if(!require(ade4)) stop("ade4 package is not installed")
 
     ## handle arguments
     method <- match.arg(method)

Modified: pkg/R/orthogram.R
===================================================================
--- pkg/R/orthogram.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/orthogram.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -4,7 +4,7 @@
                         high.scores = 0,alter=c("greater", "less", "two-sided")){
 
     ## some checks and preliminary assignements
-    if(!require(ade4)) stop("The ade4 package is not installed.")
+    ## if(!require(ade4)) stop("The ade4 package is not installed.")
 
     nobs <- length(x)
     alter <- match.arg(alter)

Modified: pkg/R/partition.R
===================================================================
--- pkg/R/partition.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/partition.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -11,7 +11,7 @@
 # listTips
 ############
 listTips <- function(x){
-    if(!require(phylobase)) stop("phylobase package is not installed")
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
 
     ## conversion from phylo, phylo4 and phylo4d
     x <- as(x, "phylo4")
@@ -37,7 +37,7 @@
 # treePart
 ###########
 treePart <- function(x, result=c("dummy", "orthobasis")){
-    if(!require(phylobase)) stop("phylobase package is not installed")
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
 
     ## conversion from phylo, phylo4 and phylo4d
     x <- as(x, "phylo4")

Modified: pkg/R/ppca.R
===================================================================
--- pkg/R/ppca.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/ppca.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -10,7 +10,7 @@
                  center=TRUE, scale=TRUE, scannf=TRUE, nfposi=1, nfnega=0){
 
     ## handle arguments
-    if(!require(ade4)) stop("The package ade4 is not installed.")
+    ## if(!require(ade4)) stop("The package ade4 is not installed.")
     if (is.character(chk <- checkPhylo4(x))) stop("bad phylo4d object: ",chk)
     ##if (is.character(chk <- checkData(x))) stop("bad phylo4d object: ",chk) : no longer needed
 
@@ -234,7 +234,7 @@
 
     ## some checks
     if (!inherits(object, "ppca"))stop("to be used with 'ppca' object")
-    if(!require(ade4)) stop("The package ade4 is not installed.")
+    ## if(!require(ade4)) stop("The package ade4 is not installed.")
 
 
     norm.w <- function(X, w) {

Modified: pkg/R/proximities.R
===================================================================
--- pkg/R/proximities.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/proximities.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -5,7 +5,7 @@
                       method=c("patristic","nNodes","oriAbouheif","Abouheif","sumDD"),
                      a=1, normalize=c("row","col","none"), symmetric=TRUE, useC=TRUE){
 
-    if(!require(phylobase)) stop("phylobase package is not installed")
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
 
     ## handle arguments
     x <- as(x, "phylo4")

Modified: pkg/R/table.phylo4d.R
===================================================================
--- pkg/R/table.phylo4d.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/table.phylo4d.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -14,7 +14,7 @@
     if (is.character(chk <- checkPhylo4(x))) stop("bad phylo4d object: ",chk)
                                         # if (is.character(chk <- checkData(x))) stop("bad phylo4d object: ",chk) <- needed?
 
-    if(!require(ape)) stop("the ape package is required")
+    ## if(!require(ape)) stop("the ape package is required")
     if(cex.label<0.1) {
         show.tip.label <- FALSE
         show.node.label <- FALSE

Modified: pkg/R/utils.R
===================================================================
--- pkg/R/utils.R	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/R/utils.R	2013-08-09 14:35:59 UTC (rev 194)
@@ -42,7 +42,7 @@
 # sp.tips
 ##########
 sp.tips <- function(x, tip1, tip2, useTipNames=FALSE, quiet=FALSE, include.mrca=TRUE){
-    if(!require(phylobase)) stop("phylobase package is not installed")
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
 
     ## conversion from phylo, phylo4 and phylo4d
     x <- as(x, "phylo4")
@@ -163,7 +163,7 @@
 # listDD
 ############
 listDD <- function(x, nameBy=c("label","number")){
-    if(!require(phylobase)) stop("phylobase package is not installed")
+    ## if(!require(phylobase)) stop("phylobase package is not installed")
 
     ## conversion from phylo, phylo4 and phylo4d
     x <- as(x, "phylo4")
@@ -186,3 +186,6 @@
     return(res)
 } # end listDD
 
