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Bill Shipley

2009-Mar-12 18:13 UTC

[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

Département de biologie

Université de Sherbrooke

Sherbrooke (Québec) J1K 2R1

Canada

(819) 821-8000, poste 62079

(819) 821-8049 FAX

 

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

 


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Joshua Reich

2009-Mar-12 18:18 UTC

head link

[R] avoiding termination of nls given convergence failure

Hi Bill,

You should have a look at the try() function that lets you enclose an
expression and handle failure in a way that prevents the entire execution
from halting.

Josh

On Thu, Mar 12, 2009 at 1:13 PM, Bill Shipley
<bill.shipley@usherbrooke.ca>wrote:
> 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
>
> Département de biologie
>
> Université de Sherbrooke
>
> Sherbrooke (Québec) J1K 2R1
>
> Canada
>
> (819) 821-8000, poste 62079
>
> (819) 821-8049 FAX
>
>
>
> http://pages.usherbrooke.ca/jshipley/recherche/
>
>
>
>
>        [[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-help@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
> and provide commented, minimal, self-contained, reproducible code.
>
>

-- 
Joshua Reich
646 256 4763
i2pi
simplicity . depth . scalability

	[[alternative HTML version deleted]]

Gabor Grothendieck

2009-Mar-12 18:23 UTC

head link

[R] avoiding termination of nls given convergence failure

If the goal here is to repeatedly run a particular model from
different starting values
then the nls2 package will do that for you.

On Thu, Mar 12, 2009 at 2:13 PM, Bill Shipley
<bill.shipley at usherbrooke.ca> wrote:> 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
>
> D?partement de biologie
>
> Universit? de Sherbrooke
>
> Sherbrooke (Qu?bec) J1K 2R1
>
> Canada
>
> (819) 821-8000, poste 62079
>
> (819) 821-8049 FAX
>
>
>
> http://pages.usherbrooke.ca/jshipley/recherche/
>
>
>
>
> ? ? ? ?[[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
> and provide commented, minimal, self-contained, reproducible code.
>
>

Ravi Varadhan

2009-Mar-12 18:24 UTC

head link

[R] avoiding termination of nls given convergence failure

?try

For example, 

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


Ravi.
----------------------------------------------------------------------------
-------

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



----------------------------------------------------------------------------
--------


-----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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