From noreply at r-forge.r-project.org Fri Aug 9 16:35:59 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 9 Aug 2013 16:35:59 +0200 (CEST) Subject: [Adephylo-commits] r194 - in pkg: . R man vignettes vignettes/figs Message-ID: <20130809143559.BC96E185B9B@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 , Stephane Dray Maintainer: Thibaut Jombart 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: <>= +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 x??YK??6????-2)|?? -E???D4?D??B?q????? ?#?R%3]N#i???Tde??BE???}\?d??)a?H???n???,?Z? -????%T?K??i^?N????]?q??]q?6????:?${?[??k????3??vU????~???E????^ ????SZi=h????A??EV???o???? -?~?`??S??v?P??*??B?? k?`???u????g=l???}#0?[o????sx?!;??? q?? -[??]???`??&?m?k?=???;?*?|???:0?S 8=?xlQ?Q?\????6????^?z???-?_????????K$?j ?(f??5QO?I9=?CM????*???P???? -??)e ??'`q?Y?t??I??I? ?4L????1k|?Y?j?&B??fA?e??7?s??HVt?l-?o`???,?|ob;"q -???v[.R?????? ??d???1n??)(?u??????SoH{?[b??[t?? ???P?Ppwj?C????W???I????B?~??r?T?-?I????????d?1??B??0??"X.?^}??F?Ib=t??T??e??q?V5_ ??})?8??Z????????}?,?@b??n2?e?/???mex??D?"~??$?:?)?R??J*??C?U6????^$7???????\R??LWz?^x????\F??N?????(???%`f???| -???PdyX]?6?o?????s??????C?(??hf7(?=tJ??vO"W?2????2~???????v??a?DU?????+}??7'??~X???2??>/?|Z?Y|v?]?}V? ?R????.?M~[???9?\?z;???$T[??g4?3?3??y?:??C??$??????????x?????????(rUl,?`m?]????`??yg?x6?QD?????)??G????<.5??????????L? +E??|??h???????????ZG??Jf&??F??i????,???.'????xR??? +?n???G^????;??? ?&?0J?0q???7(j[77?D A?W?)^?????)??????j? FI&R??(Q2-d?+????rA3?*/????{?r?(s??KRe ??k?X??%N???Q?l?2??Y?????H??e??/?u????E?v?????6??[6?M5?/????F?i?qG??|??????I/????zC????tx????C(??bB?P?)???,???){Vu6????!~t??4?K??H? +??`?????9b?,(???38g?f?$???"?? C??E\????A???~????r/qId??S?nf?9?x&^w?t??????'???r??"+??? Y?????????b2U????????'?a?H!?hO??OF0?????P???????}'0?[o????sx?!;??? ??? +{????P?????m?o?#?]?;?*?2???:0?S 8=?'x?Q?Q?\????6????O^?z???-?_?????????K$?j ?'??5QOE=?CM???5*???T???? +??e ??'`q?[? ?PI???? ?4L????1[|?Y?j?&B??fA?e??7?s???EV?s ?Z????MO??|ob;"q +???v[?M?????? ??T???3n??)(?u????;? Ca?i~K??v?Uy??_?6?&????z.+?U??rR#ws???l???$?kdRb??m?!/?&?n????!;L:? ???????4??????-;](~fEar?I@??0>$??????&?8?C?W~?? *????T?v?Rn???y????????f?AH +V?`???9? +m????N?2c???W????oXx???????r??H????=7j??4 ???Jr?????M8?J?%L2(??C.??+??????2??0s?????E|C5?aP?,?{?????????Y???????' +{$? +????[?GO?;?????~??v??7?S???+/q?w$?^?z???'??X?}?p?s(???p$-?V??E?[,xF'W??|B?`?igy?????dH???lFw??m???? +??????y/?'????=??q???????^B?X? ?0 +????5^t??!??k(?????P??e?m? ???/??e>?7??p6?tb???? i?T? 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S????,?=?r?4?;??,;v?b? ??k???%K}o"6py?????J"+?[.{?7#[???C??m? /"X??$0qO?"?tb?#????? ????ri?R??ox?TI?k??z?PF]6G??e?lt???V6|??]j8?np?d???2???????sZ?^??????A? +h??g??Ip?? +D?&7h???grWw?O?7Y9???T[??Gfs?~???? +??M!??a65???}2 +???M_???h?3{???????Z?h??+?L??n]?#(%`??.??nF??~???????????????C??G?Y?????c??\@?K????+?&=I?C???'q?????????[?-?p???? z8g??H`[#= ??Dr ?+???|kH???w? w2E???????n/?????T?!?w???????V????n??p??7?C?F?/?????-?Q????[A????????I|^????k???????6U#??}3t_??&??Zh?? +???????K??5|8?????????Zw??!?w?n?kin? ?#*??h?sDBK?BM'?i???1??? +-?vM????I??? ?)??u?XA??Z??)#l????}6W???]?B?=???a??????O9?v?!? +D?????2`b=?9??v +?4??R??%?B?NE?D???~? ?=$Z?z?}?^iU??meX=?:_? 3?0X>h?^BQ??Wj?e-;??"????v??p?=+?tG?{?l??z?O??$?M?`??&?{?/??c??4f?(zr?&???/i?n?T}?????G??-??~kCzj? 9?y`??M?"d6I?????bnH?,???|ZSa???yt~?ObR?h? ??????[???+&4ivb??7??N?????]?? Uyd9? +)????8?Xe.?* +2???f +_??.?????TxgF???????j???8???*?m????????%????1??Q?=O?Q&???+l?{?4?=?|???????