[R] Issue with 95% CI using MASS{confint}
Duncan Murdoch
murdoch.duncan at gmail.com
Wed May 27 22:28:48 CEST 2015
On 27/05/2015 4:08 PM, Jennifer Sweatman wrote:
> I am trying to run a nonlinear model looking at seasonal abundance of
> plants with the following limitations:
>
>
>
> fit.nls.s<-nls(S_a~beta+m*time+alpha*sin(w*time+phi),
>
> data= xy,
>
> start=list(beta=2.1, m=0, alpha=2, phi = 1, w = 1),
>
> upper=list(beta="inf", m="inf", alpha="inf", phi = 2*pi, w =
> "inf"),
>
> lower=list(beta="-inf", m="-inf", alpha=0, phi = 0, w =
> 0.0000001),
>
> algorithm="port")
>
>
>
> I want to know the 95% confidence intervals for all of my model
> parameters. I have been using confint from the MASS package but I’m
> getting some NA values. See output below:
>
> confint(fit.nls.s)
>
> 2.5% 97.5%
>
> beta 1.68170858 2.5635734
>
> m 0.02810172 0.0710163
>
> alpha NA 0.6755750
>
> phi NA NA
>
> w NA 1.0275199
>
> The parameters I most need 95% CIs for are alpha and w (when alpha is
> significant), but I consistently get NA for the lower limit of both. I
> have changed my Upper/Lower limits for alpha, phi, and w to +/- infinity,
> but my CIs still don’t include complete intervals. Any suggestions as to
> what is going on here?
Probably the profiling failed. You could look at
plot(profile(fit.nls.s)) to see an indication of what's going on. If
your tau values don't exceed 2 on one side of the estimate, you can't
get a confidence limit on that side. Your data may not rule out any phi
values, or may not rule out a lower limit on alpha or w.
Duncan Murdoch
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