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alessia matano

sparseM and kronecker product_R latest version

Dear all,

I just installed the new version of R, 2.10.1, and I am currently
using the package sparseM. (I also use a 64 bit windows version)

I got a problem that I never had: when I try to multiply with a
kronecker product (%x%) two sparse matrixes I get the following
message:

Error in dim(x) <- length(x) : invalid first argument

I never had this problem with previous versions of R.

May you help me?

thanks
alessia

______________________________________________
[hidden email] 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.

alessia matano

sparseM and kronecker product_R latest version

Peter Ehlers

Re: sparseM and kronecker product_R latest version

Do you have the same problem with the example
on the help page?

?'%x%-methods'

Works for me on Windows Vista (32-bit OS) and
R version 2.10.1 Patched (2010-01-05 r50896).

-Peter Ehlers

alessia matano wrote:

> Dear all,
>
> I just installed the new version of R, 2.10.1, and I am currently
> using the package sparseM. (I also use a 64 bit windows version)
>
> I got a problem that I never had: when I try to multiply with a
> kronecker product (%x%) two sparse matrixes I get the following
> message:
>
> Error in dim(x) <- length(x) : invalid first argument
>
> I never had this problem with previous versions of R.
>
> May you help me?
>
> thanks
> alessia
>
> ______________________________________________
> [hidden email] 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.
>
>

--
Peter Ehlers
University of Calgary
403.202.3921

______________________________________________
[hidden email] 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

Re: sparseM and kronecker product_R latest version

On Jan 11, 2010, at 7:55 AM, Peter Ehlers wrote:

> Do you have the same problem with the example
> on the help page?
>
> ?'%x%-methods'
>
> Works for me on Windows Vista (32-bit OS) and
> R version 2.10.1 Patched (2010-01-05 r50896).
>
> -Peter Ehlers
>
> alessia matano wrote:
>> Dear all,
>> I just installed the new version of R, 2.10.1, and I am currently
>> using the package sparseM. (I also use a 64 bit windows version)

SparseM

>> I got a problem that I never had: when I try to multiply with a
>> kronecker product (%x%) two sparse matrixes I get the following
>> message:
>> Error in dim(x) <- length(x) : invalid first argument
>> I never had this problem with previous versions of R.

I get the same error as you do when trying the example on the cited
help page using SparseM 0.83 in a 64 bit Mac version of 2.10.1

> A.csr %x% matrix(1:4,2,2)
Error in dim(x) <- length(x) : invalid first argument

> sessionInfo()
R version 2.10.1 RC (2009-12-09 r50695)
x86_64-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid splines stats graphics grDevices utils
datasets methods base

other attached packages:
[1] SparseM_0.83 Matrix_0.999375-32 Epi_1.1.10
plotrix_2.7-2 ROCR_1.0-4
[6] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1
gdata_2.6.1 gtools_2.6.1
[11] lattice_0.17-26 Design_2.3-0 Hmisc_3.7-0
survival_2.35-7

loaded via a namespace (and not attached):
[1] cluster_1.12.1 tools_2.10.1

>> May you help me?
>> thanks
>> alessia
>> ______________________________________________
> --
> Peter Ehlers
> University of Calgary
> 403.202.3921
>
> ______________________________________________

David Winsemius, MD
Heritage Laboratories
West Hartford, CT

______________________________________________
[hidden email] 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.

alessia matano

Re: sparseM and kronecker product_R latest version

Many thanks for your suggestions,

fortunately when I closed R and opeedn it again, it did not give again
that error. However, now there is something more strange happening,
related again to sparse matrix, and I am afraid it could concern
memory problems (I put 4000 of memory limit).

I am defining a matrix where I have nrow=113289, ncol=36698 such as:

D<- as.matrix.csr(0, nrow, ncol)

Error in if (length(x) == nrow * ncol) x <- matrix(x, nrow, ncol) else { :
missing value where TRUE/FALSE needed
In addition: Warning message:
In nrow * ncol : NAs produced by integer overflow

With reduced number of rows and columns it worked, so I am wondering
wether it is a problem of memory. My pc has 6gb of nmemory, and it is
64-bit windows system, but R reads only 4 has capacity.