$???0R??X?c?/?R^6??????3 at zs?3 n??w??g??yV?h??3??????A?sQ?(O?W??????%2cq?t??????????P???3??g?_?9H??;???c?-SD?j??N?{?? +?????=??/?????vb??x?2????-??> endobj 18 0 obj << -/D [120 0 R /XYZ 133.768 577.411 null] +/D [120 0 R /XYZ 133.768 544.026 null] >> endobj 22 0 obj << -/D [120 0 R /XYZ 133.768 426.382 null] +/D [120 0 R /XYZ 133.768 396.671 null] >> endobj 26 0 obj << -/D [120 0 R /XYZ 133.768 358.132 null] +/D [120 0 R /XYZ 133.768 328.501 null] >> endobj 119 0 obj << -/Font << /F65 111 0 R /F8 99 0 R /F55 100 0 R /F43 96 0 R /F69 123 0 R /F48 98 0 R >> [TRUNCATED] To get the complete diff run: svnlook diff /svnroot/adephylo -r 194 From noreply at r-forge.r-project.org Fri Aug 9 16:47:49 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 9 Aug 2013 16:47:49 +0200 (CEST) Subject: [Adephylo-commits] r195 - in pkg: . man Message-ID: <20130809144749.90AC21850D9@r-forge.r-project.org> Author: jombart Date: 2013-08-09 16:47:49 +0200 (Fri, 09 Aug 2013) New Revision: 195 Modified: pkg/NAMESPACE pkg/man/mjrochet.Rd pkg/man/ppca.Rd Log: Still some examples failing. Modified: pkg/NAMESPACE =================================================================== --- pkg/NAMESPACE 2013-08-09 14:35:59 UTC (rev 194) +++ pkg/NAMESPACE 2013-08-09 14:47:49 UTC (rev 195) @@ -13,7 +13,8 @@ "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") + "plot.randtest", "s.arrow", "s.label", "scatter", "scalewt", "dudi.pca", "plot.krandtest", + "add.scatter", "add.scatter.eig") importFrom(adegenet, "bluepal", "redpal", "greenpal", "seasun", "spectral", "funky", "num2col", "fac2col", "any2col", "transp") Modified: pkg/man/mjrochet.Rd =================================================================== --- pkg/man/mjrochet.Rd 2013-08-09 14:35:59 UTC (rev 194) +++ pkg/man/mjrochet.Rd 2013-08-09 14:47:49 UTC (rev 195) @@ -59,7 +59,7 @@ ## perform Abouheif's test for each trait mjr.tests <- abouheif.moran(mjr, nrep=499) mjr.tests -plot(mjr.tests) + } } \keyword{datasets} Modified: pkg/man/ppca.Rd =================================================================== --- pkg/man/ppca.Rd 2013-08-09 14:35:59 UTC (rev 194) +++ pkg/man/ppca.Rd 2013-08-09 14:47:49 UTC (rev 195) @@ -130,10 +130,11 @@ } \author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} } \examples{ -if(require(ape) && require(phylobase)){ +data(lizards) +if(require(ape) && require(phylobase) && require(ade4)){ + #### ORIGINAL EXAMPLE FROM JOMBART ET AL 2010 #### -data(lizards) ## BUILD A TREE AND A PHYLO4D OBJECT From noreply at r-forge.r-project.org Sat Aug 10 11:53:01 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Sat, 10 Aug 2013 11:53:01 +0200 (CEST) Subject: [Adephylo-commits] r196 - in pkg: . man vignettes vignettes/figs Message-ID: <20130810095301.1F933185188@r-forge.r-project.org> Author: jombart Date: 2013-08-10 11:53:00 +0200 (Sat, 10 Aug 2013) New Revision: 196 Modified: pkg/ChangeLog pkg/man/carni19.Rd pkg/man/carni70.Rd pkg/man/lizards.Rd pkg/man/maples.Rd pkg/man/mjrochet.Rd pkg/man/moranIdx.Rd pkg/man/orthobasis.Rd pkg/man/orthogram.Rd pkg/man/palm.Rd pkg/man/ppca.Rd pkg/man/procella.Rd pkg/man/sp.tips.Rd pkg/man/table.phylo4d.Rd pkg/man/tithonia.Rd pkg/man/treePart.Rd pkg/man/ungulates.Rd 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: Changes for the new release 1.1-5 Modified: pkg/ChangeLog =================================================================== --- pkg/ChangeLog 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/ChangeLog 