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/
