[R] how to pass matrices from C to R effectively

[Duncan Murdoch]

Hao Cen wrote:
> Hi Duncan,
>
> Thanks for your reply. I am not sure what you meant by "tell your C
> function to use the memory that R sent to it". What R can pass to C is a
> pointer to an array and the array size, assuming we are taking about the
> .C mechanism. Did you mean my C function takes that array pointer and
> generate the required matrix along the length of the array? If this is not
> what you meant, would you please give me a small example?
>   

Yes, that is what I meant.

Duncan Murdoch
>
>
> Jeff
>
>
>
> On Thu, November 12, 2009 6:53 pm, Duncan Murdoch wrote:
>   
>> On 12/11/2009 6:45 PM, Hao Cen wrote:
>>
>>     
>>> Hi,
>>>
>>>
>>> I have C code to produce a lot of matrices to be analyzed. As these
>>> matrices are large (> 1000*10000) and are a lot (> 1000), I am thinking
>>> about how to pass them from C to R effectively.
>>>
>>> Would you think about the following solution? In R, I create a wrapper
>>> function
>>>
>>> passDataFromCToR = function(row, col) { mat = matrix(0, row, col)
>>> .C("passDataFromCToR",mat)[[1]]
>>>
>>>       
>> That .C call doesn't match the header of the function below:  you didn't
>> pass row and col.
>>
>>     
>>> }
>>>
>>>
>>> It wraps the following C function
>>> void passDataFromCToR (double *m, int *row, int* col){ mymat = f() // my
>>> c function to produce a matrix // then I copy mymat to m element by
>>> element via a loop
>>>
>>> }
>>>
>>>
>>> Then to use these functions, I would write in R
>>> mat = passDataFromCToR(1000, 10000)
>>>
>>> Two issues with this approach are that 1) I have to copy the data once
>>> and 2)to the worse, in R I have to know the dimension of the matrices to
>>> be passed from C. This information is not always available.
>>>       
>> Why would you have to copy the data?  Just tell your C function to use
>> the memory that R sent to it, instead of copying entries into it.  (R may
>> be doing a copy when you extract the results, though.)
>>
>> If your C code can't use memory provided to it, then there are no simple
>> ways to avoid copying.  The complicated way is to use the .Call interface
>> instead of .C.  There are examples in Writing R Extensions. They *will*
>> require modifications to your code if it can't take a pointer to the
>> memory to use.
>>
>> For the question of the dimensions being unknown in advance:  Just write
>> two functions.  The first does the calculations up to the point where it
>> needs the memory, the second works on an appropriately sized array, that
>> your R code allocated based on the first result.  Or use the .Call()
>> interface.
>>
>> Duncan Murdoch
>>
>>
>>     
>>> I would appreciate if you share with me your thoughts on how to solve
>>> this problem better.
>>>
>>> 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.
>>>       
>>
>>     
>
> ______________________________________________
> 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.
>