Re: [R] Query: lme output

From: Andrew Robinson <A.Robinson_at_ms.unimelb.edu.au>
Date: Tue 30 May 2006 - 21:25:26 EST

You can try dissecting the output of

VarCorr(ggg)

but, once again, I can't guarantee that it's what you want because we can't fit your model, and you have not sent us a simple, reproducible example.

Andrew

On Tue, May 30, 2006 at 03:37:19AM -0700, Pryseley Assam wrote:
> Dear R-Users
>
> I have a problem accessing some values in the output from the summary of an lme fit.
>
> I fit the model below:
>
> ggg <- lme (ST~ -1 + as.factor(endp):Z.sas + as.factor(endp), data=dat4a,
> random=~-1 + as.factor(endp) + as.factor(endp):Z.sas|as.factor(trials),
> correlation = corSymm(form=~1|as.factor(trials)/as.factor(id)), weights=varIdent(form=~1|endp))
>
> hh <- summary(ggg)
> hh
>
> Below is the following part of the output of interest:
>
> Correlation Structure: General
> Formula: ~1 | as.factor(trials)/as.factor(id)
> Parameter estimate(s):
> Correlation:
> 1
> 2 0.785
> Variance function:
> Structure: Different standard deviations per stratum
> Formula: ~1 | endp
> Parameter estimates:
> -1 1
> 1.0000000 0.9692405
>
> I wish to access the value of the correlation (0.785) and the vector of the variance function estimates (1,0.969). I know these can be done throught the intervals function, but sometimes when the estimated Hessian matrix is not positive definite or something like that (i am not quite sure), the intervals function delivers an error message.
>
> Thus, i will like to ask if there is another way to access these values. I tried using the following code:
>
> hh$modelStruct$corStruct[1]
> hh$modelStruct$varStruct[1]
>
> Rather the output was:
>
> > hh$modelStruct$corStruct[1]
> [1] -1.308580
> > hh$modelStruct$varStruct[1]
> [1] -0.03124255
>
> I presume there is a way to calculate the correlation and variance function coefficients using these values.
>
> Could someone tell me how to access those values (without using the intervals function) or better still how to calculate the values from the last output values.
>
> Kind regards
> Pryseley
>
>
>
>
> ---------------------------------
>
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-- 
Andrew Robinson  
Department of Mathematics and Statistics            Tel: +61-3-8344-9763
University of Melbourne, VIC 3010 Australia         Fax: +61-3-8344-4599
Email: a.robinson_at_ms.unimelb.edu.au         http://www.ms.unimelb.edu.au

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Received on Tue May 30 21:29:58 2006

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