From bates at stat.wisc.edu  Sat Oct 24 19:06:14 2009
From: bates at stat.wisc.edu (Douglas Bates)
Date: Sat, 24 Oct 2009 12:06:14 -0500
Subject: [Rd] Confusion regarding allocating Matrices.
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On Fri, Oct 23, 2009 at 2:02 PM, Abhijit Bera <abhibera at gmail.com> wrote:
> Sorry, I made a mistake while writing the code. The declaration of Data
> should have been first.

> I still have some doubts:

Because you are making some sweeping and incorrect assumptions about
the way that the internals of R operate.  R allows for arrays to be
dynamically resized but this is accomplished internally by allocating
new storage, copying the current contents to this new location and
installing the values of the new elements.  It is an expensive
operation, which is why it is discouraged.

Your design is deeply flawed.  Go back to the drawing board.

> When you say calloc and realloc are you talking about R's C interface Calloc
> and Realloc or the regular calloc and realloc?

Either one.

> I want to feed data directly into a R matrix and grow it as required. So at
> one time I might have 100 rows coming in from a data source. The next time I
> might have 200 rows coming in from a data source. I want to be able to
> expand the R-matrix instead of creating a regular C float matrix and then
> make an R-matrix based on the new size. I just want to have one R object and
> be able to expand it's size dynamically.

R stores floating-point numbers as the C data type double, not float.
It may seem pedantic to point out distinctions like that but not when
you are writing programs.  Compilers are the ultimate pedants - they
are real sticklers for getting the details right.

As I said, it just doesn't work the way that you think it does.  The
fact that there is an R object with a certain name before and after an
operation doesn't mean it is the same R object.

> I was reading the language specs. It says that one could declare an object
> in R like this:
>
> m=matrix(nrows=10,ncols=10)
>
> and then one could assign
>
> m[101]=1.00
>
> to expand the object.
>
> but this has one problem when I do a
>
> dim(m)
>
> I get
>
> NULL instead of 10 10
>
> So what is happening here?
>
>
> I am aware that R matrices are stored in column major order.
>
> Thanks for the tip on using float *dat= REAL(Data);
>
> Regards
>
> Abhijit Bera
>
>
>
> On Fri, Oct 23, 2009 at 7:27 PM, Douglas Bates <bates at stat.wisc.edu> wrote:
>>
>> On Fri, Oct 23, 2009 at 9:23 AM, Douglas Bates <bates at stat.wisc.edu>
>> wrote:
>> > On Fri, Oct 23, 2009 at 8:39 AM, Abhijit Bera <abhibera at gmail.com>
>> > wrote:
>> >> Hi
>> >>
>> >> I'm having slight confusion.
>> >
>> > Indeed.
>> >
>> >> I plan to grow/realloc a matrix depending on the data available in a C
>> >> program.
>> >
>> >> Here is what I'm tried to do:
>> >
>> >> Data=allocMatrix(REALSXP,3,4);
>> >> SEXP Data;
>> >
>> > Those lines should be in the other order, shouldn't they?
>> >
>> > Also, you need to PROTECT Data or bad things will happen.
>> >
>> >> REAL(Data)[8]=0.001123;
>> >> REAL(Data)[200000]=0.001125;
>> >> printf("%f %f\n\n\n\n",REAL(Data)[8],REAL(Data)[200000]);
>>
>> And I forgot to mention, it is not a good idea to write REAL(Data)
>> many times like this. ?REAL is a function, not a macro and you are
>> calling the same function over and over again unnecessarily. ?It is
>> better to write
>>
>> double *dat = REAL(Data);
>>
>> and use the dat pointer instead of REAL(Data).
>>
>> >> Here is my confusion:
>> >
>> >> Do I always require to allocate the exact number of data elements in a
>> >> R
>> >> Matrix?
>> >
>> > Yes.
>> >
>> >> In the above code segment I have clearly exceeded the number of
>> >> elements that have been allocated but my program doesn't crash.
>> >
>> > Remember that when programming in C you have a lot of rope with which
>> > to hang yourself. ? You have corrupted a memory location beyond that
>> > allocated to the array but nothing bad has happened ?- yet.
>> >
>> >> I don't find any specific R functions for reallocation incase my data
>> >> set
>> >> grows. How do I reallocate?
>> >
>> > You allocate a new matrix, copy the contents of the current matrix to
>> > the new matrix, then release the old one. ?It gets tricky in that you
>> > should unprotect the old one and protect the new one but you need to
>> > watch the order of those operations.
>> >
>> > This approach is not a very good one. ?If you really need to grow an
>> > array it is better to allocate and reallocate the memory within your C
>> > code using calloc and realloc then, at the end of the calculations,
>> > allocate an R matrix and copy the results over.
>> >
>> > Also, you haven't said whether you are growing the matrix by row or by
>> > column or both. ?If you are adding rows then you can't just reallocate
>> > storage because R stores matrices in column-major order. The positions
>> > of the elements in a matrix with n+1 rows are different from those in
>> > a matrix with n rows.
>> >
>> >> Is it necessary to reallocate or is R handling
>> >> the memory management for the matrix that I have allocated?
>> >>
>> >> Regards
>> >>
>> >> Abhijit Bera
>> >>
>> >> ? ? ? ?[[alternative HTML version deleted]]
>> >>
>> >> ______________________________________________
>> >> R-devel at r-project.org mailing list
>> >> https://stat.ethz.ch/mailman/listinfo/r-devel
>> >>
>> >
>
>



[Rd] Confusion regarding allocating Matrices.
Douglas Bates