removing only rows/columns with "na" value from square ( symmetrical ) matrix.

Yes  the matrix is symmetric 
Gabor provided a partial solution:
Try this:

ix <- na.action(na.omit(replace(M, upper.tri(M), 0)))
M[-ix, -ix]

However this removes all rows containing an NA in the lower half of the 
matrix - even if the corresponding column has also been removed

I I have revised the example to show this.

thanks all for you help

in the below case I would like to retain row and column [c(1:5,7,8,10:
12),c(1:5,7,8,10:12)]
M<-matrix(sample(144),12,12)
M[10,9]<-NA
M<-as.matrix(as.dist(M))
N=M
#the above rows are to create the symmetric matrix M and a copy N
M[6,]<-NA
M[,6]<-NA
#above two rows - make corresponding row and column NA
print (M)
ix <- na.action(na.omit(replace(M, upper.tri(M), 0)))
M<-M[-ix, -ix]
print (M)

print ("however what I would like to retain is the maximum amout of data 

while removing rows or columns containing NA  ie:")
print(N [c(1:5,7,8,10:12),c(1:5,7,8,10:12)])

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thanks to all
On 21/05/2012, at 1:10 AM, peter dalgaard wrote:

On May 20, 2012, at 16:37 , Bert Gunter wrote:

Your problem is not well-defined. In your example below, why not
remove rows 1,2,6, and 10, all of which contain NA's? Is the matrix
supposed to be symmetric?

YES

Do NA's always occur symmetrically?

YES

...and even if they do, how do you decide whether to remove row/col 9 

row/col 10 in the example? (Or, for that matter, between (1 and 2) and 

In that case you might chose to remove the smallest no. of row/cols but 

"9 vs. 10", the situation is completely symmetric.) 

You either need to rethink what you want to do or clarify your 

-- Bert

On Sun, May 20, 2012 at 7:17 AM, Nevil Amos <nevil.amos at monash.edu> 

I have some square matrices with na values in corresponding rows and
columns.

M<-matrix(1:2,10,10)
M[6,1:2]<-NA
M[10,9]<-NA
M<-as.matrix(as.dist(M))
print (M)

  1 2 3 4 5 6 7 8 9 10
1   0  2 1 2 1 NA 1 2  1  2
2   2  0 1 2 1 NA 1 2  1  2
3   1  1 0 2 1  2 1 2  1  2
4   2  2 2 0 1  2 1 2  1  2
5   1  1 1 1 0  2 1 2  1  2
6  NA NA 2 2 2  0 1 2  1  2
7   1  1 1 1 1  1 0 2  1  2
8   2  2 2 2 2  2 2 0  1  2
9   1  1 1 1 1  1 1 1  0 NA
10  2  2 2 2 2  2 2 2 NA  0


How do I remove just the row/column pair( in this trivial example 

10 and column 6 and 10) containing the NA values?

so that I end up with all rows/ columns that are not NA - e.g.

1 2 3 4 5 7 8 9
1 0 2 1 2 1 1 2 1
2 2 0 1 2 1 1 2 1
3 1 1 0 2 1 1 2 1
4 2 2 2 0 1 1 2 1
5 1 1 1 1 0 1 2 1
7 1 1 1 1 1 0 2 1
8 2 2 2 2 2 2 0 1
9 1 1 1 1 1 1 1 0


if i use na omit I lose rows 1,2,6, and 9
which is not what I want.

thanks
--
Nevil Amos
Molecular Ecology Research Group
Australian Centre for Biodiversity
Monash University
CLAYTON VIC 3800
Australia

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-- 

Bert Gunter
Genentech Nonclinical Biostatistics

Internal Contact Info:
Phone: 467-7374
Website:

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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com

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