Re: [R] peak finding

From: Andrew Robinson <A.Robinson_at_ms.unimelb.edu.au>
Date: Tue, 25 Mar 2008 15:00:54 +1100

Another approach that involves more infrastructure is to fit a smooth line to your points, compute the first derivative, and look for change in sign in the first derivative.

eg

x <- c(14,15,12,11,12,13,14,15,16,15,14,13,12,11,14,12)

smoothed.dx <- predict(smooth.spline(x), deriv=1)$y

which(c(smoothed.dx,NA) > 0 & c(NA, smoothed.dx) < 0)

My experience is that this approach sometimes requires some fine-tuning, eg in fitting the smooth.

I hope that this helps

Andrew

On Mon, Mar 24, 2008 at 11:23:57PM -0400, Research Scholar wrote:
> Hi
> Thanks for replying. I meant x[4] is the start of a peak shape and x[14] is
> the end of that peak and x[9] is the maxima of the peak.
> Thanks,
> John
>
>
>
>
> On Mon, Mar 24, 2008 at 11:09 PM, <Bill.Venables_at_csiro.au> wrote:
>
> > It's hard to see how positions 4 and 14 correspond to 'peaks', they look
> > like troughs to me. So perhaps this is what you mean:
> >
> > > x <- c(14,15,12,11,12,13,14,15,16,15,14,13,12,11,14,12)
> >
> > > y <- which(x == min(x))
> > > y
> > [1] 4 14
> >
> > as a function:
> >
> > somefunction <- function(x) which(x == min(x))
> >
> >
> > Bill Venables
> > CSIRO Laboratories
> > PO Box 120, Cleveland, 4163
> > AUSTRALIA
> > Office Phone (email preferred): +61 7 3826 7251
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> > mailto:Bill.Venables_at_csiro.au
> > http://www.cmis.csiro.au/bill.venables/
> >
> > -----Original Message-----
> > From: r-help-bounces_at_r-project.org [mailto:r-help-bounces_at_r-project.org]
> > On Behalf Of Research Scholar
> > Sent: Tuesday, 25 March 2008 12:54 PM
> > To: r-help_at_r-project.org
> > Subject: [R] peak finding
> >
> > Hi all
> > Is there a function that can find the start and end position of peaks
> > in a
> > set of numbers.
> > eg.
> > x <- c(14,15,12,11,12,13,14,15,16,15,14,13,12,11,14,12)
> > y <- somefunction(x)
> >
> > y
> > 4 14
> >
> >
> > Thanks
> > John
> >
> > [[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<http://www.r-project.org/posting-guide.html>
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> >
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
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-- 
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-6410
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
http://www.ms.unimelb.edu.au/~andrewpr
http://blogs.mbs.edu/fishing-in-the-bay/

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Received on Tue 25 Mar 2008 - 04:52:45 GMT

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