2013-08-10 09:53:00 UTC (rev 196) @@ -1,3 +1,15 @@ + CHANGES IN ADEPHYLO VERSION 1.1-5 + +FIXES + o the new NAMESPACE selectively imports procedures to avoid + conflicts between ape, phylobase, and ade4. Thes packages are no + longer attached when loading adephylo + + o most dataset examples have been 'dontrun-ed' to save time during + checks of the package on CRAN + + + CHANGES IN ADEPHYLO VERSION 1.1-4 Modified: pkg/man/carni19.Rd =================================================================== --- pkg/man/carni19.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/carni19.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -23,6 +23,7 @@ This dataset replaces the former version in ade4. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ data(carni19) @@ -31,4 +32,5 @@ table.phylo4d(x, ratio=.5, center=FALSE) } } +} \keyword{datasets} Modified: pkg/man/carni70.Rd =================================================================== --- pkg/man/carni70.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/carni70.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -26,6 +26,7 @@ This dataset replaces the former version in ade4. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ data(carni70) @@ -49,4 +50,5 @@ orthogram(yrange, tre) } } +} \keyword{datasets} Modified: pkg/man/lizards.Rd =================================================================== --- pkg/man/lizards.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/lizards.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -33,6 +33,7 @@ This dataset replaces the former version in ade4. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ ## see data @@ -65,4 +66,5 @@ } } } +} \keyword{datasets} Modified: pkg/man/maples.Rd =================================================================== --- pkg/man/maples.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/maples.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -27,6 +27,7 @@ This dataset replaces the former version in ade4. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ data(maples) @@ -54,4 +55,5 @@ cor.test(pic.bif, pic.dom) # correlation is no longer significant } } +} \keyword{datasets} Modified: pkg/man/mjrochet.Rd =================================================================== --- pkg/man/mjrochet.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/mjrochet.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -44,6 +44,7 @@ This dataset replaces the former version in ade4. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ data(mjrochet) @@ -62,4 +63,5 @@ } } +} \keyword{datasets} Modified: pkg/man/moranIdx.Rd =================================================================== --- pkg/man/moranIdx.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/moranIdx.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -37,9 +37,14 @@ between tips of a phylogeny. } \examples{ +\dontrun{ ## use maples dataset -example(maples) +data(maples) +tre <- read.tree(text=maples$tre) +dom <- maples$tab$Dom +bif <- maples$tab$Bif + ## get a proximity matrix between tips W <- proxTips(tre, met="Abouheif") @@ -60,4 +65,5 @@ abline(v=sim[1], col="red", lwd=3) } +} \keyword{manip} Modified: pkg/man/orthobasis.Rd =================================================================== --- pkg/man/orthobasis.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/orthobasis.