[R] Creating a sparse matrix from a file

[Pallavi Palleti]

Hi all,

I used sparseM package for creating sparse Matrix and followed below
commands.

The sequence of commands are:

>ex <- read.table('fileName',sep=',')
> M <- as.matrix.csr(0,22638,80914)
>for (i in 1:nrow(ex)) { M[ex[i,1],ex[i,2]]<-ex[i,3]}
 
Even after 4 hours, I can still see the above command running. But, I am not
sure whether it got stuck some where.
 
Also, when I initialize matrix M and try to display the values, I can see
something like this
[1] 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2 2 2
[85] 2 2

And, after I stopped executing above initialize command from table(after 4
hours). I could see a different values.

Could some one kindly explain what these number are about and how can I test
that my command is running and not just stuck some where.

Also, it would be great if some one point me to a tutorial if any on sparse
matricies on R as I couldn't get one from internet.

Thanks
Pallavi



Pallavi Palleti wrote:
> 
> Hi David,
> 
> Thanks for your help. This is exactly what I want.
> But, I have number of rows of my matrix = 25k and columns size as 80k. So,
> when I define a matrix object, it is throwing an error saying can not
> allocate a vector of length (25K * 80k). I heard that, this data can still
> be loaded into R using sparseMatrix. However, I couldn't get a syntax for
> creating the same.  Could someone kindly help me in this regard.
> 
> Thanks
> Pallavi
> 
> 
> David Winsemius wrote:
>> 
>> 
>> On Oct 26, 2009, at 5:06 AM, Pallavi Palleti wrote:
>> 
>>>
>>> Hi all,
>>>
>>> I am new to R and learning the same. I would like to create a sparse  
>>> matrix
>>> from an existing file whose contents are in the format
>>>      "rowIndex,columnIndex,value"
>>>
>>> for ex:
>>> 1,2,14
>>> 2,4,15
>>>
>>> I would like to create a sparse matrix by taking the above as input.
>>> However, I couldn't find an example where the data was being read  
>>> from a
>>> file. I tried searching in R tutorial and also searched for the same  
>>> in web
>>> but in vain. Could some one kindly help me how to give the above  
>>> format as
>>> input in R to create a sparse matrix.
>> 
>>   ex <- read.table(textConnection("1,2,14
>>   2,4,15") , sep=",")
>>   ex
>> #  V1 V2 V3
>> #1  1  2 14
>> #2  2  4 15
>> 
>>   M <- Matrix(0, 20, 20)
>> 
>>  > M
>> #20 x 20 sparse Matrix of class "dsCMatrix"
>> 
>>   [1,] . . . . . . . . . . . . . . . . . . . .
>>   [2,] . . . . . . . . . . . . . . . . . . . .
>>   [3,] . . . . . . . . . . . . . . . . . . . .
>> snip
>> 
>>   for (i in 1:nrow(ex) ) { M[ex[i, 1], ex[i, 2] ] <- ex[i, 3] }
>> 
>>  > M
>> 20 x 20 sparse Matrix of class "dgCMatrix"
>> 
>>   [1,] . 14 .  . . . . . . . . . . . . . . . . .
>>   [2,] .  . . 15 . . . . . . . . . . . . . . . .
>>   [3,] .  . .  . . . . . . . . . . . . . . . . .
>> snip
>>  >
>> --
>> 
>> David Winsemius, MD
>> Heritage Laboratories
>> West Hartford, CT
>> 
>> ______________________________________________
>> 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.
>> 
>> 
> 
> 

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