[R] Help: lme

[Doran, Harold]

Pryseley:

You asked this question last week and received answers to that question
along with other suggestions from Doug Bates and myself. Is there some
reason the post by Andrew Robinson is not working?

Harold

> -----Original Message-----
> From: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Pryseley Assam
> Sent: Thursday, June 01, 2006 6:25 AM
> To: r-help at stat.math.ethz.ch
> Subject: [R] Help: lme
> 
> Good day R-Users,
>    
>   I have a problem accessing some values in the output from 
> the summary of an lme fit.
>    
>   
> The structure of my data is as shown below (I have attached a 
> copy of the full data).
>   
>  
>   id trials endp Z.sas       ST
>   1      1   -1         -1        42.42884
>   1      1    1         -1         48.12007
>   2      1   -1         -1        43.42878
>   2      1    1         -1         46.82817
>   3      1   -1         -1        45.56736
>   ...........................................
>   598  10  -1        1          49.59715
>   598  10   1        1          55.46324
>   599  10   -1       1          46.80873
>   599  10    1       1          53.52223
>   600  10   -1       1          48.58257
>   600  10    1       1          56.78674
>   
>  I used the following code to fit my model of interest:
>    
>   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 I 
> wish to access:
>    
>   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 through 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 you 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
>    
>    
> 
> __________________________________________________
> 
> 
>