Re: [R-sig-phylo] multi2di fails on multiPhylo objects
Hi, Klaus: thanks for the fix. There is a development version on ape-package.ird.fr: http://ape-package.ird.fr/ape_installation.html#versions This version is 4.0-0.2. The source as well as a Windows version are avaialble. The list of changes is there: http://ape-package.ird.fr/NEWS Best, Emmanuel Le 14/01/2017 à 00:43, Yan Wong a écrit : On 13 Jan 2017, at 20:37, Klaus Schliepwrote: Hi Yan, it seems we introduced a small bug with making these functions generic. Replace in the function .multi2di_ape the line phy <- reorder(phy) with phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L) and it should work. You have to recompile ape afterwards. By the way, is this likely to make it into a new release soon, or is there a dev version I can access somehow? I need to roll this out across a number of different computers, some of which I don’t have admin access to. Yan ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] multi2di fails on multiPhylo objects
On 13 Jan 2017, at 20:37, Klaus Schliepwrote: > Hi Yan, > > it seems we introduced a small bug with making these functions generic. > Replace in the function .multi2di_ape the line > phy <- reorder(phy) > with > phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L) > and it should work. You have to recompile ape afterwards. By the way, is this likely to make it into a new release soon, or is there a dev version I can access somehow? I need to roll this out across a number of different computers, some of which I don’t have admin access to. Yan ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] multi2di fails on multiPhylo objects
On 13 Jan 2017, at 20:37, Klaus Schliepwrote: > Hi Yan, > > it seems we introduced a small bug with making these functions generic. > Replace in the function .multi2di_ape the line > phy <- reorder(phy) > with > phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L) > and it should work. You have to recompile ape afterwards. That’s great, thanks. Yan ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] multi2di fails on multiPhylo objects
Hi Yan, it seems we introduced a small bug with making these functions generic. Replace in the function .multi2di_ape the line phy <- reorder(phy) with phy <- .reorder_ape(phy, "cladewise", FALSE, n, 1L) and it should work. You have to recompile ape afterwards. Cheers, Klaus On Fri, Jan 13, 2017 at 1:24 PM, Yan Wongwrote: > Thanks. I think that’s because read_nexus_phylo() doesn’t do > .compressTipLabel automatically > > n <- read_nexus_phylo("tmp.nex") > n2 <- .compressTipLabel(n) > multi2di(n2) #this causes an error. > > Unfortunately I need the .compressTipLabel functionality really. > > Yan > > > On 13 Jan 2017, at 17:06, François Michonneau < > francois.michonn...@gmail.com> wrote: > > > Hi Yan, > > > > I'm not sure about what's going on here, but it works with the rncl > > package (http://cran.r-project.org/web/packages/rncl/index.html) > > > > install.packages("rncl") > > library(rncl) > > n <- read_nexus_phylo("tmp.nex") > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.org/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
Re: [R-sig-phylo] multi2di fails on multiPhylo objects
Thanks. I think that’s because read_nexus_phylo() doesn’t do .compressTipLabel automatically n <- read_nexus_phylo("tmp.nex") n2 <- .compressTipLabel(n) multi2di(n2) #this causes an error. Unfortunately I need the .compressTipLabel functionality really. Yan On 13 Jan 2017, at 17:06, François Michonneauwrote: > Hi Yan, > > I'm not sure about what's going on here, but it works with the rncl > package (http://cran.r-project.org/web/packages/rncl/index.html) > > install.packages("rncl") > library(rncl) > n <- read_nexus_phylo("tmp.nex") ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
[R-sig-phylo] multi2di fails on multiPhylo objects
If I have a nexus file with multiple trees, and the same tips in each tree, but some trees with polytomies, like this #NEXUS BEGIN TREES; TRANSLATE 1 1, 2 2, 3 3, 4 4; TREE A = (((1,2)5,3)6,4); TREE B = ((1,2,3)6,4); END; Then when I try to resolve both trees using multi2di, I get > n <- read.nexus("tmp.nex") > multi2di(n) Error in .reorder_ape(x, order, index.only, length(x$tip.label), io) : tree apparently badly conformed What am I doing wrong? ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/