[R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus

and when I root it with only one species, the outgroup is paraphyletic and it is not true. So my questions are: (1) Is here a command for forcing a monophyly of the outgroup? (2) Is there a command for exporting this consesus tree with the PP values? Many thanks in advance Felipe Rossetto Her

Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus

Someone thought I having difficulties in MrBayes, but the point I need help is in R and not in MrBayes Thanks Felipe Rossetto Herbário FUEL Departamento de Biologia Animal e Vegetal Universidade Estadual de Londrina Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário Caixa postal

Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus

hich allows exporting the consensus with the PP values? Finally, I woud like to express my apologies to Vojtěch, please, forgive me! Any problems, please, write me Felipe Rossetto Herbário FUEL Departamento de Biologia Animal e Vegetal Universidade Estadual de Londrina Rodovia Celso Garcia Ci

Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus

bels = TRUE) plotBS(con, tree, "phylogram") -> con.l write.tree(con.l, file="c.tre") But another difficult I'm having is when I plot PP values in the consensus rooted, values > 200 appear, and I didn't find a solution for it, so, someone had the same proble

Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus

outgr, resolve.root = TRUE) consensus(tree,p=0.5,check.labels = TRUE) con<-consensus(tree,p=0.5,check.labels = TRUE) plotBS(con, tree, "phylogram") -> con.l # plot the PP or bs values in the rooted consensus write.tree(con.l, file="c.tre") Felipe Rossetto Herbário FUEL Depa

[R-sig-phylo] standard error (NaN) in model ARD

: > ARDreconstruction$se and only NaNs were detected: >[1] NaN NaN NaN NaN NaN NaN Then, that means there is not confidence in the recosntructed rates using ARD model? Then is it better ER for estimating ancestral state for this character? Many thanks Felipe Rossetto Herbário FUEL Departame

[R-sig-phylo] tip labels-stochastic mapping

"off", add=TRUE)* *text(1,1:length(mtrees[[1]]$tip),mtrees[[1]]$tip.label, pos=4,font=3)* *nodelabels(pie=pies,cex=0.6,piecol=cols)* Is there a code for maintaining the tip labels in the phylogeny with characters mapped? Mnay thanks in advance Felipe Rossetto Herbário FUEL Departamento d

[R-sig-phylo] question-state code change and simmap

nd I think analyses didn't recognise the change in state code I made in this tip, am I right? Is there a solution for that? many thanks in advance! Felipe Rossetto Herbário FUEL Departamento de Biologia Animal e Vegetal Universidade Estadual de Londrina Rodovia Celso Garcia Cid, PR 445

[R-sig-phylo] Shimodaira-Hasegawa test using per site log likelihood

ed to a matrix with rows and columns? Many thanks in advance! felipe Felipe Rossetto Herbário FUEL Departamento de Biologia Animal e Vegetal Universidade Estadual de Londrina Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário Caixa postal 10.011 CEP: 86057-970 Londrina, Paraná, Brasil C

[R-sig-phylo] problem with phylo.toBackbone

roblem related to the fact I used an ultrametric tree? Many thanks in advance felipe Felipe Rossetto Herbário FUEL Departamento de Biologia Animal e Vegetal Universidade Estadual de Londrina Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário Caixa postal 10.011 CEP: 86057-970

[R-sig-phylo] Codifying missing data and polymorphic state of characters in the same matrix

*,0.5,0.5,0.0 (polymorphic character) *Taxon_D*,0.33,0.33,0.33 (missing data) Thank you very much in advance! Felipe Rossetto [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman

[R-sig-phylo] time axis in fan style phylogeny: arcs did not appear in eps file

Dear all, I am including time axis in a circular phylogeny following this nice post http://blog.phytools.org/2018/02/another-technique-for-including-time.html where this loop is used to drawing arcs: for(i in 1:length(obj)){ a1<-0 a2<-2*pi draw.arc(0,0,radius=obj[i],a1,a2,lwd =1, col=make.trans

Re: [R-sig-phylo] time axis in fan style phylogeny: arcs did not appear in eps file

ative-methods-in-r> > (*Princeton University Press*, 2022) > > > On 6/25/2023 12:09 AM, Felipe Rossetto wrote: > > > You don't often get email from rossetto.fel...@gmail.com. Learn why this > is important <https://aka.ms/LearnAboutSenderIdentification> > >

[R-sig-phylo] command for access posterior probabilities values of pie charts obtained from make.simmap

Dear all, I am trying to find an email where Liam showed a command that allows us to get the posterior probability values of pie charts at nodes of trees resulting from make.simmap computation, but I failed to find it. Does someone know this command? If yes, I am very grateful, if it is possible t

Re: [R-sig-phylo] command for access posterior probabilities values of pie charts obtained from make.simmap

nceton.edu/books/phylogenetic-comparative-methods-in-r> > (*Princeton University Press*, 2022) > > > On 8/22/2023 11:22 AM, Felipe Rossetto wrote: > > CAUTION: EXTERNAL SENDER > > Dear all, > > I am trying to find an email where Liam showed a command that allows us