[R] Find the 50 highest values in a matrix

[Peter Ehlers]

m <- matrix(round(rnorm(4000 * 2000), 4), nr = 4000)
is.na(m) <- sample(8e6, 1e6)

system.time(
   idx <- which(
     matrix(m %in% head(sort(m, TRUE), 50),
            nr = nrow(m)), arr.ind = TRUE))

#   user  system elapsed
#   3.12    0.19    3.18

   -Peter Ehlers


On 2010-06-18 5:13, Dennis Murphy wrote:
> Hi:
>
> Here's a faked up example:
>
> a<- matrix(rnorm(4000*2000), 4000, 2000)
> # Generate some NAs in the matrix
> nr<- sample(50, 1:4000)
> nc<- sample(50, 1:2000)
> a[nr, nc]<- NA
>
> # convert to data frame:
> b<- data.frame(row = rep(1:4000, 2000), col = rep(1:2000, each = 4000),
>                            x = as.vector(a))
> # relatively time consuming...about 13.5 s on my machine
> bb<- b[rev(order(b$x, na.last = FALSE)), ]
>> bb[1:10, ]
>           row  col        x
> 691269  3269  173 5.103704
> 7815076 3076 1954 4.961544
> 4999621 3621 1250 4.953265
> 500469   469  126 4.937655
> 5878224 2224 1470 4.929150
> 4287270 3270 1072 4.913791
> 4442521 2521 1111 4.896869
> 4668867  867 1168 4.863504
> 5716575  575 1430 4.760778
> 3055274 3274  764 4.758995
>
> HTH,
> Dennis
>
>
> On Thu, Jun 17, 2010 at 10:41 PM, uschlecht<ulrich.schlecht at stanford.edu>wrote:
>
>>
>> Hi,
>>
>> I have a huge matrix (4000 * 2000 data points) and I would like to retrieve
>> the coordinates (column and row) for the top 50 (or x) values. Some
>> positions in the matrix have NA as a value. These should be discarded.
>>
>> My current method is to replace all NAs by 0, then rank all the values and
>> then extract the positions with the 50 highest ranks. It is very
>> time-consuming!
>>
>> Is there a simpler way to do this?
>>
>> Thank you,
>> Ulrich
>>
>> --
>> View this message in context:
>> http://r.789695.n4.nabble.com/Find-the-50-highest-values-in-a-matrix-tp2259721p2259721.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
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>>
>
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