# Re: [R] peak finding

From: stephen sefick <ssefick_at_gmail.com>
Date: Tue, 25 Mar 2008 10:35:56 -0400

I am not sure how to implement this in R, but beam forming, used in geophysics, sounds like an alternative. We are currently looking at this with the help of a matlab guru to look at the shift in the dissolved oxygen peaks as you go down river. This assumes that you have an array of reading sepperated by space. Schumway's book mentions this.

On Tue, Mar 25, 2008 at 11:25 AM, Robert A LaBudde <ral_at_lcfltd.com> wrote:
> At 10:48 PM 3/24/2008, Chistos wrote:
> >John,
> >
> >There is a peak finding algorithm attributed to Prof. Ripley in the R-help
> >archive. It has a span parameter which might give you something close to
> >what you seem to be looking for.
> >
> >http://finzi.psych.upenn.edu/R/Rhelp02a/archive/33097.html
> >
> >-Christos
>
> Finding peaks and valleys has several issues:
>
> 1. Impact of noise.
> 2. Mathematical smoothness of the underlying signal.
> 3. Boundary conditions at the beginning and end of the data series.
> 4. Bias from smoothing.
>
> If the noise is not too bad, I'd try fitting a smoothing spline, and
> then use the null derivative points to punctuate the extrema.
>
> If the noise is severe, you probably will need some domain knowledge,
> and will end up with perhaps locally weighted regression, followed by
> extrema search.
>
> For cases where the noise is trivial, the following short function
> might be useful in picking off peaks (and symmetrically modified, valleys):
>
> #findpeaks()
> #find peaks in (x,y) curve
> findpeaks<- function(x, y) {
> nx<- length(x)
> ny<- length(y)
> if (nx != ny) {
> print ('>> findpeaks01: x and y must be same length!')
> stop
> }
> ipeak<- NULL
> xpeak<- NULL
> ypeak<- NULL
> yprv<- y[1]
> for (i in 1:ny) {
> ynext<- ifelse(i==ny,y[ny],y[i+1])
> if(yprv < y[i] & y[i] > ynext) { #found local peak
> ipeak<- c(ipeak,i)
> xpeak<- c(xpeak,x[i])
> ypeak<- c(ypeak,y[i])
> }
> yprv<- y[i]
> }
> return(data.frame(ipeak,x=xpeak,y=ypeak))
> }
>
> Trivial though it may be, it actually works quite well for its
> intended purpose.
>
> ================================================================
> Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: ral_at_lcfltd.com
> Least Cost Formulations, Ltd. URL: http://lcfltd.com/
> 824 Timberlake Drive Tel: 757-467-0954
> Virginia Beach, VA 23464-3239 Fax: 757-467-2947
>
> "Vere scire est per causas scire"
>
>
>
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> and provide commented, minimal, self-contained, reproducible code.
>

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