Remove rows in R matrix where all data is NA

Question

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Removing empty rows of a data file in R

How would I remove rows from a matrix or data frame where all elements in the row are NA?

So to get from this:

     [,1] [,2] [,3]
[1,]    1    6   11
[2,]   NA   NA   NA
[3,]    3    8   13
[4,]    4   NA   NA
[5,]    5   10   NA

to this:

     [,1] [,2] [,3]
[1,]    1    6   11
[2,]    3    8   13
[3,]    4   NA   NA
[4,]    5   10   NA

Because the problem with na.omit is that it removes rows with any NAs and so would give me this:

     [,1] [,2] [,3]
[1,]    1    6   11
[2,]    3    8   13

The best I have been able to do so far is use the apply() function:

> x[apply(x, 1, function(y) !all(is.na(y))),]
     [,1] [,2] [,3]
[1,]    1    6   11
[2,]    3    8   13
[3,]    4   NA   NA
[4,]    5   10   NA

but this seems quite convoluted (is there something simpler that I am missing?)....

Thanks.

score 75 · Accepted Answer · edited Jun 06 '18 at 13:30

75

Solutions using rowSums() generally outperform apply() ones:

m <- structure(c( 1,  NA,  3,  4,  5, 
                  6,  NA,  8, NA, 10, 
                 11,  NA, 13, NA, NA), 
               .Dim = c(5L, 3L))

m[rowSums(is.na(m)) != ncol(m), ]

     [,1] [,2] [,3]
[1,]    1    6   11
[2,]    3    8   13
[3,]    4   NA   NA
[4,]    5   10   NA

edited Jun 06 '18 at 13:30

divibisan

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answered Jun 24 '11 at 18:02

IRTFM

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This is the same solution as the linked question, except the number of columns is hard-coded. – Joshua Ulrich Jun 24 '11 at 18:29
I see that you are right. Will vote to close. – IRTFM Jun 24 '11 at 18:34

score 44 · Answer 2 · edited Feb 11 '15 at 23:30

44

Sweep a test for all(is.na()) across rows, and remove where true. Something like this (untested as you provided no code to generate your data -- dput() is your friend):

 R> ind <- apply(X, 1, function(x) all(is.na(x)))
 R> X <- X[ !ind, ]

edited Feb 11 '15 at 23:30

Ben

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answered Jun 24 '11 at 17:50

Dirk Eddelbuettel

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maybe slower but I like it because it expresses the logic better – Ben Bolker Jun 24 '11 at 21:33
This option works with non-numeric data too. but the apply solution in the linked questions avoids the index and does it in one line. – orville jackson Oct 17 '16 at 20:29

Remove rows in R matrix where all data is NA

2 Answers2

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