+
+
+

Modified: pkg/man/abouheif.Rd
===================================================================
--- pkg/man/abouheif.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/abouheif.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -72,7 +72,8 @@
   classical Moran's I test. \cr
 }
 \examples{
-if(require(ade4)){
+
+if(require(ade4)&& require(ape) && require(phylobase)){
 ## load data
 data(ungulates)
 tre <- read.tree(text=ungulates$tre)

Modified: pkg/man/bullseye.Rd
===================================================================
--- pkg/man/bullseye.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/bullseye.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -8,7 +8,7 @@
   uses and is compatible with ape's \code{\link[ape]{plot.phylo}}.
 }
 \usage{
-bullseye(phy, traits=NULL, col.tips.by=NULL, col.pal=seasun,
+bullseye(phy, traits=NULL, col.tips.by=NULL, col.pal=spectral,
          circ.n=6, circ.bg=transp("royalblue",.1), circ.unit=NULL,
          legend=TRUE, leg.posi="bottomleft", leg.title="", leg.bg="white",
          traits.inset=1.1, traits.space=0.05, traits.pch=19, traits.cex=1,
@@ -55,6 +55,7 @@
 }
 \author{Thibaut Jombart \email{tjombart at imperial.ac.uk}}
 \examples{
+if(require(ape) && require(phylobase) && require(adegenet)){
 
 data(lizards)
 tre <- read.tree(text=lizards$hprA) # make a tree
@@ -70,5 +71,6 @@
          edge.width=2)
 
 }
+}
 \keyword{hplot}
 \keyword{multivariate}

Modified: pkg/man/carni19.Rd
===================================================================
--- pkg/man/carni19.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/carni19.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -23,9 +23,12 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+if(require(ape) && require(phylobase)){
+
 data(carni19)
 tre <- read.tree(text=carni19$tre)
 x <- phylo4d(tre, data.frame(carni19$bm))
 table.phylo4d(x, ratio=.5, center=FALSE)
 }
+}
 \keyword{datasets}

Modified: pkg/man/carni70.Rd
===================================================================
--- pkg/man/carni70.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/carni70.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -26,7 +26,10 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+if(require(ape) && require(phylobase)){
+
 data(carni70)
+rownames(carni70$tab) <- gsub("_", ".", rownames(carni70$tab))
 tre <- read.tree(text=carni70$tre)
 x <- phylo4d(tre, carni70$tab)
 table.phylo4d(x)
@@ -41,9 +44,9 @@
 orthogram(size, tre)
 
 ## transform range and test for a phylogenetic signal
-yrange <- scalewt(carni70$tab)[,2]
+yrange <- scale(carni70$tab)[,2]
 names(yrange) <- row.names(carni70$tab)
 orthogram(yrange, tre)
-
 }
+}
 \keyword{datasets}

Modified: pkg/man/lizards.Rd
===================================================================
--- pkg/man/lizards.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/lizards.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -33,6 +33,8 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+if(require(ape) && require(phylobase)){
+
 ## see data
 data(lizards)
 liz.tr <- read.tree(tex=lizards$hprA) # make a tree
@@ -62,4 +64,5 @@
 
 }
 }
+}
 \keyword{datasets}

Modified: pkg/man/maples.Rd
===================================================================
--- pkg/man/maples.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/maples.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -27,6 +27,8 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+if(require(ape) && require(phylobase)){
+
 data(maples)
 
 ## see the tree
@@ -51,4 +53,5 @@
 pic.dom <- pic(dom, tre)
 cor.test(pic.bif, pic.dom) # correlation is no longer significant
 }
+}
 \keyword{datasets}

Modified: pkg/man/mjrochet.Rd
===================================================================
--- pkg/man/mjrochet.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/mjrochet.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -44,6 +44,8 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+if(require(ape) && require(phylobase)){
+
 data(mjrochet)
 tre <- read.tree(text=mjrochet$tre) # make a tree
 traits <- log((mjrochet$tab))
@@ -58,6 +60,6 @@
 mjr.tests <- abouheif.moran(mjr, nrep=499)
 mjr.tests
 plot(mjr.tests)
-
 }
+}
 \keyword{datasets}

Modified: pkg/man/orthobasis.Rd
===================================================================
--- pkg/man/orthobasis.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/orthobasis.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -74,6 +74,7 @@
 
