Thanks a lot Emmanuel. It works perfectly. Amitiés, Jérémie. ---- Jérémie Bardin, Dr.
CR2P - Centre de Recherche en Paléontologie - ParisSorbonne Université - MNHN - CNRS Site Jussieu, Tour 46-56, 5°et. 4 place Jussieu, 75252 Paris Cedex 05 tel. +331.44.27.51.77. jeremie.bar...@upmc.fr / jbar...@mnhn.fr / jeremiebar...@yahoo.fr Le mercredi 23 janvier 2019 à 15:55:01 UTC+1, Emmanuel Paradis <emmanuel.para...@ird.fr> a écrit : Hi Jérémie, You're correct: the current version of write.tree() scales with n^2. This seems to be related to calling the generic '[[' operator. You can modify the code with the usual fix(write.tree), then insert these two lines: phy <- .uncompressTipLabel(phy) class(phy) <- NULL right before the 'for' loop, save and close. You may need to use the modified code once or twice (with a small tree) so that R might byte-compile it. I've tried it with the 2027025 trees generared by allTrees(9,rooted=T) and it took 8.5 mins (instead of the predicted 28 hrs with the current code). Best, Emmanuel Le 23/01/2019 à 10:51, Jérémie Bardin a écrit : > Hi all, > I tried to export 2 millions trees to a .tre file with write.tree. This never > ends, thus i tried to get why and realized that the time to write the .tre > depends exponentially on the number of trees. > > trees<-allTrees(9,rooted=T)to<-seq(10000,2000000,10000)durations<-NAfor(i in > 1:length(to)) { ptm <- proc.time() write.tree(trees[1:to[i]], file = > "test.tre") durations[i]<-(proc.time() - ptm)[3]} > I do not really get why it is not nearly linear. Any explanation? > Cheers, Jérémie > ---- > Jérémie Bardin, Dr. > > CR2P - Centre de Recherche en Paléontologie - ParisSorbonne Université - MNHN > - CNRS > Site Jussieu, Tour 46-56, 5°et. > 4 place Jussieu, 75252 Paris Cedex 05 > tel. +331.44.27.51.77. > jeremie.bar...@upmc.fr / jbar...@mnhn.fr / jeremiebar...@yahoo.fr > > [[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/fPLqvOj4 > > [[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/