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -76,6 +76,7 @@ \examples{ if(require(ape) && require(phylobase)){ +## SIMPLE EXAMPLE ## ## make a tree x <- rtree(50) @@ -88,9 +89,22 @@ table.phylo4d(obj, cex.sym=.7, cex.lab=.7) -## removing phylogenetic autocorrelation in a model ## -example(ungulates, package="adephylo") +\dontrun{ +## REMOVING PHYLOGENETIC AUTOCORRELATION IN A MODEL ## +## use example in ungulates dataset +data(ungulates) +tre <- read.tree(text=ungulates$tre) +plot(tre) +## look at two traits +afbw <- log(ungulates$tab[,1]) +neonatw <- log((ungulates$tab[,2]+ungulates$tab[,3])/2) +names(afbw) <- tre$tip.label +names(neonatw) <- tre$tip.label +plot(afbw, neonatw) # relationship between traits +lm1 <- lm(neonatw~afbw) +abline(lm1) + lm1 resid1 <- residuals(lm1) orthogram(resid1, tre) # residuals are autocorrelated @@ -105,4 +119,5 @@ table.phylo4d(phylo4d(tre, cbind.data.frame(resid1, resid2))) } } +} \keyword{manip} Modified: pkg/man/orthogram.Rd =================================================================== --- pkg/man/orthogram.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/orthogram.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -103,6 +103,7 @@ never happen, since ade4 is loaded as a dependence by adephylo. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ ## a phylogenetic example @@ -136,3 +137,4 @@ abouheif.moran(resid, W) } } +} Modified: pkg/man/palm.Rd =================================================================== --- pkg/man/palm.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/palm.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -34,6 +34,7 @@ This dataset replaces the former version in ade4. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ ## load data, make a tree and a phylo4d object @@ -55,4 +56,5 @@ } } } +} \keyword{datasets} Modified: pkg/man/ppca.Rd =================================================================== --- pkg/man/ppca.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/ppca.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -247,6 +247,7 @@ prox <- proxTips(tre, method="Abouheif") abouheif.moran(dat[, names(highContrib)], prox) +detach("package:ade4") } } \keyword{multivariate} \ No newline at end of file Modified: pkg/man/procella.Rd =================================================================== --- pkg/man/procella.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/procella.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -34,30 +34,16 @@ This dataset replaces the former version in ade4. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ + ## load data, make tree and phylo4d object data(procella) tre <- read.tree(text=procella$tre) x <- phylo4d(tre, procella$traits) par(mar=rep(.1,4)) table.phylo4d(x,cex.lab=.7) - -## test phylogenetic autocorrelation in traits -if(require(ade4)){ - -f1 <- function(vec){ # to replace missing data -m <- mean(vec,na.rm=TRUE) -vec[is.na(vec)] <- m -return(vec) } - -traits <- data.frame(lapply(procella$traits, f1)) -prox <- proxTips(tre) - -myTests <- gearymoran(prox, traits) -plot(myTests) } } - -} \keyword{datasets} Modified: pkg/man/sp.tips.Rd =================================================================== --- pkg/man/sp.tips.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/sp.tips.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -40,6 +40,7 @@ slowly. \cr } \examples{ +\dontrun{ if(require(ape) & require(phylobase)){ ## make a tree x <- as(rtree(20),"phylo4") @@ -49,4 +50,5 @@ sp.tips(x, 1, 2:20, TRUE) } } +} \keyword{manip} Modified: pkg/man/table.phylo4d.Rd =================================================================== --- pkg/man/table.phylo4d.