 }
 \examples{
+if(require(ape) && require(phylobase)){
 
 ## make a tree
 x <- rtree(50)
@@ -102,6 +103,6 @@
 
 ## see the difference
 table.phylo4d(phylo4d(tre, cbind.data.frame(resid1, resid2)))
-
 }
+}
 \keyword{manip}

Modified: pkg/man/orthogram.Rd
===================================================================
--- pkg/man/orthogram.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/orthogram.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -103,6 +103,8 @@
   never happen, since ade4 is loaded as a dependence by adephylo.
 }
 \examples{
+if(require(ape) && require(phylobase)){
+
 ## a phylogenetic example
 data(ungulates)
 tre <- read.tree(text=ungulates$tre)
@@ -132,5 +134,5 @@
 ## Abouheif's test
 W <- proxTips(tre, method="oriAbouheif") # proximity matrix
 abouheif.moran(resid, W)
-
 }
+}

Modified: pkg/man/palm.Rd
===================================================================
--- pkg/man/palm.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/palm.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -34,6 +34,8 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+if(require(ape) && require(phylobase)){
+
 ## load data, make a tree and a phylo4d object
 data(palm)
 tre <- read.tree(text=palm$tre)
@@ -52,4 +54,5 @@
 plot(phylAutoTests)
 }
 }
+}
 \keyword{datasets}

Modified: pkg/man/ppca.Rd
===================================================================
--- pkg/man/ppca.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/ppca.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -130,6 +130,7 @@
  }
 \author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
 \examples{
+if(require(ape) && require(phylobase)){
 
 #### ORIGINAL EXAMPLE FROM JOMBART ET AL 2010 ####
 data(lizards)
@@ -246,4 +247,5 @@
 abouheif.moran(dat[, names(highContrib)], prox)
 
 }
+}
 \keyword{multivariate}
\ No newline at end of file

Modified: pkg/man/procella.Rd
===================================================================
--- pkg/man/procella.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/procella.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -34,6 +34,7 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+if(require(ape) && require(phylobase)){
 ## load data, make tree and phylo4d object
 data(procella)
 tre <- read.tree(text=procella$tre)
@@ -56,6 +57,7 @@
 myTests <- gearymoran(prox, traits)
 plot(myTests)
 }
+}
 
 }
 \keyword{datasets}

Modified: pkg/man/tithonia.Rd
===================================================================
--- pkg/man/tithonia.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/tithonia.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -39,6 +39,8 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+if(require(ape) && require(phylobase)){
+
 data(tithonia)
 tre <- read.tree(text=tithonia$tre)
 traits <- log(tithonia$tab + 1)
@@ -60,4 +62,5 @@
 gearymoran(prox2, traits)
 }
 }
+}
 \keyword{datasets}

Modified: pkg/man/ungulates.Rd
===================================================================
--- pkg/man/ungulates.Rd	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/man/ungulates.Rd	2013-08-09 14:35:59 UTC (rev 194)
@@ -32,6 +32,7 @@
   This dataset replaces the former version in ade4.
 }
 \examples{
+if(require(ape) && require(phylobase)){
 ## load data
 data(ungulates)
 tre <- read.tree(text=ungulates$tre)
@@ -49,6 +50,6 @@
 
 ## test phylogenetic inertia in residuals
 orthogram(residuals(lm1), x) 
-
 }
+}
 \keyword{datasets}

Modified: pkg/vignettes/adephylo.Rnw
===================================================================
--- pkg/vignettes/adephylo.Rnw	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/vignettes/adephylo.Rnw	2013-08-09 14:35:59 UTC (rev 194)
@@ -133,8 +133,11 @@
 (\url{http://r-forge.r-project.org/}).  In all cases, the latest version of \code{adephylo} can be
 found from \url{http://r-forge.r-project.org/R/?group_id=303}.  \\
 
-When loading the package, dependencies are also loaded:
+We load \textit{adephylo}, alongside some useful packages:
 <<load>>=
+library(ape)
+library(phylobase)
+library(ade4)
 library(adephylo)
 search()
 @

Modified: pkg/vignettes/adephylo.pdf
===================================================================
--- pkg/vignettes/adephylo.pdf	2013-05-20 16:33:39 UTC (rev 193)
+++ pkg/vignettes/adephylo.pdf	2013-08-09 14:35:59 UTC (rev 194)
@@ -106,24 +106,28 @@
 << /S /GoTo /D [70 0 R  /Fit ] >>
 endobj
 90 0 obj <<
-/Length 1891      
+/Length 1889      
 /Filter /FlateDecode
 >>
 stream
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adephylo -r 194