Can I add the suggestion that you do:
ace.ER<-ace(setNames(MCTree[,2],MCTree[,1]),phy=tree,
type="discrete",model=“ER”)
otherwise it will 'work', but ace will not notice if the row order of
MCTree is not the same as tree$tip.label.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: [email protected]
blog: http://blog.phytools.org
On 3/13/2015 2:30 PM, [email protected] wrote:
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).
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