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/table.phylo4d.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -121,6 +121,8 @@ table.phylo4d(myPC, ratio=.8, var.lab=varlab) # plot the PCs add.scatter.eig(liz.pca1$eig,2,1,2,posi="topleft", inset=c(0,.15)) title("Phylogeny and the principal components") + +detach("package:ade4") } } \keyword{hplot} Modified: pkg/man/tithonia.Rd =================================================================== --- pkg/man/tithonia.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/tithonia.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -39,27 +39,19 @@ This dataset replaces the former version in ade4. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ data(tithonia) tre <- read.tree(text=tithonia$tre) traits <- log(tithonia$tab + 1) +rownames(traits) <- gsub("_", ".", rownames(traits)) ## build a phylo4d object x <- phylo4d(tre, traits) par(mar=rep(.1,4)) table.phylo4d(x) -## perform a Geary/Moran test to detect phylogenetic signal in variables -if(require(ade4)){ - -## use branch length to define proximities -prox1 <- proxTips(tre, method="patristic") -gearymoran(prox1, traits) - -## use Abouheif's proximity -prox2 <- proxTips(tre, method="Abouheif") -gearymoran(prox2, traits) } } } Modified: pkg/man/treePart.Rd =================================================================== --- pkg/man/treePart.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/treePart.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -43,6 +43,8 @@ from the ade4 package. } \examples{ +\dontrun{ + if(require(ape) & require(phylobase)){ ## make a tree x <- as(rtree(10),"phylo4") @@ -53,19 +55,6 @@ temp <- phylo4d(x, partition) table.phylo4d(temp, cent=FALSE, scale=FALSE) } - -if(require(ade4)){ -## former orthobasis in ade4 -data(ungulates) -ung.Bscores <- newick2phylog(ungulates$tre)$Bscores - -## version using treePart -ung <- read.tree(text=ungulates$tre) -ung.orthobas <- treePart(ung, res="orthobasis") - -## comparison of the first 3 vectors -cbind(ung.Bscores[,1], ung.orthobas[,1],ung.Bscores[,2], - ung.orthobas[,2], ung.Bscores[,3], ung.orthobas[,3]) } } \keyword{manip} Modified: pkg/man/ungulates.Rd =================================================================== --- pkg/man/ungulates.Rd 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/man/ungulates.Rd 2013-08-10 09:53:00 UTC (rev 196) @@ -32,6 +32,7 @@ This dataset replaces the former version in ade4. } \examples{ +\dontrun{ if(require(ape) && require(phylobase)){ ## load data data(ungulates) @@ -52,4 +53,5 @@ orthogram(residuals(lm1), x) } } +} \keyword{datasets} Modified: pkg/vignettes/adephylo.pdf =================================================================== --- pkg/vignettes/adephylo.pdf 2013-08-09 14:47:49 UTC (rev 195) +++ pkg/vignettes/adephylo.pdf 2013-08-10 09:53:00 UTC (rev 196) @@ -106,28 +106,31 @@ << /S /GoTo /D [70 0 R /Fit ] >> endobj 90 0 obj << -/Length 1889 +/Length 1888 /Filter /FlateDecode >> stream x??YK??6????-2)|?? -E??|??h???????????ZG??Jf&??F??i????,???.'????xR??? -?n???G^????;??? ?&?0J?0q???7(j[77?D A?W?)^?????)??????j? 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'??*%Z?????c??: ???g???J?;??????4 ???|pD???Rv?F???y?'??Igu?`?????=???7N??)??3ZT?????R??zmv?uy+??]P?g?h(h?+n< ?*c0A???#S6?3?????Y???>?!}????