Re: [R] removeing only rows/columns with na value from square ( symmetrical ) matrix.
On Sun, May 20, 2012 at 10:54 AM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
On Sun, May 20, 2012 at 10:52 AM, Gabor Grothendieck
ggrothendi...@gmail.com wrote:
On Sun, May 20, 2012 at 10:17 AM, Nevil Amos nevil.a...@monash.edu wrote:
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 row 6 and
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
Try this:
ix - na.action(na.omit(replace(M, upper.tri(M), 0)))
M[-ix, -ix]
and here is a minor variation which is slightly shorter:
ix - complete.cases(replace(M, upper.tri(M), 0))
M[ix, ix]
Please keep all follow ups on the original thread.
Here is a greedy algorithm to iteratively drop the column and row with
the most NAs.
dropNA - function(M) {
while(any(is.na(M))) {
ix - which.max(colSums(is.na(M)))
M - M[-ix, -ix]
}
M
}
dropNA(M)
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] removeing only rows/columns with na value from square ( symmetrical ) matrix.
Hello,
Try
while(TRUE){
ix - apply(M, 2, function(x) sum(is.na(x)))
if(all(ix == 0)) break
ix - max(which(ix == max(ix)))
M - M[-ix , -ix]
}
M
Note that in the original there's really no difference between columns 9
and 10.
If in the above code you use 'min', column 9 is removed and it's still a
minimum of removals.
(Like in any case of a tie.)
Hope this helps,
Rui Barradas
Em 21-05-2012 11:00, Nevil Amos nevil.a...@monash.edu escreveu:
Date: Mon, 21 May 2012 00:17:10 +1000
From: Nevil Amosnevil.a...@monash.edu
To:r-help@r-project.org
Subject: [R] removeing only rows/columns with na value from square (
symmetrical ) matrix.
Message-ID:
CAGUDtZJOW7x3sjZsnqf7uAQN6gKFg+EMqq=-hbqkgcwggaj...@mail.gmail.com
Content-Type: text/plain
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 row 6 and
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
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] removeing only rows/columns with na value from square ( symmetrical ) matrix.
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 row 6 and 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 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removeing only rows/columns with na value from square ( symmetrical ) matrix.
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? Do NA's always occur symmetrically? You either need to rethink what you want to do or clarify your statement of it. -- Bert On Sun, May 20, 2012 at 7:17 AM, Nevil Amos nevil.a...@monash.edu wrote: 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 row 6 and 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 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removeing only rows/columns with na value from square ( symmetrical ) matrix.
On Sun, May 20, 2012 at 10:17 AM, Nevil Amos nevil.a...@monash.edu wrote: 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 row 6 and 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 Try this: ix - na.action(na.omit(replace(M, upper.tri(M), 0))) M[-ix, -ix] -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removeing only rows/columns with na value from square ( symmetrical ) matrix.
On Sun, May 20, 2012 at 10:52 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Sun, May 20, 2012 at 10:17 AM, Nevil Amos nevil.a...@monash.edu wrote: 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 row 6 and 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 Try this: ix - na.action(na.omit(replace(M, upper.tri(M), 0))) M[-ix, -ix] and here is a minor variation which is slightly shorter: ix - complete.cases(replace(M, upper.tri(M), 0)) M[ix, ix] -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] removeing only rows/columns with na value from square ( symmetrical ) matrix.
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? Do NA's always occur symmetrically? ...and even if they do, how do you decide whether to remove row/col 9 or row/col 10 in the example? (Or, for that matter, between (1 and 2) and 6. In that case you might chose to remove the smallest no. of row/cols but in 9 vs. 10, the situation is completely symmetric.) You either need to rethink what you want to do or clarify your statement of it. -- Bert On Sun, May 20, 2012 at 7:17 AM, Nevil Amos nevil.a...@monash.edu wrote: 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 row 6 and 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 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
