[R] Pseudo-Voigt fit

Spencer Graves spencer.graves at pdf.com
Fri Sep 2 04:17:01 CEST 2005

	  I haven't seen a reply to this question, so I will attempt a few 
remarks in spite of some confusion about what you are asking.

	  1.  The function to use for parameter estimation depends on ths 
structure of the data.  My all-around preference for many purposes is 
for "optim", but I've used "nls", "fitdistr" (in the MASS package) and 
others in different circumstances.

	  2.  If you are doing nonlinear estimation with, e.g., optim, I 
suggest you request "hessian=TRUE".  The eigenvalues of the hessian will 
tell you if it is ill conditioned.  If it is, you might consider 
reparameterizing the model.

	  3.  I try to avoid using reserved words like "c".  R can often 
determine what you want from the context, but there are exceptions.  I 
try to avoid that problem by testing a name at a command prompt before I 
use it.  If it returns, "object not found", I'm fine;  if not, I try 
something different.

	  4.  Following the posting guide! 
"http://www.R-project.org/posting-guide.html" can on average increase 
the likelihood that you will receive helpful suggestions quickly.  (I've 
learned that people rarely respond to my incoherent screams;  when they 
do, it's rarely helpful.  I've reluctantly learned that there is often 
no substutute for reading the *#@%* manual.)

	  I'd be shocked if this answered your question, but I hope it is 
helpful nonetheless.
	  spencer graves

ppancoska at notes.cc.sunysb.edu wrote:

> Hi, I am sorry for this question, but I am trying to speed up an
> application....
> I will need to fit many x-y data sets (input from text files) to
> 4-parameter Pseudo-Voigt peak function.
> Until now I used SigmaPlot macro to do it (enclosed just in case...)
> peaksign(q) = if(total(q)>q[1], 1, -1)
> xatymin(q,r) = xatymax(q,max(r)-r)
> [Parameters]
> a = if(peaksign(y)>0, max(y), min(y)) ''Auto {{previous: 60.8286}}
> b = fwhm(x,abs(y))/2 ''Auto {{previous: 0.656637}}
> c = .5 ''Auto {{previous: 6.82973e-010}}
> x0 = if(peaksign(y)>0, xatymax(x,y), xatymin(x,y)) ''Auto {{previous:
> 3.19308}}
> [Equation]
> f = a*(c*(1/(1+((x-x0)/b)^2))+(1-c)*exp(-0.5*((x-x0)/b)^2))
> fit f to y
>  (manageable for ~100), but it looks like the next project would need to
> process ~1000 member sets.
> I am not as familiar with R to find the right info (although I can use R in
> general).
> I am also nearly sure that there should be a solution to this task "out
> there" ready to be modified...
> Could you be so kind and direct me please to the right package or web-site
> with examples?
> Thank you very much
> Dr. Petr Pancoska
> Department of Pathology
> SUNY Stony Brook, NY 11794
> phone:          (631)-444-3030
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Spencer Graves, PhD
Senior Development Engineer
PDF Solutions, Inc.
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