Hi Jen.
Try changing to a matrix first (from a data frame). [I.e.,
p<-as.matrix(p); p2<-phyDat(p,type="USER",levels=c(0,1)) ]
I'm not sure why this works, but it seems to. - Liam
More details below.
When I do:
p<-matrix(c(1,0,0,0,1,0,1,0,1,0,
1,1,0,1,1,0,0,1,0,0,
1,0,0,1,0,1,0,0,1,0,
0,1,0,1,1,1,0,0,0,0,
0,0,0,1,1,1,1,0,1,0),5,10,byrow=T)
dimnames(p)<-list(c("A","B","C","D","E"),paste("X",1:10,sep=""))
p2<-phyDat(p,type="USER",levels=c(0,1))
I get:
> p2
5 sequences with 10 character and 9 different site patterns.
The states are 0 1
However:
p<-as.data.frame(p)
p2<-phyDat(p,type="USER",levels=c(0,1))
Gives me:
> p2
10 sequences with 5 character and 5 different site patterns.
The states are 0 1
--
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 1/9/2012 9:14 AM, J Greenwood wrote:
Hi all,
I am having a problem with getting parsimony scores in Phangorn and have
found that the program is not reading in my datafile the way I expect it.
I have 10 characters and 5 taxa, but phangorn seems to read this the
opposite way round.
Can anybody help? Details follow,
thanks,
Jen
I made a test dataset to try and work out the problem which is the
following:
p<-read.table(file="tab_phangorn.txt", header=T)
p
X1 X2 X3 X4 X5 X6 X7 X8 X9 X10
A 1 0 0 0 1 0 1 0 1 0
B 1 1 0 1 1 0 0 1 0 0
C 1 0 0 1 0 1 0 0 1 0
D 0 1 0 1 1 1 0 0 0 0
E 0 0 0 1 1 1 1 0 1 0
Where A-E are taxa and X1-X10 are characters.
I then tried converting it to phyDat format which gives the following:
p2<-phyDat(p, type="USER", levels=c(0,1))
p2
10 sequences with 5 character and 5 different site patterns.
The states are 0 1
str(p2)
List of 10
$ X1 : int [1:5] 2 2 2 1 1
$ X2 : int [1:5] 1 2 1 2 1
$ X3 : int [1:5] 1 1 1 1 1
$ X4 : int [1:5] 1 2 2 2 2
$ X5 : int [1:5] 2 2 1 2 2
$ X6 : int [1:5] 1 1 2 2 2
$ X7 : int [1:5] 2 1 1 1 2
$ X8 : int [1:5] 1 2 1 1 1
$ X9 : int [1:5] 2 1 2 1 2
$ X10: int [1:5] 1 1 1 1 1
- attr(*, "class")= chr "phyDat"
- attr(*, "weight")= int [1:5] 1 1 1 1 1
- attr(*, "nr")= int 5
- attr(*, "nc")= int 2
- attr(*, "index")= int [1:5] 1 2 3 4 5
- attr(*, "levels")= num [1:2] 0 1
- attr(*, "allLevels")= chr [1:3] "0" "1" "?"
- attr(*, "type")= chr "USER"
- attr(*, "contrast")= num [1:3, 1:2] 1 0 1 0 1 1
It has read the data in the opposite way round to the way i was
expecting, which was odd, but I transposed the matrix anyway, but got
the same output:
ptrans<-t(p)
ptrans
A B C D E
X1 1 1 1 0 0
X2 0 1 0 1 0
X3 0 0 0 0 0
X4 0 1 1 1 1
X5 1 1 0 1 1
X6 0 0 1 1 1
X7 1 0 0 0 1
X8 0 1 0 0 0
X9 1 0 1 0 1
X10 0 0 0 0 0
ptrans2
10 sequences with 5 character and 5 different site patterns.
The states are 0 1
str(ptrans2)
List of 10
$ X1 : int [1:5] 2 2 2 1 1
$ X2 : int [1:5] 1 2 1 2 1
$ X3 : int [1:5] 1 1 1 1 1
$ X4 : int [1:5] 1 2 2 2 2
$ X5 : int [1:5] 2 2 1 2 2
$ X6 : int [1:5] 1 1 2 2 2
$ X7 : int [1:5] 2 1 1 1 2
$ X8 : int [1:5] 1 2 1 1 1
$ X9 : int [1:5] 2 1 2 1 2
$ X10: int [1:5] 1 1 1 1 1
- attr(*, "class")= chr "phyDat"
- attr(*, "weight")= int [1:5] 1 1 1 1 1
- attr(*, "nr")= int 5
- attr(*, "nc")= int 2
- attr(*, "index")= int [1:5] 1 2 3 4 5
- attr(*, "levels")= num [1:2] 0 1
- attr(*, "allLevels")= chr [1:3] "0" "1" "?"
- attr(*, "type")= chr "USER"
- attr(*, "contrast")= num [1:3, 1:2] 1 0 1 0 1 1
Can anyone explain to me what I am doing wrong? How can I get the phyDat
format to hold my information correctly?
----------------------
J Greenwood
jenny.greenw...@bristol.ac.uk
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