Thanks for your help
alessia

2010/1/11 David Winsemius <[hidden email]>:

>
> On Jan 11, 2010, at 7:55 AM, Peter Ehlers wrote:
>
>> Do you have the same problem with the example
>> on the help page?
>>
>> ?'%x%-methods'
>>
>> Works for me on Windows Vista (32-bit OS) and
>> R version 2.10.1 Patched (2010-01-05 r50896).
>>
>> -Peter Ehlers
>>
>> alessia matano wrote:
>>>
>>> Dear all,
>>> I just installed the new version of R, 2.10.1, and I am currently
>>> using the package sparseM. (I also use a 64 bit windows version)
>
> SparseM
>
>>> I got a problem that I never had: when I try to multiply with a
>>> kronecker product (%x%) two sparse matrixes I get the following
>>> message:
>>> Error in dim(x) <- length(x) : invalid first argument
>>> I never had this problem with previous versions of R.
>
> I get the same error as you do when trying the example on the cited help
> page using SparseM 0.83 in a 64 bit Mac version of 2.10.1
>
>> A.csr %x% matrix(1:4,2,2)
> Error in dim(x) <- length(x) : invalid first argument
>
>> sessionInfo()
> R version 2.10.1 RC (2009-12-09 r50695)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid splines stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] SparseM_0.83 Matrix_0.999375-32 Epi_1.1.10 plotrix_2.7-2
> ROCR_1.0-4
> [6] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1 gdata_2.6.1
> gtools_2.6.1
> [11] lattice_0.17-26 Design_2.3-0 Hmisc_3.7-0
> survival_2.35-7
>
> loaded via a namespace (and not attached):
> [1] cluster_1.12.1 tools_2.10.1
>
>
>
>>> May you help me?
>>> thanks
>>> alessia
>>> ______________________________________________
>>
>> --
>> Peter Ehlers
>> University of Calgary
>> 403.202.3921
>>
>> ______________________________________________
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
>

______________________________________________
[hidden email] 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.

RKoenker

Re: sparseM and kronecker product_R latest version

In reply to this post by David Winsemius

I can't reproduce this on my mac:

> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-apple-darwin9.8.0

locale:
[1] C

attached base packages:
[1] graphics grDevices datasets utils stats methods base

other attached packages:
[1] fortunes_1.3-7 quantreg_4.44 SparseM_0.83

loaded via a namespace (and not attached):
[1] tools_2.10.1

url: www.econ.uiuc.edu/~roger Roger Koenker
email [hidden email] Department of Economics
vox: 217-333-4558 University of Illinois
fax: 217-244-6678 Urbana, IL 61801

On Jan 11, 2010, at 8:00 AM, David Winsemius wrote:

>
> On Jan 11, 2010, at 7:55 AM, Peter Ehlers wrote:
>
>> Do you have the same problem with the example
>> on the help page?
>>
>> ?'%x%-methods'
>>
>> Works for me on Windows Vista (32-bit OS) and
>> R version 2.10.1 Patched (2010-01-05 r50896).
>>
>> -Peter Ehlers
>>
>> alessia matano wrote:
>>> Dear all,
>>> I just installed the new version of R, 2.10.1, and I am currently
>>> using the package sparseM. (I also use a 64 bit windows version)
>
> SparseM
>
>>> I got a problem that I never had: when I try to multiply with a
>>> kronecker product (%x%) two sparse matrixes I get the following
>>> message:
>>> Error in dim(x) <- length(x) : invalid first argument
>>> I never had this problem with previous versions of R.
>
> I get the same error as you do when trying the example on the cited help page using SparseM 0.83 in a 64 bit Mac version of 2.10.1
>
> > A.csr %x% matrix(1:4,2,2)
> Error in dim(x) <- length(x) : invalid first argument
>
> > sessionInfo()
> R version 2.10.1 RC (2009-12-09 r50695)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] grid splines stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] SparseM_0.83 Matrix_0.999375-32 Epi_1.1.10 plotrix_2.7-2 ROCR_1.0-4
> [6] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1 gdata_2.6.1 gtools_2.6.1
> [11] lattice_0.17-26 Design_2.3-0 Hmisc_3.7-0 survival_2.35-7
>
> loaded via a namespace (and not attached):
> [1] cluster_1.12.1 tools_2.10.1
>
>
>
>>> May you help me?
>>> thanks
>>> alessia
>>> ______________________________________________
>> --
>> Peter Ehlers
>> University of Calgary
>> 403.202.3921
>>
>> ______________________________________________
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT

