Ok, will check. No need of a script to match names between files? ____________________________________________________________ David Costantini Professor of Conservation Physiology Muséum National d'Histoire Naturelle, CNRS 7 rue Cuvier 75005 Paris, France Tel.: +33.(0)1.40.79.53.74 Associate Editor Functional Ecology http://davidcostantini.wordpress.com/ https://twitter.com/DavidZool http://scholar.google.com/citations?user=nBSC4-EAAAAJ&hl=it
----- Original Message ----- From: Jarrod Hadfield <j.hadfi...@ed.ac.uk> To: David Costantini <david.costant...@mnhn.fr> Cc: r-sig-phylo <r-sig-phylo@r-project.org> Sent: Thu, 20 May 2021 12:22:54 +0200 (CEST) Subject: Re: [R-sig-phylo] phylogenetic correction and MCMC model Hi, This error always turns out to be mispellings on the part of the user. Perhaps you have trailing white space in them? Cheers, Jarrod On 19/05/2021 09:09, David Costantini wrote: > This email was sent to you by someone outside the University. > You should only click on links or attachments if you are certain that the > email is genuine and the content is safe. > > Hi Jarrod > there were actually a few misspelled names, but R > still tells me 'some levels of animal do not have a row entry in ginverse' > Might there be another reason for that? > cheers > d > > ____________________________________________________________ > David Costantini > Professor of Conservation Physiology > Muséum National d'Histoire Naturelle, CNRS > 7 rue Cuvier > 75005 Paris, France > Tel.: +33.(0)1.40.79.53.74 > Associate Editor Functional Ecology > http://davidcostantini.wordpress.com/ > https://twitter.com/DavidZool > http://scholar.google.com/citations?user=nBSC4-EAAAAJ&hl=it > > ----- Original Message ----- > From: "Jarrod Hadfield" <j.hadfi...@ed.ac.uk> > To: "David COSTANTINI" <david.costant...@mnhn.fr> > Cc: "r-sig-phylo" <r-sig-phylo@r-project.org> > Sent: Monday, 17 May, 2021 21:34:34 > Subject: Re: [R-sig-phylo] phylogenetic correction and MCMC model > > Hi, > > chronos adds a chronos class to the object, creating problems. Anything > wrong with using: > > phylo<-read.nexus("output.nex") > phylo<- di2multi(phylo) > inv.phylo<-inverseA(phylo) > > ? > > Cheers, > > Jarrod > > > On 17/05/2021 19:47, David Costantini wrote: >> This email was sent to you by someone outside the University. >> You should only click on links or attachments if you are certain that the >> email is genuine and the content is safe. >> >> Hi Jarrod >> here are the scripts: >> phylo<-read.nexus("output.nex") >> phylo$edge.length <- phylo$edge.length[1 + .0000001] >> phylo_ultra=chronos(phylo, lambda=0) >> is.ultrametric(phylo_ultra) >> tree.unmatched <- multi2di(phylo_ultra, random=TRUE) >> plotTree(tree.unmatched,fsize=0.6) >> inv.phylo<-inverseA(tree.unmatched,nodes="TIPS",scale=TRUE) >> >> When I do plotTree, I can visualise the tree. >> but the original file looks like a list, here is just an extract of the >> original file output.nex: >> >> #NEXUS BEGIN TREES; TREE tree_2467 = >> ((Anguilla_anguilla:274.35321211,(((Oreochromis_tanganicae:128.00000000,((Channa_argus:94.28562300,((Scophthalmus_maximus:64.40000000,Paralichthys_dentatus:64.40000000)'14':19.14618300,Seriola_quinqueradiata:83.54618300)'13':10.73944000)'11':15.71437700,(((Gasterosteus_aculeatus:94.90000000,Perca_flavescens:94.90000000)'10':15.10000000,((Siganus_vulpinus:99.80000000,(Lutjanus_peru:99.80000000,Argyrosomus_regius:99.80000000)'19':0.00000000)'9':10.20000000,Sparus_aurata:110.00000000)'22':0.00000000)'8':0.00000000,(Zosterisessor_ophiocephalus:56.20000000,Ponticola_eurycephalus:56.20000000)'6':53.80000000)'30':0.00000000)'29':18.00000000)'27':78.33545792,((Salmo_salar:12.51368429,Salmo_trutta:12.51368429)'35':33.20842500,Oncorhynchus_mykiss:45.72210929)'43':160.61334863).........;END; >> >> >> thanks! >> d >> >> PS. If I drop TIPS, I have the same message. >> >> ____________________________________________________________ >> David Costantini >> Professor of Conservation Physiology >> Muséum National d'Histoire Naturelle, CNRS >> 7 rue Cuvier >> 75005 Paris, France >> Tel.: +33.(0)1.40.79.53.74 >> Associate Editor Functional Ecology >> http://davidcostantini.wordpress.com/ >> https://twitter.com/DavidZool >> http://scholar.google.com/citations?user=nBSC4-EAAAAJ&hl=it >> >> ----- Original Message ----- >> From: "Jarrod Hadfield" <j.hadfi...@ed.ac.uk> >> To: "David COSTANTINI" <david.costant...@mnhn.fr>, "r-sig-phylo" >> <r-sig-phylo@r-project.org> >> Sent: Monday, 17 May, 2021 19:48:59 >> Subject: Re: [R-sig-phylo] phylogenetic correction and MCMC model >> >> Hi David, >> >> It looks like phylo_ultra might be a list? Is phylo_ultra[[1]] a tree? >> >> Also, don't use nodes="TIPS"; this is just to demonstrate how poor the >> algorithm is when you don't use the expanded inverse. I see people using >> nodes="TIPS" a lot - where does this code come from? >> >> Cheers, >> >> Jarrod >> >> On 17/05/2021 16:06, David Costantini wrote: >>> This email was sent to you by someone outside the University. >>> You should only click on links or attachments if you are certain that the >>> email is genuine and the content is safe. >>> >>> Dear All >>> I am trying to apply a phylogenetic correction to an MCMC model, but I have >>> problems in making the inverse matrix. I can visualise the treeplot very >>> well, but when I use the script: >>> inv.phylo<-inverseA(phylo_ultra,nodes="TIPS",scale=TRUE) >>> >>> R tells me that there is an error: >>> >>> Error in pedigree[, 2] : incorrect number of dimensions >>> In addition: Warning message: >>> In if (attr(pedigree, "class") == "phylo") { : >>> >>> Do you have any experience with this? I couldn't find a solution so far. >>> Thanks in advance >>> David >>> >>> >>> [[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/ >> The University of Edinburgh is a charitable body, registered in Scotland, >> with registration number SC005336. Is e buidheann carthannais a th’ ann an >> Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh SC005336. _______________________________________________ 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/
