R help - Feb 2008 - Removing columns that are all NA from a matrix

Hi,

I guess this might be a FAQ or something, and there's probably a nice 
simple way to do it, but I can't think of it:

Given a matrix, I want to remove columns that are _entirely_ filled with 
NAs (partial NAs are fine).

How please?

Thanks,

Martin

data <- data[ , !apply(is.na(data), 2, all)]

(or something like that)

G.

On Thu, Feb 14, 2008 at 12:59:46PM +0000, Martin Waller
wrote:
> Hi,
> 
> I guess this might be a FAQ or something, and there's probably a nice 
> simple way to do it, but I can't think of it:
> 
> Given a matrix, I want to remove columns that are _entirely_ filled with 
> NAs (partial NAs are fine).
> 
> How please?
> 
> Thanks,
> 
> Martin
> 
> ______________________________________________
> R-help at 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.
-- 
Csardi Gabor <csardi at rmki.kfki.hu>    UNIL DGM

On 2/14/2008 7:59 AM, Martin Waller wrote:
> Hi,
> 
> I guess this might be a FAQ or something, and there's probably a nice 
> simple way to do it, but I can't think of it:
> 
> Given a matrix, I want to remove columns that are _entirely_ filled with 
> NAs (partial NAs are fine).
> 
> How please?
mymat[,which(colMeans(is.na(mymat)) < 1)]
> Thanks,
> 
> Martin
> 
> ______________________________________________
> R-help at 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. 
-- 
Chuck Cleland, Ph.D.
NDRI, Inc.
71 West 23rd Street, 8th floor
New York, NY 10010
tel: (212) 845-4495 (Tu, Th)
tel: (732) 512-0171 (M, W, F)
fax: (917) 438-0894

try this:

mat <- matrix(rnorm(42), 6, 7)
mat[sample(42, 10)] <- NA
mat[, c(3,5)] <- NA

ind <- colSums(is.na(mat)) != nrow(mat)
mat
mat[, ind]


I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
     http://www.student.kuleuven.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "Martin Waller" <martinej.waller at ntlworld.com>
To: <r-help at stat.math.ethz.ch>
Sent: Thursday, February 14, 2008 1:59 PM
Subject: [R] Removing columns that are all NA from a matrix

> Hi,
>
> I guess this might be a FAQ or something, and there's probably a 
> nice
> simple way to do it, but I can't think of it:
>
> Given a matrix, I want to remove columns that are _entirely_ filled 
> with
> NAs (partial NAs are fine).
>
> How please?
>
> Thanks,
>
> Martin
>
> ______________________________________________
> R-help at 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.
> 

Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm

On 14-Feb-08 12:59:46, Martin Waller wrote:
> Hi,
> I guess this might be a FAQ or something, and there's
> probably a nice simple way to do it, but I can't think of it:
> 
> Given a matrix, I want to remove columns that are _entirely_
> filled with NAs (partial NAs are fine).
> 
> How please?
> 
> Thanks,
> Martin
It probably isn't a FAQ (it's a somewhat special question)
but the following illustrates one way to do it:

  M<-cbind(c(1,2,3,4),c(1,2,NA,4),c(NA,NA,NA,NA))
  M
##     [,1] [,2] [,3]
##[1,]    1    1   NA
##[2,]    2    2   NA
##[3,]    3   NA   NA
##[4,]    4    4   NA
  apply(M,2,function(x){!all(is.na(x))})
##[1]  TRUE  TRUE FALSE
  M[,apply(M,2,function(x){!all(is.na(x))})]
##     [,1] [,2]
##[1,]    1    1
##[2,]    2    2
##[3,]    3   NA
##[4,]    4    4

Ted.

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E-Mail: (Ted Harding) <Ted.Harding at manchester.ac.uk>
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Date: 14-Feb-08                                       Time: 13:14:20
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Thanks to all who responded - great stuff!

Martin

Martin Waller wrote:
> Hi,
> 
> I guess this might be a FAQ or something, and there's probably a nice 
> simple way to do it, but I can't think of it:
> 
> Given a matrix, I want to remove columns that are _entirely_ filled with 
> NAs (partial NAs are fine).
> 
> How please?
> 
> Thanks,
> 
> Martin
> 
> ______________________________________________
> R-help at 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.
>