On 11.06.2012 11:45, Ceci Tam wrote:
diag(n) is alright when n = 5e3, it took 0.7 sec on my machine for
diag(5e3). However, it's slow when n = 23000, diag(23000) took 15 sec
1. As others have said already, for huge data, the Matrix implementation
for diagonals is the right idea, since it actually does know how to
calculate things without actually using and saving the elements of the
diagonal explicitly.
2. Such a huge matrix (23000x23000) does not work on all available
machines and the OP tried to make the example code portable.
3. What timing do you expect?
I'd expect (assuming O(n) for the numbers of elements in the matrix) a
ratio of round(23000^2/5000^2)=21 and actually you reported round(15/0.7)=21
Best,
Uwe Ligges
On 11 June 2012 17:43, Ceci Tam<yeeching...@gmail.com> wrote:
diag(n) is alright when n = 5e3, it took 0.7 sec on my machine for
diag(5e3). However, it's slow when n = 23000, diag(23000) took 15 sec
On 9 June 2012 06:32, R. Michael Weylandt<michael.weyla...@gmail.com>wrote:
On Fri, Jun 8, 2012 at 5:31 PM, R. Michael Weylandt
<michael.weyla...@gmail.com> wrote:
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.
Sorry -- the regular base function is not a generic in this case.
Everything else still holds though. (Same tricks to find things work
with print which becomes both an S3 and S4 generic on loading Matrix)
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.gra...@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
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