Re: [R] Show Progress in loop
On Mon, 10 Oct 2005, Philippe Grosjean wrote:
> Hello,
>
> You must explicitly use print(), show() on an object -here, use
> print(i)- in a loop or alternatively, use cat() to display string like:
> cat("loop", i, "\n")
>
> With RGui under Windows, there is another subtility: if you have turn on
> 'Misc -> Buffered output' (it is ON by default), all output are delayed
> until the end of the command processing. You need to use flush.console()
> to tell to print i immediatelly within a loop. The best synthax is
> (since the command is only usable under Windows):
Not so: all systems have it. It is also useful on MacOS X. All this is
on the help page.
This is in the rw-FAQ: it seems we have lost the convention of not
answering FAQs but referring people to the appropriate FAQ.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
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Re: [R] Show Progress in loop
Rainer M. Krug wrote:
>Hi
>
>I have a loop which is doing time consuming calculations and I would
>like to be able to have some feedback on where it is in it's
>calculations. I tried to simply show the counter variable in the loop,
>but id doesn't work as all display seems to be delayed until the loop is
>completed. Is there any way of displaying the progress of a loop?
>
>Rainer
>
>The loop:
>
>for (i in 2:Result$NoSims)
>{
> ppp <- runifpoint(Result$NoPlants)
> K <- Kest(ppp)
> Result$LSim[i,] <- sqrt(K$iso / pi) - K$r
> CM <- (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
> Result$SigCM[i] <- sum(CM, na.rm=TRUE)
> i #}
>
>
>
Hi,
You can simply include a command like
cat("loop: " , i, "\n")
inside your loop.
EJ
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Re: [R] Show Progress in loop
Rainer M. Krug a écrit :
> Hi
> I have a loop which is doing time consuming calculations and I would
> like to be able to have some feedback on where it is in it's
> calculations. I tried to simply show the counter variable in the loop,
> but id doesn't work as all display seems to be delayed until the loop is
> completed. Is there any way of displaying the progress of a loop?
>
> for (i in 2:Result$NoSims)
> {
> ...
> i # }
>
Hi,
for your last line, use :
print(i);
flush.console(); #<== now displays in the loop
hih
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Re: [R] Show Progress in loop
"Rainer M. Krug" <[EMAIL PROTECTED]> writes:
> I put print(i) in the loop instead of i, but it still only prints (in
> the Windows R GUI) i after it finished the calculations.
> I guess it might be due to the output buffering you mentioned - but how
> do I unset it?
Using the user friendly interface... (it's on one of the top menus),
or, as Uwe suggested, stick in flush.console() after the print(i).
-p
> Rainer
>
> Peter Dalgaard wrote:
> > "Rainer M. Krug" <[EMAIL PROTECTED]> writes:
> >
> >
> >>Hi
> >>
> >>I have a loop which is doing time consuming calculations and I would
> >>like to be able to have some feedback on where it is in it's
> >>calculations. I tried to simply show the counter variable in the loop,
> >>but id doesn't work as all display seems to be delayed until the loop is
> >>completed. Is there any way of displaying the progress of a loop?
> >>
> >>Rainer
> >>
> >>The loop:
> >>
> >>for (i in 2:Result$NoSims)
> >>{
> >>ppp <- runifpoint(Result$NoPlants)
> >>K <- Kest(ppp)
> >>Result$LSim[i,] <- sqrt(K$iso / pi) - K$r
> >>CM <- (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
> >>Result$SigCM[i] <- sum(CM, na.rm=TRUE)
> >>i # >>}
> >
> >
> > Just print(i) and if on Windows, remember to unset output buffering.
