Hi Hannah, if you provide MCTree then I guess the first column is the species and the second column is the character vector. Try providing only the state vector. I think in this case “length” does count the length of your MCTree data.frame which would be 2 and not the length of your character vector in the data.frame.
So try this: ace.ER<-ace(MCTree[,2],phy=tree,type="discrete",model=“ER”) Hope this works... Best, Franz MSc. Franz Krah Mycology, Phylogenetics, PCM http://www.biodiv.wzw.tum.de/index.php?id=18 <http://www.biodiv.wzw.tum.de/index.php?id=18> currently at Clark University > On 13 Mar 2015, at 12:16, Hannah west <[email protected]> wrote: > > > > > > > Dear All, > > I am trying to do an ancestral state reconstruction in R using the package > 'ape'. I have tried trimming my tree in BayesTraits and in R itself, and the > resulting tree reports as having 573 species tips, which is the same as my > dataset. As far as I can tell everything is loading properly, but every time > I try running the ACE codes R returns the following error message; > Error in ace(MCTree, phy = tree, type = "discrete", model = "ER") : > length of phenotypic and of phylogenetic data do not match. > > The code I'm using is > ace.ER<-ace(MCTree,phy=tree,type="discrete",model="ER") > > My data summary loads as > 'data.frame': 573 obs. of 2 variables: > $ Species: Factor w/ 573 levels "Abeomelomys_sevia",..: 251 10 16 17 18 25 30 > 31 32 54 ... > $ MCAll : int 0 0 0 0 0 0 0 0 0 0 ... > > My tree loads as > List of 4 > $ edge : int [1:1144, 1:2] 574 575 576 576 577 577 578 578 579 579 ... > $ edge.length: num [1:1144] 64.6 27.3 55.2 3.6 51.6 33.3 18.3 0.1 18.2 18.2 > ... > $ Nnode : int 572 > $ tip.label : chr [1:573] "Abeomelomys_sevia" "Abrothrix_longipilis" > "Abrothrix_olivaceus" "Acerodon_celebensis" ... > - attr(*, "class")= chr "phylo" > - attr(*, "order")= chr "cladewise" > > And as you can see the tips and data strings should match in length. > > Any help would be much appreciated. Thank you! > > (This is my first submission to one of these help threads so let me know if I > miss anything vital). > > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/[email protected]/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
