From noreply at r-forge.r-project.org Wed Nov 20 21:04:40 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 20 Nov 2013 21:04:40 +0100 (CET) Subject: [Adephylo-commits] r197 - pkg Message-ID: <20131120200440.BB2EC18518B@r-forge.r-project.org> Author: sdray Date: 2013-11-20 21:04:40 +0100 (Wed, 20 Nov 2013) New Revision: 197 Modified: pkg/DESCRIPTION pkg/NAMESPACE Log: Update the import for ade4 methods Modified: pkg/DESCRIPTION =================================================================== --- pkg/DESCRIPTION 2013-08-10 09:53:00 UTC (rev 196) +++ pkg/DESCRIPTION 2013-11-20 20:04:40 UTC (rev 197) @@ -5,8 +5,8 @@ Author: Thibaut Jombart , Stephane Dray Maintainer: Thibaut Jombart Suggests: -Depends: methods -Imports: phylobase, ape, ade4, adegenet +Depends: methods, ade4 +Imports: phylobase, ape, 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 2013-08-10 09:53:00 UTC (rev 196) +++ pkg/NAMESPACE 2013-11-20 20:04:40 UTC (rev 197) @@ -13,7 +13,7 @@ "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.krandtest", + "s.arrow", "s.label", "scatter", "scalewt", "dudi.pca", "add.scatter", "add.scatter.eig") importFrom(adegenet, "bluepal", "redpal", "greenpal", "seasun", "spectral", "funky", From noreply at r-forge.r-project.org Fri Nov 22 22:17:54 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 22 Nov 2013 22:17:54 +0100 (CET) Subject: [Adephylo-commits] r198 - pkg/R Message-ID: <20131122211754.81F4F185329@r-forge.r-project.org> Author: sdray Date: 2013-11-22 22:17:54 +0100 (Fri, 22 Nov 2013) New Revision: 198 Modified: pkg/R/orthogram.R Log: Upate calls to ade4 methods Modified: pkg/R/orthogram.R =================================================================== --- pkg/R/orthogram.R 2013-11-20 20:04:40 UTC (rev 197) +++ pkg/R/orthogram.R 2013-11-22 21:17:54 UTC (rev 198) @@ -185,14 +185,14 @@ nclass <- as.integer (nrepet/25) nclass <- min(c(nclass,40)) } - plot.randtest (as.randtest (w$R2Max[-1],w$R2Max[1],call=match.call()),main = "R2Max",nclass=nclass) + plot(as.randtest (w$R2Max[-1],w$R2Max[1],call=match.call()),main = "R2Max",nclass=nclass) if (posinega !=0) { - plot.randtest (as.randtest (w$ratio[-1],w$ratio[1],call=match.call()),main = "Ratio",nclass=nclass) + plot(as.randtest (w$ratio[-1],w$ratio[1],call=match.call()),main = "Ratio",nclass=nclass) } else { - plot.randtest (as.randtest (w$SkR2k[-1],w$SkR2k[1],call=match.call()),main = "SkR2k",nclass=nclass) + plot(as.randtest (w$SkR2k[-1],w$SkR2k[1],call=match.call()),main = "SkR2k",nclass=nclass) } - plot.randtest (as.randtest (w$Dmax[-1],w$Dmax[1],call=match.call()),main = "DMax",nclass=nclass) - plot.randtest (as.randtest (w$SCE[-1],w$SCE[1],call=match.call()),main = "SCE",nclass=nclass) + plot(as.randtest (w$Dmax[-1],w$Dmax[1],call=match.call()),main = "DMax",nclass=nclass) + plot(as.randtest (w$SCE[-1],w$SCE[1],call=match.call()),main = "SCE",nclass=nclass) w$param <- w$observed <- w$vecpro <- NULL w$phylo95 <- w$sig025 <- w$sig975 <- NULL From noreply at r-forge.r-project.org Mon Nov 25 16:06:42 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 25 Nov 2013 16:06:42 +0100 (CET) Subject: [Adephylo-commits] r199 - pkg/man Message-ID: <20131125150642.DF104185AE7@r-forge.r-project.org> Author: sdray Date: 2013-11-25 16:06:41 +0100 (Mon, 25 Nov 2013) New Revision: 199 Modified: pkg/man/ppca.Rd Log: Update loading/unloading of ade4 Modified: pkg/man/ppca.Rd =================================================================== --- pkg/man/ppca.Rd 2013-11-22 21:17:54 UTC (rev 198) +++ pkg/man/ppca.Rd 2013-11-25 15:06:41 UTC (rev 199) @@ -132,7 +132,7 @@ \examples{ data(lizards) -if(require(ape) && require(phylobase) && require(ade4)){ +if(require(ape) && require(phylobase)){ #### ORIGINAL EXAMPLE FROM JOMBART ET AL 2010 #### @@ -247,7 +247,6 @@ prox <- proxTips(tre, method="Abouheif") abouheif.moran(dat[, names(highContrib)], prox) -detach("package:ade4") } } -\keyword{multivariate} \ No newline at end of file +\keyword{multivariate} From noreply at r-forge.r-project.org Fri Nov 29 10:12:55 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 29 Nov 2013 10:12:55 +0100 (CET) Subject: [Adephylo-commits] r200 - pkg/man Message-ID: <20131129091255.E0B3B1852B0@r-forge.r-project.org> Author: sdray Date: 2013-11-29 10:12:55 +0100 (Fri, 29 Nov 2013) New Revision: 200 Modified: pkg/man/table.phylo4d.Rd Log: Correct some ade4 load/unload calls Modified: pkg/man/table.phylo4d.Rd =================================================================== --- pkg/man/table.phylo4d.Rd 2013-11-25 15:06:41 UTC (rev 199) +++ pkg/man/table.phylo4d.Rd 2013-11-29 09:12:55 UTC (rev 200) @@ -122,7 +122,6 @@ 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} From noreply at r-forge.r-project.org Fri Nov 29 16:46:03 2013 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 29 Nov 2013 16:46:03 +0100 (CET) Subject: [Adephylo-commits] r201 - pkg Message-ID: <20131129154603.691481865D4@r-forge.r-project.org> Author: sdray Date: 2013-11-29 16:46:01 +0100 (Fri, 29 Nov 2013) New Revision: 201 Modified: pkg/DESCRIPTION Log: Release of adephylo 1.1-6 Modified: pkg/DESCRIPTION =================================================================== --- pkg/DESCRIPTION 2013-11-29 09:12:55 UTC (rev 200) +++ pkg/DESCRIPTION 2013-11-29 15:46:01 UTC (rev 201) @@ -1,6 +1,6 @@ Package: adephylo -Version: 1.1-5 -Date: 2013/08/09 +Version: 1.1-6 +Date: 2013/11/29 Title: adephylo: exploratory analyses for the phylogenetic comparative method. Author: Thibaut Jombart , Stephane Dray Maintainer: Thibaut Jombart