[R] How to build a large identity matrix faster?

[R. Michael Weylandt]

For the matter and hand, you can probably get to it by simply trying
base:::diag. In this case, it's not too hard because what you're
seeing is the S4 generic that the Matrix package is defining _over_
the regular base function generic.

More generally, going down the rabbit hole of S4:

As it suggests, first try

showMethods("diag")

and you'll see a long list of types. The parallel to the *.default
method is the one with signature "ANY" so you can try that:

getMethod("diag", "ANY")

which gets you where you need to be.

Hope this helps,
Michael

On Fri, Jun 8, 2012 at 5:11 PM, Spencer Graves
<spencer.graves at structuremonitoring.com> wrote:
>      How can one get the source code for diag?  I tried the following:
>
>
>> diag
> standardGeneric for "diag" defined from package "base"
>
> function (x = 1, nrow, ncol)
> standardGeneric("diag")
> <environment: 0x0000000009dc1ab0>
> Methods may be defined for arguments: x, nrow, ncol
> Use  showMethods("diag")  for currently available ones.
>
>
>      How can I look at the code past the methods dispatch?
>
>
>> methods('diag')
> [1] diag.panel.splom
> Warning message:
> In methods("diag") : function 'diag' appears not to be generic
>
>
>      So "diag" is an S4 generic.  I tried the following:
>
>
>> dumpMethods('diag', file='diag.R')
>> readLines('diag.R')
> character(0)
>
>
>      More generally, what do you recommend I read to learn about S4
> generics?  I've read fair portions of Chambers (1998, 2008), which produced
> more frustration than enlightenment for me.
>
>
>      Thanks,
>      Spencer
>
>
> On 6/8/2012 12:07 PM, Uwe Ligges wrote:
>>
>> I quickly looked at it, and the difference comes from:
>>
>> n <- 5e3
>> system.time(x <- array(0, c(n, n))) # from diag()
>> system.time(x <- matrix(0, n, n))   # from Rdiag()
>>
>> Replaced in R-devel.
>>
>> Best,
>> Uwe Ligges
>>
>>
>>
>> On 07.06.2012 12:11, Spencer Graves wrote:
>>>
>>> On 6/7/2012 2:27 AM, Rui Barradas wrote:
>>>>
>>>> Hello,
>>>>
>>>> To my great surprise, on my system, Windows 7, R 15.0, 32 bits, an R
>>>> version is faster!
>>>
>>>
>>> I was also surprised, Windows 7, R 2.15.0, 64-bit
>>>
>>>
>>> > rbind(diag=t1, Rdiag=t2, ratio=t1/t2)
>>> user.self sys.self elapsed user.child sys.child
>>> diag 0.72 0.080000 0.81 NA NA
>>> Rdiag 0.09 0.030000 0.12 NA NA
>>> ratio 8.00 2.666667 6.75 NA NA
>>> >
>>> > sessionInfo()
>>> R version 2.15.0 (2012-03-30)
>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252
>>> [2] LC_CTYPE=English_United States.1252
>>> [3] LC_MONETARY=English_United States.1252
>>> [4] LC_NUMERIC=C
>>> [5] LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] splines stats graphics grDevices utils datasets methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] fda_2.2.9 Matrix_1.0-6 lattice_0.20-6 zoo_1.7-7
>>>
>>> loaded via a namespace (and not attached):
>>> [1] grid_2.15.0 tools_2.15.0
>>> >
>>>
>>>
>>> Spencer
>>>>
>>>>
>>>>
>>>> Rdiag <- function(n){
>>>> m <- matrix(0, nrow=n, ncol=n)
>>>> m[matrix(rep(seq_len(n), 2), ncol=2)] <- 1
>>>> m
>>>> }
>>>>
>>>> Rdiag(4)
>>>>
>>>> n <- 5e3
>>>> t1 <- system.time(d1 <- diag(n))
>>>> t2 <- system.time(d2 <- Rdiag(n))
>>>> all.equal(d1, d2)
>>>> rbind(diag=t1, Rdiag=t2, ratio=t1/t2)
>>>>
>>>>
>>>> Anyway, why don't you create it once, save a copy and use it many times?
>>>>
>>>> Hope this helps,
>>>>
>>>> Rui Barradas
>>>>
>>>> Em 07-06-2012 08:55, Ceci Tam escreveu:
>>>>>
>>>>> Hello, I am trying to build a large size identity matrix using
>>>>> diag(). The
>>>>> size is around 23000 and I've tried diag(23000), that took a long time.
>>>>> Since I have to use this operation several times in my program, the
>>>>> running
>>>>> time is too long to be tolerable. Are there any alternative for
>>>>> diag(N)?
>>>>> Thanks
>>>>>
>>>>> Cheers,
>>>>> yct
>>>>>
>>>>> [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> 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.
>
>
> ______________________________________________
> 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.