Martin Maechler

Re: sparseM and kronecker product_R latest version

In reply to this post by alessia matano

>>>>> "am" == alessia matano <[hidden email]>
>>>>> on Mon, 11 Jan 2010 15:38:39 +0100 writes:

am> Many thanks for your suggestions,
am> fortunately when I closed R and opeedn it again, it did not give again
am> that error. However, now there is something more strange happening,
am> related again to sparse matrix, and I am afraid it could concern
am> memory problems (I put 4000 of memory limit).

am> I am defining a matrix where I have nrow=113289, ncol=36698 such as:

am> D<- as.matrix.csr(0, nrow, ncol)

am> Error in if (length(x) == nrow * ncol) x <- matrix(x, nrow, ncol) else { :
am> missing value where TRUE/FALSE needed
am> In addition: Warning message:
am> In nrow * ncol : NAs produced by integer overflow

am> With reduced number of rows and columns it worked, so I am wondering
am> wether it is a problem of memory.

It's not; rather a "trap" that the programmers of SparseM fell
into (I did too, in the past): Your nrow and ncol are so
large that nrow * ncol is larger than R's maximal integer,
( == .Machine$integer.max which is 2^31 - 1 on all current versions of R)
and so overflows to NA and such leads to the
"missing value" warning you see.

am> My pc has 6gb of nmemory, and it is
am> 64-bit windows system, but R reads only 4 has capacity.

am> Thanks for your help
am> alessia

As a side note:
As co-author of R package 'Matrix' in to which we have put a
large amount of work and which is nowadays a recommended package
(i.e., also part of every R distribution),
I do wonder why you don't use 'Matrix' for sparse matrix
computing in R.

Best regards,
Martin Maechler, ETH Zurich

am> 2010/1/11 David Winsemius <[hidden email]>:
>>
>> On Jan 11, 2010, at 7:55 AM, Peter Ehlers wrote:
>>
>>> Do you have the same problem with the example
>>> on the help page?
>>>
>>> ?'%x%-methods'
>>>
>>> Works for me on Windows Vista (32-bit OS) and
>>> R version 2.10.1 Patched (2010-01-05 r50896).
>>>
>>> -Peter Ehlers
>>>
>>> alessia matano wrote:
>>>>
>>>> Dear all,
>>>> I just installed the new version of R, 2.10.1, and I am currently
>>>> using the package sparseM. (I also use a 64 bit windows version)
>>
>> SparseM
>>
>>>> I got a problem that I never had: when I try to multiply with a
>>>> kronecker product (%x%) two sparse matrixes I get the following
>>>> message:
>>>> Error in dim(x) <- length(x) : invalid first argument
>>>> I never had this problem with previous versions of R.
>>
>> I get the same error as you do when trying the example on the cited help
>> page using SparseM 0.83 in a 64 bit Mac version of 2.10.1
>>
>>> A.csr %x% matrix(1:4,2,2)
>> Error in dim(x) <- length(x) : invalid first argument
>>
>>> sessionInfo()
>> R version 2.10.1 RC (2009-12-09 r50695)
>> x86_64-apple-darwin9.8.0
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] grid splines stats graphics grDevices utils datasets
>> methods base
>>
>> other attached packages:
>> [1] SparseM_0.83 Matrix_0.999375-32 Epi_1.1.10 plotrix_2.7-2
>> ROCR_1.0-4
>> [6] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1 gdata_2.6.1
>> gtools_2.6.1
>> [11] lattice_0.17-26 Design_2.3-0 Hmisc_3.7-0
>> survival_2.35-7
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.12.1 tools_2.10.1
>>
>>
>>
>>>> May you help me?
>>>> thanks
>>>> alessia
>>>> ______________________________________________
>>>
>>> --
>>> Peter Ehlers
>>> University of Calgary
>>> 403.202.3921
>>>
>>> ______________________________________________
>>
>> David Winsemius, MD
>> Heritage Laboratories
>> West Hartford, CT
>>
>>

am> ______________________________________________
am> [hidden email] mailing list
am> https://stat.ethz.ch/mailman/listinfo/r-help
am> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
am> and provide commented, minimal, self-contained, reproducible code.

______________________________________________
[hidden email] 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.

alessia matano

Re: sparseM and kronecker product_R latest version

Many thanks for it.

However it is strange that when I put the numbers rather than ncol(R)
(a matrix with ncol=36698) it worked. Look below

> dim(res2)
[1] 170471 25822
> D<- as.matrix.csr(0,nrow(tmpb),25822)
> D<- as.matrix.csr(0,nrow(tmpb),ncol(res2))
Error in if (length(x) == nrow * ncol) x <- matrix(x, nrow, ncol) else { :
missing value where TRUE/FALSE needed
In addition: Warning message:
In nrow * ncol : NAs produced by integer overflow

But probably it is true what you said, anyway.
So, do you suggest me to use directly the simple matrix command? or a
kind of sparse matrix within your package?!? Many thanks again.

