[R] how to skip NA columns ?

[Mike Lonergan]

Ryszard,

1) with your example, I get:

>t(na.omit(t(o)))
     [,1] [,2]
[1,]    1    7
[2,]    2    8
[3,]    3    9
attr(,"na.action")
[1] 2
attr(,"na.action")attr(,"class")
[1] "omit"
>

in which the first attr statement seems to say that the old column 2 has
been removed
( and this information can be recovered with things like:
   > t<-t(na.omit(t(o)))
   > attr(t,"na.action")[1]
)

2) are you sure your solution is so bad? I did:

> o<-matrix(c(1,2,3,rep(NA,3),7,8,9),3,3)
> ot<-t(o)
> date();for(i in 1:10000) t(na.omit(t(o)));date()
[1] "Thu Jun 20 14:48:53 2002"
[1] "Thu Jun 20 14:49:02 2002"
> date();for(i in 1:10000) na.omit(ot);date()
[1] "Thu Jun 20 14:49:13 2002"
[1] "Thu Jun 20 14:49:20 2002"
>

which seems to suggest that (for this toy example at least) the transposes
are taking around 30% of the time. Similarly for a slightly bigger example:

> o100<-matrix(c(1,NA),100,100,byrow=TRUE)
> ot100<-t(o100)
> date();for(i in 1:1000) t(na.omit(t(o100)));date()
[1] "Thu Jun 20 14:54:40 2002"
[1] "Thu Jun 20 14:54:52 2002"
> date();for(i in 1:1000) na.omit(o100);date()
[1] "Thu Jun 20 14:55:10 2002"
[1] "Thu Jun 20 14:55:19 2002"
>

While the exact times will be machine dependent, I'd guess the ratios are
likely to be fairly consistent. So, unless your code does lots of this and
little else, I'd suggest finding something else to fret about!

Cheers,

Mike.

     > -----Original Message-----
     > From: owner-r-help at stat.math.ethz.ch
     > [mailto:owner-r-help at stat.math.ethz.ch]On Behalf Of
     > Czerminski, Ryszard
     > Sent: 20 June 2002 12:58
     > To: r-help at stat.math.ethz.ch
     > Subject: [R] how to skip NA columns ?
     >
     >
     > R-helpers!
     >
     > na.omit() can be used to remove rows with NA's
     > but how can I remove columns ? and remember, which columns
     > have been removed
     > ?
     >
     > I guess I can do t(na.omit(t(o))) as shown below, but this
     > probably creates
     > a lot of overhead and I do not know which columns
     > have been removed.
     >
     > Yours,
     >
     > R
     >
     > > o
     >      [,1] [,2] [,3]
     > [1,]    1   NA    7
     > [2,]    2   NA    8
     > [3,]    3   NA    9
     > > t(na.omit(t(o)))
     >      [,1] [,2]
     > [1,]    1    7
     > [2,]    2    8
     > [3,]    3    9
     >
     > Ryszard Czerminski   phone: (781)994-0479
     > ArQule, Inc.         email:ryszard at arqule.com
     > 19 Presidential Way  http://www.arqule.com
     > Woburn, MA 01801     fax: (781)994-0679
     >
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