> >
>
>
>
> --
> NEW TELEPHONE NUMBER
> Tel: +27 - (0)72 808 2975 (w)
>
> Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
> Biology (UCT)
>
> Department of Conservation Ecology
> University of Stellenbosch
> Matieland 7602
> South Africa
>
> Tel: +27 - (0)72 808 2975 (w)
> Fax: +27 - (0)21 808 3304
> Cell: +27 - (0)83 9479 042
>
> email:[EMAIL PROTECTED]
> [EMAIL PROTECTED]
>
> __
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>
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
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Re: [R] Show Progress in loop
Hello,
You must explicitly use print(), show() on an object -here, use
print(i)- in a loop or alternatively, use cat() to display string like:
cat("loop", i, "\n")
With RGui under Windows, there is another subtility: if you have turn on
'Misc -> Buffered output' (it is ON by default), all output are delayed
until the end of the command processing. You need to use flush.console()
to tell to print i immediatelly within a loop. The best synthax is
(since the command is only usable under Windows):
> for (i in 1:10) {
> print(i)# You must use print explicitly within a loop
> # or, better, use: cat("loop", i, "\n")
> # Next command is to overcome buffered output in RGui
> if (.Platform$OS.type == "windows") flush.console()
> # Next command simulates a "long" process (taking 1 sec)
> Sys.sleep(1)
> # ... your loop code here...
> }
Alternatively, you can use the progress() function in svMisc package
(SciViews bundle). Load svMisc and look at its online help... you have
several examples of use.
> library(svMisc)
> ?progress
Best,
Philippe Grosjean
..<°}))><
) ) ) ) )
( ( ( ( (Prof. Philippe Grosjean
) ) ) ) )
( ( ( ( (Numerical Ecology of Aquatic Systems
) ) ) ) ) Mons-Hainaut University, Pentagone (3D08)
( ( ( ( (Academie Universitaire Wallonie-Bruxelles
) ) ) ) ) 8, av du Champ de Mars, 7000 Mons, Belgium
( ( ( ( (
) ) ) ) ) phone: + 32.65.37.34.97, fax: + 32.65.37.30.54
( ( ( ( (email: [EMAIL PROTECTED]
) ) ) ) )
( ( ( ( (web: http://www.umh.ac.be/~econum
) ) ) ) ) http://www.sciviews.org
( ( ( ( (
..
Rainer M. Krug wrote:
> Hi
>
> I have a loop which is doing time consuming calculations and I would
> like to be able to have some feedback on where it is in it's
> calculations. I tried to simply show the counter variable in the loop,
> but id doesn't work as all display seems to be delayed until the loop is
> completed. Is there any way of displaying the progress of a loop?
>
> Rainer
>
> The loop:
>
> for (i in 2:Result$NoSims)
> {
> ppp <- runifpoint(Result$NoPlants)
> K <- Kest(ppp)
> Result$LSim[i,] <- sqrt(K$iso / pi) - K$r
> CM <- (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
> Result$SigCM[i] <- sum(CM, na.rm=TRUE)
> i # }
>
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Re: [R] Show Progress in loop
Thanks - flush.console() did the trick.
As you might guess, I am quite new to R. I like the idea of vectorizing
the calculation, but I guess it is not possible in this case - I will
ask in a new thread.
Thanks,
Rainer
Uwe Ligges wrote:
> Rainer M. Krug wrote:
>
>> Hi
>>
>> I have a loop which is doing time consuming calculations and I would
>> like to be able to have some feedback on where it is in it's
>> calculations. I tried to simply show the counter variable in the loop,
>> but id doesn't work as all display seems to be delayed until the loop
>> is completed. Is there any way of displaying the progress of a loop?
>>
>> Rainer
>>
>> The loop:
>>
>> for (i in 2:Result$NoSims)
>> {
>> ppp <- runifpoint(Result$NoPlants)
>> K <- Kest(ppp)
>> Result$LSim[i,] <- sqrt(K$iso / pi) - K$r
>> CM <- (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
>> Result$SigCM[i] <- sum(CM, na.rm=TRUE)
>> i #> }
>>
>
>
> - Update your console (I guess you are on Windows?) by using
> flush.console().
> - You might want to measure time consumption, hence see ?Rprof.
> - Save some more time by moving as much as possible out of your loop by
> doing it in a vectorized way (I don't know all the functions you are
> using, hence cannot make any further recommendations).
>
> Uwe Ligges
--
NEW TELEPHONE NUMBER
Tel:+27 - (0)72 808 2975 (w)
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
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Re: [R] Show Progress in loop
I put print(i) in the loop instead of i, but it still only prints (in
the Windows R GUI) i after it finished the calculations.
I guess it might be due to the output buffering you mentioned - but how
do I unset it?