Moreover unfortunately I then run the procedure of quantile fixed
effects elaborated by Koenker on a sample of 276000 observations, and
even if I am using a 64 bit machine with 6 gigabyte of Ram (and we
will raise it to 16 giga) he gives me the error :

Error: cannot allocate vector of size 155.4 Mb

and R cannot read more than 4 giga of RAM (even if I have 6).
Any suggestion to overcome this problem? Otherwise I have to randomly
subsample my data, which is a pity when you have such an amount of
information.

2010/1/11 Martin Maechler <[hidden email]>:

>>>>>> "am" == alessia matano <[hidden email]>
>>>>>> on Mon, 11 Jan 2010 15:38:39 +0100 writes:
>
> am> Many thanks for your suggestions,
> am> fortunately when I closed R and opeedn it again, it did not give again
> am> that error. However, now there is something more strange happening,
> am> related again to sparse matrix, and I am afraid it could concern
> am> memory problems (I put 4000 of memory limit).
>
> am> I am defining a matrix where I have nrow=113289, ncol=36698 such as:
>
> am> D<- as.matrix.csr(0, nrow, ncol)
>
> am> Error in if (length(x) == nrow * ncol) x <- matrix(x, nrow, ncol) else { :
> am> missing value where TRUE/FALSE needed
> am> In addition: Warning message:
> am> In nrow * ncol : NAs produced by integer overflow
>
> am> With reduced number of rows and columns it worked, so I am wondering
> am> wether it is a problem of memory.
>
> It's not; rather a "trap" that the programmers of SparseM fell
> into (I did too, in the past): Your nrow and ncol are so
> large that nrow * ncol is larger than R's maximal integer,
> ( == .Machine$integer.max which is 2^31 - 1 on all current versions of R)
> and so overflows to NA and such leads to the
> "missing value" warning you see.
>
> am> My pc has 6gb of nmemory, and it is
> am> 64-bit windows system, but R reads only 4 has capacity.
>
> am> Thanks for your help
> am> alessia
>
> As a side note:
> As co-author of R package 'Matrix' in to which we have put a
> large amount of work and which is nowadays a recommended package
> (i.e., also part of every R distribution),
> I do wonder why you don't use 'Matrix' for sparse matrix
> computing in R.
>
> Best regards,
> Martin Maechler, ETH Zurich
>
>
> am> 2010/1/11 David Winsemius <[hidden email]>:
> >>
> >> On Jan 11, 2010, at 7:55 AM, Peter Ehlers wrote:
> >>
> >>> Do you have the same problem with the example
> >>> on the help page?
> >>>
> >>> ?'%x%-methods'
> >>>
> >>> Works for me on Windows Vista (32-bit OS) and
> >>> R version 2.10.1 Patched (2010-01-05 r50896).
> >>>
> >>> -Peter Ehlers
> >>>
> >>> alessia matano wrote:
> >>>>
> >>>> Dear all,
> >>>> I just installed the new version of R, 2.10.1, and I am currently
> >>>> using the package sparseM. (I also use a 64 bit windows version)
> >>
> >> SparseM
> >>
> >>>> I got a problem that I never had: when I try to multiply with a
> >>>> kronecker product (%x%) two sparse matrixes I get the following
> >>>> message:
> >>>> Error in dim(x) <- length(x) : invalid first argument
> >>>> I never had this problem with previous versions of R.
> >>
> >> I get the same error as you do when trying the example on the cited help
> >> page using SparseM 0.83 in a 64 bit Mac version of 2.10.1
> >>
> >>> A.csr %x% matrix(1:4,2,2)
> >> Error in dim(x) <- length(x) : invalid first argument
> >>
> >>> sessionInfo()
> >> R version 2.10.1 RC (2009-12-09 r50695)
> >> x86_64-apple-darwin9.8.0
> >>
> >> locale:
> >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >>
> >> attached base packages:
> >> [1] grid splines stats graphics grDevices utils datasets
> >> methods base
> >>
> >> other attached packages:
> >> [1] SparseM_0.83 Matrix_0.999375-32 Epi_1.1.10 plotrix_2.7-2
> >> ROCR_1.0-4
> >> [6] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1 gdata_2.6.1
> >> gtools_2.6.1
> >> [11] lattice_0.17-26 Design_2.3-0 Hmisc_3.7-0
> >> survival_2.35-7
> >>
> >> loaded via a namespace (and not attached):
> >> [1] cluster_1.12.1 tools_2.10.1
> >>
> >>
> >>
> >>>> May you help me?
> >>>> thanks
> >>>> alessia
> >>>> ______________________________________________
> >>>
> >>> --
> >>> Peter Ehlers
> >>> University of Calgary
> >>> 403.202.3921
> >>>
> >>> ______________________________________________
> >>
> >> David Winsemius, MD
> >> Heritage Laboratories
> >> West Hartford, CT
> >>
> >>
>
> am> ______________________________________________
> am> [hidden email] mailing list
> am> https://stat.ethz.ch/mailman/listinfo/r-help
> am> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> am> and provide commented, minimal, self-contained, reproducible code.
>

