Hi Cahn
Have you tried the "verbose" argument to gnls?
That will make gnls() print out information on each iteration before it
throws the error.
Steve McKinney
________________________________________
From: Chaehyung Ahn [cahn88 at gmail.com]
Sent: February 4, 2010 12:47 PM
To: Steven McKinney
Cc: r-sig-mixed-models at r-project.org
Subject: Re: [R-sig-ME] nonlinear models with warnOnly
Hi Steven,
Thank you for your reply.
But I need to this to prevent the error from stopping the iteration. I need to count how many time the model fits without error.
cahn
On Thu, Feb 4, 2010 at 3:29 PM, Steven McKinney <smckinney at bccrc.ca<mailto:smckinney at bccrc.ca>> wrote:
> -----Original Message-----
> From: r-sig-mixed-models-bounces at r-project.org<mailto:r-sig-mixed-models-bounces at r-project.org> [mailto:r-sig-mixed-<mailto:r-sig-mixed->
> models-bounces at r-project.org<mailto:models-bounces at r-project.org>] On Behalf Of Chaehyung Ahn
> Sent: Thursday, February 04, 2010 9:36 AM
> To: r-sig-mixed-models at r-project.org<mailto:r-sig-mixed-models at r-project.org>
> Subject: [R-sig-ME] nonlinear models with warnOnly
>
> Dear list,
>
> I need to make nls() or gnls() function to return something like "NA"
> when
> it fails to fit. I found I can use "warnOnly", but I cannot make it
> work.
>
> In the following program. I intentionally make it fail by making very
> wrong
> initial values, but the "out" is empty. What is wrong with my approach?
>
> Many thanks in advance!
>
> library(nlme)
> out<- gnls(conc~SSbiexp(time,A,lalpha,B,lbeta),
> start=list(A=-1,lalpha=2,B=20,lbeta=4),
> weights=varPower(fixed=1),control=list(warnOnly=TRUE),
> data=Indometh,subset=Subject==1)
Have you explored using the "try()" or "tryCatch()"
strategies?
out <- try(gnls(conc~SSbiexp(time,A,lalpha,B,lbeta),
start=list(A=-1,lalpha=2,B=20,lbeta=4),
weights=varPower(fixed=1),
data=Indometh,subset=Subject==1))
Then if the fit fails, variable "out" will have class "try-error"
so you can check the class of out and decide what to do etc.
(I tried your example in R 2.10.1 on a Mac and R 2.9.2 on a PC and
get an error that I haven't been able to track down yet.
> require("nlme")
Loading required package: nlme
> out<- gnls(conc~SSbiexp(time,A,lalpha,B,lbeta),
+ start=list(A=-1,lalpha=2,B=20,lbeta=4),
+ weights=varPower(fixed=1),control=list(warnOnly=TRUE),
+ data=Indometh,subset=Subject==1)
Error: object 'convIter' not found
>
>
> out<- try(gnls(conc~SSbiexp(time,A,lalpha,B,lbeta),
+ start=list(A=-1,lalpha=2,B=20,lbeta=4),
+ weights=varPower(fixed=1),
+ data=Indometh,subset=Subject==1))
Error : object 'convIter' not found
>
)
Best
Steve McKinney
>
>
>
>
> --
> Chaehyung Ahn, Ph.D.
> 4033 Remington Oaks Circle
> Cary, NC 27519
> Daum Cafe: http://cafe.daum.net/biometrika
> Blog: http://cahn88.blogspot.com/
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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Steven McKinney, Ph.D.
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney -at- bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
--
Chaehyung Ahn, Ph.D.
4033 Remington Oaks Circle
Cary, NC 27519
Daum Cafe: http://cafe.daum.net/biometrika
Blog: http://cahn88.blogspot.com/