I think this'll work, depending on how you store your data. # assumes a tree 'phy' and a dataframe, 'df', with first column of tip names, and second column of values for (i in 1:dim(df)[1]) { # find index of edge length idx <- which(phy$edge[,2] == which(phy$tip.label == df[1,i])); # apply it. this assume you want to extend it, not just set it phy$edge.length[idx] <- phy$edge.length[idx] + as.numeric(df[i,2]); }
Probably a nicer way to do it without a loop... JWB ________________________________________ Joseph W. Brown Post-doctoral Researcher, Smith Laboratory University of Michigan Department of Ecology & Evolutionary Biology Room 2071, Kraus Natural Sciences Building Ann Arbor MI 48109-1079 josep...@umich.edu > On 26 Jul, 2017, at 11:57, William Gearty <wgea...@stanford.edu> wrote: > > That's definitely helpful, Joseph, but I'll need to extend the tips to > varying amounts. > > Basically, I performed a tip-dating analysis using constraints based on the > FADs of a bunch of fossils. > However, now some of the analyses I want to perform require that the tips > extend to the species' extinctions, so I need to extend them to the LADs (or > farther, I suppose). > How would I, given a vector of LAD ages for the tips, extend the tips to > those ages? > > On Wed, Jul 26, 2017 at 8:50 AM, Joseph W. Brown <josep...@umich.edu > <mailto:josep...@umich.edu>> wrote: > If you want to just extend all tips by a constant amount you can do this: > > # extend terminal edges by arbitrary amount (here: 13) > idx <- which(phy$edge[,2] < (phy$Nnode + 1)); > phy$edge.length[idx] <- phy$edge.length[idx] + 13; > > HTH. > Joseph. > ________________________________________ > Joseph W. Brown > Post-doctoral Researcher, Smith Laboratory > University of Michigan > Department of Ecology & Evolutionary Biology > Room 2071, Kraus Natural Sciences Building > Ann Arbor MI 48109-1079 > josep...@umich.edu <mailto:josep...@umich.edu> > > > >> On 26 Jul, 2017, at 11:39, David Bapst <dwba...@gmail.com >> <mailto:dwba...@gmail.com>> wrote: >> >> Not sure what you mean by extending tips, Will. Could you describe a >> small example? >> -Dave >> >> On Fri, Jul 21, 2017 at 5:15 PM, William Gearty <wgea...@stanford.edu >> <mailto:wgea...@stanford.edu>> wrote: >>> Hi all, >>> >>> Before I go ahead and wrote a whole script, I was wondering if there is a >>> function or script out there for extending tips (or setting the ages of >>> tips) given a list of taxa and ages? >>> I haven't found anything, but perhaps I'm searching the wrong phrase(s). >>> >>> Thanks, >>> Will >>> >>> -- >>> William Gearty >>> PhD Candidate, Paleobiology >>> Department of Geological Sciences >>> Stanford School of Earth, Energy & Environmental Sciences >>> williamgearty.com <http://williamgearty.com/> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> <mailto:R-sig-phylo@r-project.org> >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >>> Searchable archive at >>> http://www.mail-archive.com/r-sig-phylo@r-project.org/ >>> <http://www.mail-archive.com/r-sig-phylo@r-project.org/> >> >> >> >> -- >> David W. Bapst, PhD >> https://github.com/dwbapst/paleotree <https://github.com/dwbapst/paleotree> >> >> _______________________________________________ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> <mailto:R-sig-phylo@r-project.org> >> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >> <https://stat.ethz.ch/mailman/listinfo/r-sig-phylo> >> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ >> <http://www.mail-archive.com/r-sig-phylo@r-project.org/> > > > > > -- > William Gearty > PhD Candidate, Paleobiology > Department of Geological Sciences > Stanford School of Earth, Energy & Environmental Sciences > williamgearty.com <http://williamgearty.com/> [[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/