David Winsemius

Re: sparseM and kronecker product_R latest version

In reply to this post by RKoenker

I had an earlier problem where cutting and pasting from a help window
caused obscure problems. Prof Ripley suggested trying example() and
that did show that the example on the help page "worked". I just ran
example(`%x%`), as well as example(matrix.csr) and encountered no
errors. I also tried re-entering the first example on the help page
and am still getting the error. It looks as though the help page that
comes up with help(`%x%`) is similar to the second example suite. But
it's not precisely the same.

For me it's not a problem, since I'm not using SparseM at the moment.
I was just trying to help out the OP. I still should probably a)
restart an run without Matrix loaded, and b) upgrade to a more recent
R, but I have a number of models and datasets that I am working on and
those efforts take precedence.

> n1 <- 10
> n2 <- 10
> p <- 6
> y <- rnorm(n1)
> a <- rnorm(n1*p)
> a[abs(a)<0.5] <- 0
> A <- matrix(a,n1,p)
> A.csr <- as.matrix.csr(A)
> b <- rnorm(n2*p)
> b[abs(b)<1.0] <- 0
> B <- matrix(b,n2,p)
> B.csr <- as.matrix.csr(B)
>
> # matrix transposition and multiplication
> A.csr%*%t(B.csr)
elided output.... no error

>
> # kronecker product
> A.csr %x% matrix(1:4,2,2)
Error in dim(x) <- length(x) : invalid first argument

Also tried kronecker():

> kronecker(A.csr, matrix(1:36, 10,10))
Error in dim(x) <- length(x) : invalid first argument

--
David.

On Jan 11, 2010, at 10:02 AM, Roger Koenker wrote:

> I can't reproduce this on my mac:
>
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] graphics grDevices datasets utils stats methods base
>
> other attached packages:
> [1] fortunes_1.3-7 quantreg_4.44 SparseM_0.83
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
>
> url: www.econ.uiuc.edu/~roger Roger Koenker
> email [hidden email] Department of Economics
> vox: 217-333-4558 University of Illinois
> fax: 217-244-6678 Urbana, IL 61801
>
> On Jan 11, 2010, at 8:00 AM, David Winsemius wrote:
>
>>
>> On Jan 11, 2010, at 7:55 AM, Peter Ehlers wrote:
>>
>>> Do you have the same problem with the example
>>> on the help page?
>>>
>>> ?'%x%-methods'
>>>
>>> Works for me on Windows Vista (32-bit OS) and
>>> R version 2.10.1 Patched (2010-01-05 r50896).
>>>
>>> -Peter Ehlers
>>>
>>> alessia matano wrote:
>>>> Dear all,
>>>> I just installed the new version of R, 2.10.1, and I am currently
>>>> using the package sparseM. (I also use a 64 bit windows version)
>>
>> SparseM
>>
>>>> I got a problem that I never had: when I try to multiply with a
>>>> kronecker product (%x%) two sparse matrixes I get the following
>>>> message:
>>>> Error in dim(x) <- length(x) : invalid first argument
>>>> I never had this problem with previous versions of R.
>>
>> I get the same error as you do when trying the example on the cited
>> help page using SparseM 0.83 in a 64 bit Mac version of 2.10.1
>>
>>> A.csr %x% matrix(1:4,2,2)
>> Error in dim(x) <- length(x) : invalid first argument
>>
>>> sessionInfo()
>> R version 2.10.1 RC (2009-12-09 r50695)
>> x86_64-apple-darwin9.8.0
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] grid splines stats graphics grDevices utils
>> datasets methods base
>>
>> other attached packages:
>> [1] SparseM_0.83 Matrix_0.999375-32 Epi_1.1.10
>> plotrix_2.7-2 ROCR_1.0-4
>> [6] gplots_2.7.4 caTools_1.10 bitops_1.0-4.1
>> gdata_2.6.1 gtools_2.6.1
>> [11] lattice_0.17-26 Design_2.3-0 Hmisc_3.7-0
>> survival_2.35-7
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.12.1 tools_2.10.1
>>
>>
>>
>>>> May you help me?
>>>> thanks
>>>> alessia
>>>> ______________________________________________
>>> --
>>> Peter Ehlers
>>> University of Calgary
>>> 403.202.3921
>>>
>>> ______________________________________________
>>
>> David Winsemius, MD
>> Heritage Laboratories
>> West Hartford, CT
>

