Tristan, It's alright. To be honest, I am (and should be) quite embarrassed that I overlooked an ape function... I was a nice warm-up exercise, nonetheless, and I can see how to extend it to handle dates for non-ultrametric fossil trees, which is a case not covered by compute.brtimes, and would make a nice addition for paleotree.
Glad we could help! Cheers, -Dave On Wed, Oct 28, 2015 at 9:03 AM, Tristan Lefebure <tristan.lefeb...@gmail.com> wrote: > David, Emmanuel, many thanks! > > chrono3 <- compute.brtime(tr, bt) > all.equal.numeric(chrono$edge.length, chrono3$edge.length) > #TRUE > all.equal.numeric(chrono$edge.length, as.numeric(chrono2$edge.length)) > #also TRUE > > PS: sorry David, I feel kinda responsible for this lost 16 minutes... > > > > On Wed, Oct 28, 2015 at 3:53 PM, Emmanuel Paradis <emmanuel.para...@ird.fr> > wrote: > >> Hi Tristan, >> >> See compute.brtime in ape. >> >> Cheers, >> >> Emmanuel >> >> >> Le 28/10/2015 15:31, Tristan Lefebure a écrit : >> >>> Greetings all, >>> >>> Does anyone know a way to transform branching times into branch length of >>> a >>> chronogram. Like the inverse function of ape::branching.time() ? >>> >>> say you have a chronogram named chrono: >>> >>> tr <- chrono >>> tr$edge.length <- NULL >>> bt <- branching.times(chrono) >>> chrono2 <- magical.function.here(bt, tr) >>> >>> here I want : >>> >>> all(chrono2$edge.length == chrono$edge.length) >>> >>> This would be helpful in situations such as parsing the mcmctree output >>> (mcmc.txt) that are made of sampled branching times by the MCMC (a big >>> table with row=iteration and col=node age) and then, say, run the same >>> diversification analysis on the MCMC trees to get some credibility >>> intervals on the diversification parameters. >>> >>> Thanks ! >>> >>> -- >>> Tristan >>> >>> [[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/ >>> >>> >>> Pour nous remonter une erreur de filtrage, veuillez vous rendre ici : >>> http://f.security-mail.net/301eSIrvP0A >>> >>> >>> >> > > [[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/ -- David W. Bapst, PhD Adjunct Asst. Professor, Geology and Geol. Eng. South Dakota School of Mines and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html _______________________________________________ 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/
