Looks like this may be because your row names in your data frame have
spaces, while your tree tip labels do not.
Try:
rownames(example)<-sub(" ","",rownames(example))
example<-example[tree$tip.label,]
Help?
- Liam
--
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://phytools.blogspot.com
On 5/9/2012 5:13 PM, Agus Camacho wrote:
Dear all,
I had the same problem as T. Gamble and tried the advice from L. Revell
and Rich over my own tree (attached), all of the hints produced a df
with Nas. Also, I cant see any difference between rownames on my matrix
and tree tip labels...
Could anyone give me a hint about what i am doing wrong here?
Thanks in advance,
Agus
PS: There it goes what I did:
First from Liam's hint:
example<- read.csv("example.csv",header=TRUE,row.names=1)
example
vara varb
C. leiolepis 1 a
C. nicterus 2 b
C. sinebrachiatus 3 c
S. catimbau 4 a
N. ablephara 5 b
P. erythrocercus 6 c
P. tetradactylus 7 a
V. rubricauda 8 b
V. rubricaudavac 9 c
M. maximiliani 10 a
P. paeminosus 11 b
tree$tip.label
[1]"C.leiolepis" "C.nicterus" "C.sinebrachiatus" "S.catimbau"
[5]"N.ablephara" "P.erythrocercus" "P.tetradactylus" "V.rubricauda"
[9]"V.rubricaudavac" "M.maximiliani" "P.paeminosus"
example<-example[tree$tip.label,]
example
vara varb
NA NA<NA>
NA.1 NA<NA>
NA.2 NA<NA>
NA.3 NA<NA>
NA.4 NA<NA>
NA.5 NA<NA>
NA.6 NA<NA>
NA.7 NA<NA>
NA.8 NA<NA>
NA.9 NA<NA>
NA.10 NA<NA>
Now, Rich's hint:
match(tree$tip.label, rownames(example)) -> match
match
[1] NA NA NA NA NA NA NA NA NA NA NA
--
Agustín Camacho Guerrero.
Doutorando em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Biociências, USP.
Rua do Matão, trav. 14, nº 321, Cidade Universitária,
São Paulo - SP, CEP: 05508-090, Brasil.
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