No, unfortunately not. It works perfectly fine with other kinds of files. Everything, but these ones...The program that generates them does not have any helpful specifications regarding this format ..*.trees
On Mon, Jun 20, 2011 at 5:55 AM, Bhoom [via R] < ml-node+3610421-1897267921-239...@n4.nabble.com> wrote: > Does read.nexus work for you? > > Bhoom > > On Sun, Jun 19, 2011 at 5:04 PM, Andra Tolbus <[hidden > email]<http://user/SendEmail.jtp?type=node&node=3610421&i=0>>wrote: > > > > Dear all, > > > > I am trying to create a consensus skyline plot using the "ape" > > package(newbie). > > I have a nexus file that looks like the one from above containing > many > > trees. (my_file.trees) > > > > #NEXUS > > begin trees; [Treefile generated by sim_coal.exe (Laurent Excoffier)] > > > > tree true_tree_1 = [&U] (((13.1:6, 43.1:5):12, 28.1:14):284, (((((21.1:0, > > > (20.1:1, 4.1:0):0):1, ((37.1:0, (23.1:0, 29.1:0):0):0, 15.1:0):3):7, > > (36.1:3, (40.1:0, 26.1:1):2):1):2, ((16.1:0, 33.1:0):3, (10.1:0, > > 18.1:0):2):8):46, ((((6.1:1, (11.1:0, 34.1:0):0):2, 2.1:1):19, (((38.1:4, > > > (35.1:4, ((8.1:0, 42.1:0):1, 22.1:0):3):2):0, ((5.1:2, (27.1:0, > > 39.1:0):0):0, (17.1:0, 30.1:0):1):4):8, ((31.1:0, ((41.1:0, (7.1:0, > > 25.1:1):0):0, 3.1:0):3):0, (12.1:0, (14.1:0, 1.1:0):0):0):13):10):14, > > (((24.1:0, 9.1:0):0, 32.1:0):1, 19.1:0):25):20):206); > > tree true_tree_2 = [&U] ((((37.1:4, ((36.1:0, 25.1:0):0, 39.1:0):2):0, > > 33.1:1):2, (1.1:0, 43.1:0):1):81, (((((21.1:1, (38.1:1, 14.1:1):0):3, > > (((29.1:0, 35.1:0):1, 4.1:1):1, ((41.1:1, (24.1:0, ((8.1:0, 32.1:0):0, > > 7.1:0):0):1):0, (10.1:2, (6.1:1, (26.1:1, (15.1:0, > > 16.1:0):0):0):0):2):0):4):1, (28.1:1, (3.1:1, 13.1:0):0):7):12, > (((22.1:5, > > (((2.1:1, 34.1:1):0, 19.1:0):3, (18.1:0, 42.1:0):3):0):0, 17.1:0):3, > > (27.1:14, (((30.1:0, 23.1:0):1, 31.1:0):1, 5.1:2):5):3):5):9, ((11.1:0, > > 9.1:1):0, (12.1:0, (20.1:0, 40.1:1):1):3):23):67); > > > > I haven't managed to read this file content using the *read.tree* > function > > .. > > > > Error in if (tp[3] != "") obj$node.label <- tp[3] : > > missing value where TRUE/FALSE needed > > > > Does anyone know first of all, why I cannot read this file (not even with > > > read.nexus function)? And secondly how can one generate an "average" > > skyline > > plot from several trees? > > > > Thank you in advance! > > Cheers! > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > [hidden email] > > <http://user/SendEmail.jtp?type=node&node=3610421&i=1>mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > [[alternative HTML version deleted]] > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=3610421&i=2>mailing > list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://r.789695.n4.nabble.com/Skyline-plots-from-several-trees-in-newick-format-tp3609929p3610421.html > To unsubscribe from Skyline plots from several trees in newick format, click > here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=3609929&code=YW5kcmFsaWEudG9sYnVzQGdtYWlsLmNvbXwzNjA5OTI5fC0yMTEyNjI2Njc2>. > > -- View this message in context: http://r.789695.n4.nabble.com/Skyline-plots-from-several-trees-in-newick-format-tp3609929p3610452.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