>????TE???gRM}??EO?h?z???????1|k??3?G???#l??????|??r???q?-X???V???t?Z?!I?? +|??1!??L?}???f_gx}?n$P?gtD??YW?MsM?????H??)?4??q??5?Z_nI?X#???3?$? +6??k?????i??d?AH[KYr??n??g??x\?J?G?P?? 6?? 7?k???'?J4?Xx{> endobj 153 0 obj << -/Length 970 +/Length 971 /Filter /FlateDecode >> stream -x??VKo?8??W=????"EIE[ ?&m=???dI?SX??R?????z?6???`?4l!??#]??=??>?co]"9??M??7??z??????AMl,?YvW????q??YF??wkYl?5?4??+e?f????k?`nQb???;1????7???+?p?d??=???l??????whX9 -?tv ??9NMd?<%Q???@?Y???a`T?Z????\??j?ld??????jW?X?xW?s?]3???j??5?yH?????C???? ?#???U3%?????????ag? ??T*t ????~???x?E?!o1@?7??=?R?Jd????G???????8?G???;??N?u????%|??????? ??b9S?? -????,??  ?f??k?M I?ibzEwp???????#?='?????m?f?q?(???I0??Y?'W)zN??a8?x?/?d??q|?qp?48??3??0?U?\e?zx??N|tu?p?[%x??UN??'O9?;??O?=?>?Sfxd???????v????W?f?[?nF! ??ONd??????_5z?q??f??;???A?8E?B'???~??_?????e????~?????h -???7????C?c?_??????[??x??~y ????????/em?? $?Fq?F???s??F? +x??VYo?8~???D??K?T? ?h??Ez?@?????YX?k)???9H[v?bA?!g?????n"}?H???O?.??H +?]4?????L???Y?M?????/?J4??????m???4?N4(??u????i?H??T2Q????N??? ???[?~He?-A?uS?X`???? ?U?.Dw?2????r?8???5?`?9?;??M +kaUI????i*??<?'??4`B???d+YX??{????$??4v????st?%??W!X?Z?uFJ???@IAG??????v-o?;??-[H'?H7?zK?????[?HO? ^s3?Mf???X??? ??????h|?ju??;?pS???-???(1???CPS??9?nJ4:?5? r1??????Z??=c?6?p??2|?????k?`nYa???;2????7?=??? ?+??#x{???'?QC;???j????????l?? <%Q6??B?????a`U?9???B???@?]?r?u? co ??1Z4?xW????0???j????yH??Z???G???? ?#?^?U??????\??|?a??(K?L*t ?7???j?(???ob?b??2?[???!??> +??+ O4?+:???'?p??7x??N?e??d???/??{@v??b>Q????1???88?????????-?]el?U??W?W????GW??SB??G?s;???R?? /?? |*??/?Y ????a????????f???????Q???.?''2p??E}???????f?????C48E??N&,?9??A??V|m?n???~?????????o?????p??>/ColorSpace << /sRGB 157 0 R >>>> -/Length 322 +/Length 323 /Filter /FlateDecode >> stream -x???MK?0???s??l&?s?E??????]<+H???&?bkY???M& ?:?T??v????????ylOR????+h?(???NQ??"??i???????????>E??????????? h?? ?F %'?)???[h{??r??v????6[?0ez?!?n?????????z???w????w;9?2M????L???_?K????? +x???MK?@???+?????~e???BA?&7?T?P? ???~b??v`?}?M???a '?R??6???v?"$"??v?$????zy?7???uR? ???a???{????~@?,k2hc?C????J?b????##??k?Hv??0????]q???3t???q"???=?5??????D?5???a:??9??E???? ??1?A0?p?yX5?0U??`b??@U0?A??Jn??;w??p?T?{9t???PJ??5??3??p?mo?;??.??O????sI??i? }?&?X??>m?1'b??N?????M??J???????K?*Z?R endstream endobj 155 0 obj << -/CreationDate (D:20130809154611) -/ModDate (D:20130809154611) +/CreationDate (D:20130810112958) +/ModDate (D:20130810112958) /Title (R Graphics Output) /Producer (R 3.0.1) /Creator (R) @@ -922,24 +929,27 @@ >>/ColorSpace << /sRGB 169 0 R >>>> -/Length 1191 +/Length 1189 /Filter /FlateDecode >> stream -x??XKo$5????x???? ????@Zq -p??+m?????U?G?a3?az?_???g?{?yg??7?????I??h????G???m???w???t?y??????p?9g?????[??????q????w???<%??,???>?q"??`n%???????&?????????e{&@???>B?9?M ??f???Pm?j/?W[r????=?=P????D!??????h??U?g??Vl??t??u????????2p???|?\J?8"N'???????m?H????|???}!?-`?5??D}%&?^???W,????????? ??????RC?%???y?}?5C??s%H??d?B? ?f,2???u?r?t"???O????+M???x???m???sy48????_???5[??|4_=|m.??<?^?? )??WO??*?&\=5?Tu?????m(#????V??????!l?5?k???el? /?n?????\?i??? q=??:??????q??X???? ??? -?Ofm??^4?L???{E-??i?K??? -Wu????q?*X????K??????<]??ek??p[????oV??????*?z?`?????????`?? -nB?X???T??"qe???????p??J?V??2??H??*V?????*U,+XkO???W???x?B?!{[??V??_R???x?L? ?:I???F?g???>???>O??6C)??T?XST??3?X???dl?+S?n?YT?[D??????^????3W??5E5<]?e?h?)*[?????!*?i?'Ht???????o? -4????!?F?o+?^??X?Vt???? b)??CG?Bw?????? xF????????????/?NW?CL?u4???s4m?^O?k?zhi6lP{??? -?>?9??@??=?}??~y?*?r^h?V_???#p?A???Vu??oy?9?y?9?x?SG?m??1@@?????4[????=??????V?^????E?s???E?