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Hao Cen

2009-Nov-11 14:38 UTC

[R] dividing a matrix by positive sum or negative sum depending on the sign

Hi,

I have a matrix with positive numbers, negative numbers, and NAs. An
example of the matrix is as follows

-1 -1 2 NA
3 3 -2 -1
1 1 NA -2

I need to compute a scaled version of this matrix. The scaling method is
dividing each positive numbers in each row by the sum of positive numbers
in that row and  dividing each negative numbers in each row by the sum of
absolute value of negative numbers in that row.

So the resulting matrix would be

-1/2 -1/2 2/2 NA
3/6 3/6 -2/3 -1/3
1/2 1/2 NA -2/2

Is there an efficient way to do that in R? One way I am using is

1. rowSums for positive numbers in the matrix
2. rowSums for negative numbers in the matrix
3. sweep(mat, 1, posSumVec, posDivFun)
4. sweep(mat, 1, negSumVec, negDivFun)

posDivFun = function(x,y) {
        xPosId = x>0 & !is.na(x)
        x[xPosId] = x[xPosId]/y[xPosId]
        return(x)
}

negDivFun = function(x,y) {
        xNegId = x<0 & !is.na(x)
        x[xNegId] = -x[xNegId]/y[xNegId]
        return(x)
}

It is not fast enough though. This scaling is to be applied to large data
sets repetitively. I would like to make it as fast as possible. Any
thoughts on improving it would be appreciated.

Thanks

Jeff

Dimitris Rizopoulos

2009-Nov-11 15:36 UTC

head link

[R] dividing a matrix by positive sum or negative sum depending on the sign

one approach is the following:

mat <- rbind(c(-1, -1, 2, NA), c(3, 3, -2, -1), c(1, 1, NA, -2))

mat / ave(abs(mat), row(mat), sign(mat), FUN = sum)


I hope it helps.

Best,
Dimitris


Hao Cen wrote:> Hi,
> 
> I have a matrix with positive numbers, negative numbers, and NAs. An
> example of the matrix is as follows
> 
> -1 -1 2 NA
> 3 3 -2 -1
> 1 1 NA -2
> 
> I need to compute a scaled version of this matrix. The scaling method is
> dividing each positive numbers in each row by the sum of positive numbers
> in that row and  dividing each negative numbers in each row by the sum of
> absolute value of negative numbers in that row.
> 
> So the resulting matrix would be
> 
> -1/2 -1/2 2/2 NA
> 3/6 3/6 -2/3 -1/3
> 1/2 1/2 NA -2/2
> 
> Is there an efficient way to do that in R? One way I am using is
> 
> 1. rowSums for positive numbers in the matrix
> 2. rowSums for negative numbers in the matrix
> 3. sweep(mat, 1, posSumVec, posDivFun)
> 4. sweep(mat, 1, negSumVec, negDivFun)
> 
> posDivFun = function(x,y) {
>         xPosId = x>0 & !is.na(x)
>         x[xPosId] = x[xPosId]/y[xPosId]
>         return(x)
> }
> 
> negDivFun = function(x,y) {
>         xNegId = x<0 & !is.na(x)
>         x[xNegId] = -x[xNegId]/y[xNegId]
>         return(x)
> }
> 
> It is not fast enough though. This scaling is to be applied to large data
> sets repetitively. I would like to make it as fast as possible. Any
> thoughts on improving it would be appreciated.
> 
> Thanks
> 
> Jeff
> 
> ______________________________________________
> 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.
> 
-- 
Dimitris Rizopoulos
Assistant Professor
Department of Biostatistics
Erasmus University Medical Center

Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
Tel: +31/(0)10/7043478
Fax: +31/(0)10/7043014

David Winsemius

2009-Nov-11 15:57 UTC

head link

[R] dividing a matrix by positive sum or negative sum depending on the sign

On Nov 11, 2009, at 10:36 AM, Dimitris Rizopoulos wrote:
> one approach is the following:
>
> mat <- rbind(c(-1, -1, 2, NA), c(3, 3, -2, -1), c(1, 1, NA, -2))
>
> mat / ave(abs(mat), row(mat), sign(mat), FUN = sum)
Very elegant. My solution was a bit more pedestrian, but may have some  
speed advantage:

t( apply(mat, 1, function(x) ifelse( x <0, -x/sum(x[x<0], na.rm=T), x/ 
sum(x[x>0], na.rm=T) ) ) )


 > system.time(replicate(10000, t( apply(mat, 1, function(x) ifelse( x  
<0, -x/sum(x[x<0], na.rm=T), x/sum(x[x>0], na.rm=T) ) ) ) ) )
    user  system elapsed
   5.958   0.027   5.977

 > system.time(replicate(10000, mat / ave(abs(mat), row(mat),  
sign(mat), FUN = sum) ) )
    user  system elapsed
  12.886   0.064  12.886

-- 
David>
>
> I hope it helps.
>
> Best,
> Dimitris
>
>
> Hao Cen wrote:
>> Hi,
>> I have a matrix with positive numbers, negative numbers, and NAs. An
>> example of the matrix is as follows
>> -1 -1 2 NA
>> 3 3 -2 -1
>> 1 1 NA -2
>> I need to compute a scaled version of this matrix. The scaling  
>> method is
>> dividing each positive numbers in each row by the sum of positive  
>> numbers
>> in that row and  dividing each negative numbers in each row by the  
>> sum of
>> absolute value of negative numbers in that row.
>> So the resulting matrix would be
>> -1/2 -1/2 2/2 NA
>> 3/6 3/6 -2/3 -1/3
>> 1/2 1/2 NA -2/2
>> Is there an efficient way to do that in R? One way I am using is
>> 1. rowSums for positive numbers in the matrix
>> 2. rowSums for negative numbers in the matrix
>> 3. sweep(mat, 1, posSumVec, posDivFun)
>> 4. sweep(mat, 1, negSumVec, negDivFun)
>> posDivFun = function(x,y) {
>>        xPosId = x>0 & !is.na(x)
>>        x[xPosId] = x[xPosId]/y[xPosId]
>>        return(x)
>> }
>> negDivFun = function(x,y) {
>>        xNegId = x<0 & !is.na(x)
>>        x[xNegId] = -x[xNegId]/y[xNegId]
>>        return(x)
>> }
>> It is not fast enough though. This scaling is to be applied to  
>> large data
>> sets repetitively. I would like to make it as fast as possible. Any
>> thoughts on improving it would be appreciated.
>> Thanks
>> Jeff
>> ______________________________________________
>> 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.
>
> -- 
> Dimitris Rizopoulos
> Assistant Professor
> Department of Biostatistics
> Erasmus University Medical Center
>
> Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands
> Tel: +31/(0)10/7043478
> Fax: +31/(0)10/7043014
>
> ______________________________________________
> 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.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT

R help - Nov 2009 - dividing a matrix by positive sum or negative sum depending on the sign

[R] dividing a matrix by positive sum or negative sum depending on the sign

[R] dividing a matrix by positive sum or negative sum depending on the sign

[R] dividing a matrix by positive sum or negative sum depending on the sign