[R] how to specify starting values in varIdent() of lme()

[toby909 at gmail.com]

Douglas Bates wrote:
> On 6/1/07, toby909 at gmail.com <toby909 at gmail.com> wrote:
> 
>>I was reading the help but just did not get how to specify starting values for
>>varIdent() of the lme() function, although I managed to do it for corSymm().
> 
> 
>>Do I specify the values just as they are printed out in an output, like c(1,
>>1.3473, 1.0195). Or do I need to take the residual and multiply it with these
>>like c(0.2235, 0.2235*1.3473, 0.2235*1.0195)
>>or any other form that I dont know of?
> 
> 
> Strangely enough you specify it in the form described in
> 
> ?varIdent
> 
> Look at the description of the value argument.
> 

Now the list knows how to find the help of the varIdent function.

For my situation, I think R does not like expressions like 2=1.94..., "2" 
supposed to serve as label....

summary(m3 <- lme(score~timef-1, dtaa, ~timef-1|orgid, corSymm(svc,~1|orgid/id), 
varIdent(c(1.94,1.05),~1|time),,,na.omit,lmeControl(1000,1000,,,2000,,,1,1)))

Error in varIdent(c(1.94, 1.05), ~1 | time) :
         Initial values must have group names in varIdent


summary(m3 <- lme(score~timef-1, dtaa, ~timef-1|orgid, corSymm(svc,~1|orgid/id), 
varIdent(c(2=1.94,3=1.05),~1|time),,,na.omit,lmeControl(1000,1000,,,2000,,,1,1)))

Error: syntax error in "summary(m3 <- lme(score~timef-1, dtaa, ~timef-1|orgid, 
corSymm(svc,~1|orgid/id), varIdent(c(2="



Without starting values:

Linear mixed-effects model fit by REML
  Data: dtaa
         AIC      BIC   logLik
   -697.0142 -601.366 363.5071

Random effects:
  Formula: ~timef - 1 | orgid
  Structure: General positive-definite, Log-Cholesky parametrization
          StdDev     Corr
timef1   0.02974621 timef1 timef2
timef2   0.05790348 0.923
timef3   0.03745570 0.921  0.999
Residual 0.22385809

Correlation Structure: General
  Formula: ~1 | orgid/id
  Parameter estimate(s):
  Correlation:
   1     2
2 0.503
3 0.578 0.475
Variance function:
  Structure: Different standard deviations per stratum
  Formula: ~1 | time
  Parameter estimates:
        1        2        3
1.000000 1.411556 1.002088
Fixed effects: score ~ timef - 1
             Value   Std.Error   DF   t-value p-value
timef1 -0.3813594 0.006800189 4253 -56.08070       0
timef2 -0.2551952 0.010747688 4253 -23.74419       0
timef3 -0.3939206 0.007296932 4253 -53.98441       0
  Correlation:
        timef1 timef2
timef2 0.625
timef3 0.675  0.666

Standardized Within-Group Residuals:
        Min         Q1        Med         Q3        Max
-1.1898841 -0.5756576 -0.4576534  0.2810892  4.1498533

Number of Observations: 4347
Number of Groups: 92






> 
>>Thanks Toby
>>
>>
>>
>>
>>
>>Linear mixed-effects model fit by REML
>>  Data: dtaa
>>        AIC       BIC   logLik
>>   -788.783 -692.5656 409.3915
>>
>>Random effects:
>>  Formula: ~timef - 1 | orgid
>>  Structure: General positive-definite, Log-Cholesky parametrization
>>          StdDev     Corr
>>timef1   0.04398482 timef1 timef2
>>timef2   0.07910354 1
>>timef3   0.03648411 1      1
>>Residual 0.22350583
>>
>>Correlation Structure: General
>>  Formula: ~1 | orgid/id
>>  Parameter estimate(s):
>>  Correlation:
>>   1     2
>>2 0.487
>>3 0.597 0.440
>>Variance function:
>>  Structure: Different standard deviations per stratum
>>  Formula: ~1 | time
>>  Parameter estimates:
>>        1        2        3
>>1.000000 1.347341 1.019529
>>Fixed effects: score ~ timef - 1
>>             Value   Std.Error   DF   t-value p-value
>>timef1 -0.3846847 0.007627811 4421 -50.43186       0
>>timef2 -0.2727646 0.012012786 4421 -22.70619       0
>>timef3 -0.3961244 0.007180147 4421 -55.16939       0
>>  Correlation:
>>        timef1 timef2
>>timef2 0.735
>>timef3 0.746  0.670
>>
>>Standardized Within-Group Residuals:
>>        Min         Q1        Med         Q3        Max
>>-1.4659548 -0.5982929 -0.4096429  0.3101507  4.0911728
>>
>>Number of Observations: 4515
>>Number of Groups: 92
>>
>>______________________________________________
>>R-help at stat.math.ethz.ch mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>>and provide commented, minimal, self-contained, reproducible code.
>>
> 
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>