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

From: <toby909_at_gmail.com>
Date: Mon, 04 Jun 2007 12:30:00 -0700

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.
>

______________________________________________
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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. Received on Mon 04 Jun 2007 - 19:38:11 GMT

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