Martin Maechler

Re: sparseM and kronecker product_R latest version

In reply to this post by alessia matano

>>>>> "am" == alessia matano <[hidden email]>
>>>>> on Mon, 11 Jan 2010 16:20:57 +0100 writes:

am> Many thanks for it.
am> However it is strange that when I put the numbers rather than ncol(R)
am> (a matrix with ncol=36698) it worked. Look below

>> dim(res2)
am> [1] 170471 25822
>> D<- as.matrix.csr(0,nrow(tmpb),25822)
>> D<- as.matrix.csr(0,nrow(tmpb),ncol(res2))
am> Error in if (length(x) == nrow * ncol) x <- matrix(x, nrow, ncol) else { :
am> missing value where TRUE/FALSE needed
am> In addition: Warning message:
am> In nrow * ncol : NAs produced by integer overflow

am> But probably it is true what you said, anyway.

yes, it is true.
The clue is that typeof(25822) is "double" and not "integer".

am> So, do you suggest me to use directly the simple matrix command? or a
am> kind of sparse matrix within your package?!?

the latter, e.g.,

library(Matrix)
D <- Matrix(0, nrow = 113289, ncol=36698)
## or
D. <- sparseMatrix(x=double(0), i=integer(0), j=integer(0),
dims = c(113289,36698))
identical(D, D.) ##--> TRUE

## and, e.g.,

> Dk <- kronecker(D, Diagonal(x=5:2))
> identical(Dk, D %x% Diagonal(x = 5:2))
[1] TRUE
> dim(D)
[1] 113289 36698
> dim(Dk)
[1] 453156 146792
>

Regards,
Martin Maechler, ETH Zurich

______________________________________________
[hidden email] 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.

alessia matano

Re: sparseM and kronecker product_R latest version

I see, now I got it.

and thanks for the example with matrix.
best
alessia

2010/1/12 Martin Maechler <[hidden email]>:

>>>>>> "am" == alessia matano <[hidden email]>
>>>>>> on Mon, 11 Jan 2010 16:20:57 +0100 writes:
>
> am> Many thanks for it.
> am> However it is strange that when I put the numbers rather than ncol(R)
> am> (a matrix with ncol=36698) it worked. Look below
>
> >> dim(res2)
> am> [1] 170471 25822
> >> D<- as.matrix.csr(0,nrow(tmpb),25822)
> >> D<- as.matrix.csr(0,nrow(tmpb),ncol(res2))
> am> Error in if (length(x) == nrow * ncol) x <- matrix(x, nrow, ncol) else { :
> am> missing value where TRUE/FALSE needed
> am> In addition: Warning message:
> am> In nrow * ncol : NAs produced by integer overflow
>
> am> But probably it is true what you said, anyway.
>
> yes, it is true.
> The clue is that typeof(25822) is "double" and not "integer".
>
> am> So, do you suggest me to use directly the simple matrix command? or a
> am> kind of sparse matrix within your package?!?
>
> the latter, e.g.,
>
> library(Matrix)
> D <- Matrix(0, nrow = 113289, ncol=36698)
> ## or
> D. <- sparseMatrix(x=double(0), i=integer(0), j=integer(0),
> dims = c(113289,36698))
> identical(D, D.) ##--> TRUE
>
> ## and, e.g.,
>
>> Dk <- kronecker(D, Diagonal(x=5:2))
>> identical(Dk, D %x% Diagonal(x = 5:2))
> [1] TRUE
>> dim(D)
> [1] 113289 36698
>> dim(Dk)
> [1] 453156 146792
>>
>
> Regards,
> Martin Maechler, ETH Zurich
>