Rainer
Peter Dalgaard wrote:
> "Rainer M. Krug" <[EMAIL PROTECTED]> writes:
>
>
>>Hi
>>
>>I have a loop which is doing time consuming calculations and I would
>>like to be able to have some feedback on where it is in it's
>>calculations. I tried to simply show the counter variable in the loop,
>>but id doesn't work as all display seems to be delayed until the loop is
>>completed. Is there any way of displaying the progress of a loop?
>>
>>Rainer
>>
>>The loop:
>>
>>for (i in 2:Result$NoSims)
>>{
>> ppp <- runifpoint(Result$NoPlants)
>> K <- Kest(ppp)
>> Result$LSim[i,] <- sqrt(K$iso / pi) - K$r
>> CM <- (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
>> Result$SigCM[i] <- sum(CM, na.rm=TRUE)
>> i #>}
>
>
> Just print(i) and if on Windows, remember to unset output buffering.
>
--
NEW TELEPHONE NUMBER
Tel:+27 - (0)72 808 2975 (w)
Rainer M. Krug, Dipl. Phys. (Germany), MSc Conservation
Biology (UCT)
Department of Conservation Ecology
University of Stellenbosch
Matieland 7602
South Africa
Tel:+27 - (0)72 808 2975 (w)
Fax:+27 - (0)21 808 3304
Cell: +27 - (0)83 9479 042
email: [EMAIL PROTECTED]
[EMAIL PROTECTED]
__
R-help@stat.math.ethz.ch mailing list
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Re: [R] Show Progress in loop
Rainer M. Krug wrote:
> Hi
>
> I have a loop which is doing time consuming calculations and I would
> like to be able to have some feedback on where it is in it's
> calculations. I tried to simply show the counter variable in the loop,
> but id doesn't work as all display seems to be delayed until the loop is
> completed. Is there any way of displaying the progress of a loop?
>
> Rainer
>
> The loop:
>
> for (i in 2:Result$NoSims)
> {
> ppp <- runifpoint(Result$NoPlants)
> K <- Kest(ppp)
> Result$LSim[i,] <- sqrt(K$iso / pi) - K$r
> CM <- (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
> Result$SigCM[i] <- sum(CM, na.rm=TRUE)
> i # }
>
- Update your console (I guess you are on Windows?) by using
flush.console().
- You might want to measure time consumption, hence see ?Rprof.
- Save some more time by moving as much as possible out of your loop by
doing it in a vectorized way (I don't know all the functions you are
using, hence cannot make any further recommendations).
Uwe Ligges
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Re: [R] Show Progress in loop
"Rainer M. Krug" <[EMAIL PROTECTED]> writes:
> Hi
>
> I have a loop which is doing time consuming calculations and I would
> like to be able to have some feedback on where it is in it's
> calculations. I tried to simply show the counter variable in the loop,
> but id doesn't work as all display seems to be delayed until the loop is
> completed. Is there any way of displaying the progress of a loop?
>
> Rainer
>
> The loop:
>
> for (i in 2:Result$NoSims)
> {
> ppp <- runifpoint(Result$NoPlants)
> K <- Kest(ppp)
> Result$LSim[i,] <- sqrt(K$iso / pi) - K$r
> CM <- (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
> Result$SigCM[i] <- sum(CM, na.rm=TRUE)
> i # }
Just print(i) and if on Windows, remember to unset output buffering.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
R-help@stat.math.ethz.ch mailing list
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[R] Show Progress in loop
Hi
I have a loop which is doing time consuming calculations and I would
like to be able to have some feedback on where it is in it's
calculations. I tried to simply show the counter variable in the loop,
but id doesn't work as all display seems to be delayed until the loop is
completed. Is there any way of displaying the progress of a loop?
Rainer
The loop:
for (i in 2:Result$NoSims)
{
ppp <- runifpoint(Result$NoPlants)
K <- Kest(ppp)
Result$LSim[i,] <- sqrt(K$iso / pi) - K$r
CM <- (Result$LSim[i,] * Result$LSim[i,]) / abs(K$r[2] - K$r[1])
Result$SigCM[i] <- sum(CM, na.rm=TRUE)
i #
