[R-sig-finance] RE: [R] How to make R faster?
andy_liaw at merck.com
Wed Jan 26 00:06:58 CET 2005
A few things to add to what Spencer said:
- Please give more info about your setup, as the posting guide asks you to
(e.g., R version, OS [which Linux distro and which release?], hardware).
These things matter! As an example, the time it takes to start an R process
was dramatically reduced since R-2.0.0. If you are using older version, you
need to upgrade.
- See the example section of ?Startup, which has an example of how to
specify packages to be loaded at startup.
- There's a section on profiling R code in the `Writing R Extensions'
manual, that may help you pinpoint the bottleneck.
- Sometimes re-thinking the organization of the computation or algorithm can
make a huge difference. I remember reading in an old computing book the
staggering difference between FFT and doing the computation the naïve way.
> From: Spencer Graves
> My standard algorithm for improving speed is as follows:
> 1. Identify what takes the most time.
> 2. Try to find ways in R to speed it up, e.g.,
> converting loops
> to vector operations. Many tasks in R can be performed in a
> variety of
> different ways to get the same result but with different time.
> 3. If that fails, convert the most time consuming part into
> compiled code and link to it.
> Use "system.time" to time a single expression and
> "proc.time" to
> store the time at multiple places in your code; precede any
> test with
> garbage collection (gc) to reduce variations in the answers.
> An "R site search" (www.r-project.org -> Search -> "R site
> search") for "timing R" produced 126 hits, the second of which gave
> "system.time"; you might skim the rest for other ideas. A similar
> search for "compute speed" produced 64 hits, some of which will
> doubtless interest you if you haven't already read them.
> For more help on this, please be more specific, e.g., following
> the posting guide! "http://www.R-project.org/posting-guide.html".
> hope this helps. spencer graves
> ebashi wrote:
> >Dear R users;
> >I am using R for a project. I have some PHP forms that
> >pass parameters to R for calculations, and publish the
> >result in HTML format by CGIwithR. I'm using a Linux
> >machine and every things work perfectly. However, it
> >is too slow, it takes 5 to 10 seconds to run, and
> >even if I start R from the Shell it takes the same
> >amount of time, which is probably due to installing
> >packages. My first question is that how can i make R
> >run faster? and second if I am supposed to reduce the
> >packages which are being loaded at initiation of R,
> >how can I limit it to only the packages that i want?
> >and third how can i make R not to get open each time,
> >and let it sit on the server so that, when i pass
> >something to it , i get result faster?
> >R-help at stat.math.ethz.ch mailing list
> >PLEASE do read the posting guide!
> R-help at stat.math.ethz.ch mailing list
> PLEASE do read the posting guide!
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