[R] peak finding

[stephen sefick]

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()
>  #Copyright 2007 by Robert A LaBudde, all rights reserved
>  #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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>



-- 
Let's not spend our time and resources thinking about things that are
so little or so large that all they really do for us is puff us up and
make us feel like gods. We are mammals, and have not exhausted the
annoying little problems of being mammals.

	-K. Mullis