Hi all; I want to print system.time whenever I execute any command. It takes too much time to type "system.time()" function to all command. is there any solution on it? And, apply(matrix,1,cumsum) command is too slow to some large matrix. is there any function like rowCumSums ? thank u! -- View this message in context: http://r.789695.n4.nabble.com/to-print-system-time-always-tp4648314.html Sent from the R help mailing list archive at Nabble.com.
Here is a faster solution to your 'apply'; use 'sapply' instead:> str(x)num [1:1000000, 1:30] 0.0346 0.4551 0.66 0.8528 0.5494 ...> system.time(y <- apply(x, 1, cumsum))user system elapsed 13.24 0.61 14.02> system.time(ys <- sapply(1:col, function(a) cumsum(x[,a])))user system elapsed 1.40 0.14 1.59 On Sat, Nov 3, 2012 at 11:52 AM, mrzung <mrzung46 at gmail.com> wrote:> Hi all; > > I want to print system.time whenever I execute any command. > > It takes too much time to type "system.time()" function to all command. > > is there any solution on it? > > And, > > apply(matrix,1,cumsum) command is too slow to some large matrix. > > is there any function like rowCumSums ? > > thank u! > > > > -- > View this message in context: http://r.789695.n4.nabble.com/to-print-system-time-always-tp4648314.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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.-- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? Tell me what you want to do, not how you want to do it.
On 03.11.2012 16:52, mrzung wrote:> Hi all; > > I want to print system.time whenever I execute any command. > > It takes too much time to type "system.time()" function to all command. > > is there any solution on it?See ?Rprof on how to profile your code.> > And, > > apply(matrix,1,cumsum) command is too slow to some large matrix. > > is there any function like rowCumSums ?You had: result1 <- apply(matrix,1,cumsum) This is only "slow", if you have lots of rows. Now "think in matrices" how to to that: b <- sapply(1:ncol(matrix), function(i) c(rep(1, i), rep(0, ncol(matrix)-i) result2 <- t(x %*% b) This is roughly 10 times faster on a 1000000 x 10 matrix. Check the results: all.equal(result1, result2) Uwe Ligges> thank u! > > > > -- > View this message in context: http://r.789695.n4.nabble.com/to-print-system-time-always-tp4648314.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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. >
I use notepad++ on Windows, so it is easy to add a "hotkey" that will
surround a block of code that you want to execute with:
system.time({......code to run......})
Usually you don't want it around each statement. I use the following
function to have it print out CPU and memory usage at various
locations in my script since it allows me to see the progress and
where time might be going:
"my.stats" <-
local({
# local variables to hold the last times
# first two variables are the elasped and CPU times from the last report
Level <- 1
MaxLevel <- 30
Stack <- matrix(0, ncol=2, nrow=MaxLevel)
function(text = "stats", reset=FALSE, oper="")
{
procTime <- proc.time()[1:3] # get current metrics
if (reset){ # setup to mark timing from this point
Level <<- 1 # reset the Level
Stack[Level, ] <<- c(procTime[3], procTime[1] + procTime[2])
}
if (oper == "push"){
if (Level < MaxLevel) Level <<- Level + 1
Stack[Level, ] <<- c(procTime[3], procTime[1] + procTime[2])
}
.caller <- sys.calls()
if (length(.caller) == 1) .caller <- "Rgui"
else .caller <- as.character(.caller[[length(.caller) - 1]])[1]
cat(sprintf("%s (%d) - %s : %s <%.1f %.1f> %.1f :
%.1fMB\n",
text,
Level,
.caller,
format(Sys.time(), format="%H:%M:%S"),
procTime[1] + procTime[2] - Stack[Level, 2],
procTime[3] - Stack[Level, 1],
procTime[3],
memory.size()))
if ((oper == "pop") && (Level > 1)) Level <<-
Level - 1
else if (oper == "reset") Level <<- 1
invisible(flush.console()) # force a write to the console
}
})
It produces output like this:
> my.stats('start')
start (1) - Rgui : 14:53:16 <39.2 597822.1> 597822.1 :
1213.8MB> system.time(for(i in 1:col) ym[, i] <- cumsum(x[,i]))
user system elapsed
1.77 0.01 1.80> my.stats('done')
done (1) - Rgui : 14:53:23 <41.0 597828.6> 597828.6 : 1213.8MB
This says that between 'start' and 'done', 1.8 CPU seconds
were used
(41.0 - 39.2) which is what syste.time was reporting.
On Sat, Nov 3, 2012 at 11:52 AM, mrzung <mrzung46 at gmail.com>
wrote:> Hi all;
>
> I want to print system.time whenever I execute any command.
>
> It takes too much time to type "system.time()" function to all
command.
>
> is there any solution on it?
>
> And,
>
> apply(matrix,1,cumsum) command is too slow to some large matrix.
>
> is there any function like rowCumSums ?
>
> thank u!
>
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/to-print-system-time-always-tp4648314.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> 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.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.