[R] nls.control()

Ranney, Steven
Wed, 03 Sep 2008 19:07:59 -0000

>>
>> and I'm trying to fit a simple Von Bertalanffy growth curve with
program:
>>
>> VonB=nls(TL~Linf*(1-exp(-k*(age-t0))), data=box5.4,
>>     start=list(Linf=1000, k=0.1, t0=0.1), trace=TRUE)
>>...
>> Everything works as it should right up until the confint(VonB)
statement.
>>When I ask
>> for the confidence intervals, R goes through the process then stops and
gives
>>
>> "Error in prof$getProfile() :
>>   step factor 0.000488281 reduced below 'minFactor' of
0.000976562".
>>
>> However, when I use nls.control=(minFactor=0.000001) OR
>> nls.control(minFactor=0.000001),

>In my experience, it never helps to reduce the control factors once this
error
>comes up; it is a problem that by profiling you hit a boundary where
>convergence problems are serious.
>
>Suggestions: first, try with some smaller p-value, e.g. 0.8 or 0.7 instead
of
>the default of 0.95; profiling will stay in safer region.
>
>It may be possible to use algorithm "port" in combination with
lower/upper, but
>I am not sure if this is honoured by profile.
>
>Dieter

I adjusted the nls() statement by adding the algorithm="port"
statement.  Without changing the
confint(vonB) request or including a lower/upper statement (I'm still not
sure what they do),
I was given

         2.5%     97.5%
Linf 462.8386        NA
k          NA 0.6944959
t0         NA 0.7973458

It's not until I get down to confint(VonB, level=.31) that I get confidence
interval values for
all of the parameter estimates in the model.  Any thoughts or ideas as to why?


Steven H. Ranney

Graduate Research Assistant (Ph.D)
USGS Montana Cooperative Fishery Research Unit
Montana State University
P.O. Box 173460
Bozeman, MT 59717-3460

phone: (406) 994-6643
fax: (406) 994-7479


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