[R] avoiding termination of nls given convergence failure

[Ravi Varadhan]

?try

For example, 

 for (i in 1:n) {
 
 try (fit <- nls(...), silent=TRUE)
  if (class(fit) != "try-error") dowhateverthatneedstobedonewiththeresults
  else fit <- NA
}


Ravi.
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Ravi Varadhan, Ph.D.

Assistant Professor, The Center on Aging and Health

Division of Geriatric Medicine and Gerontology 

Johns Hopkins University

Ph: (410) 502-2619

Fax: (410) 614-9625

Email: rvaradhan at jhmi.edu

Webpage:  http://www.jhsph.edu/agingandhealth/People/Faculty/Varadhan.html



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-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Bill Shipley
Sent: Thursday, March 12, 2009 2:13 PM
To: R-help
Subject: [R] avoiding termination of nls given convergence failure

Hello.  I have a script in which I repeatedly fit a nonlinear regression to
a series of data sets using nls and the port algorithm from within a loop.
The general structure of the loop is:

 for(i in 1:n){

 extract relevant vectors of dependent and independent variables 

 estimate starting values for Amax and Q.LCP




fit<-nls(photosynthesis~fit.Mitcherlich(irradiance,Amax,LCP,Q.LCP),data=temp
,


start=list(Amax=Astart,Q.LCP=x,LCP=33),control=list(maxiter=100,tol=5e-4),

            na.action=na.omit,trace=T,algorithm="port",lower=c(0,0,0))



}



Despite trying to estimate good starting values, the nls function
occasionally experiences problems with convergence.  When this happens the
function stops and prints an error message, thus preventing the loop from
continuing.  Is there some what of detecting the convergence problem while
preventing the nls function from stopping when this happens, so that the
loop can continue?



Bill Shipley

North American Editor, Annals of Botany

Dipartement de biologie

Universiti de Sherbrooke

Sherbrooke (Quibec) J1K 2R1

Canada

(819) 821-8000, poste 62079

(819) 821-8049 FAX



http://pages.usherbrooke.ca/jshipley/recherche/




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