Re: [R-sig-phylo] Rooting a tree with a basal polytomy
Perfect, thanks. Yan On 7 Feb 2017, at 13:40, Emmanuel Paradiswrote: > Hi, > > If you have a single tree (object of class "phylo") > > phy$root.edge <- 0 > > If there are several trees in your NEXUS file (then phy is of class > "multiPhylo"): > > for (i in seq_along(phy)) phy[[i]]$root.edge <- 0 ___ 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] Rooting a tree with a basal polytomy
Hi, If you have a single tree (object of class "phylo") phy$root.edge <- 0 If there are several trees in your NEXUS file (then phy is of class "multiPhylo"): for (i in seq_along(phy)) phy[[i]]$root.edge <- 0 Best, Emmanuel Le 07/02/2017 à 13:17, Yan Wong a écrit : Sorry if this is a trivial question, but I have some (rooted) nexus trees with polytomies at the root. When I read them in using read.nexus() they are treated as unrooted. What’s the easiest way to tell R that they are intended to be rooted, even though the root is a polytomy? There’s no ‘force.rooted’ option to any of the tree reading routines that I can see. Cheers 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/ Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : http://f.security-mail.net/307Q0KTUtCj ___ 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] Rooting a tree with a basal polytomy
Sorry if this is a trivial question, but I have some (rooted) nexus trees with polytomies at the root. When I read them in using read.nexus() they are treated as unrooted. What’s the easiest way to tell R that they are intended to be rooted, even though the root is a polytomy? There’s no ‘force.rooted’ option to any of the tree reading routines that I can see. Cheers 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/