[R] lme to determine if there is a group effect

[Bert Gunter]

I never used the groupedData structure, precisely because I found it
confusing, but I think:

1. group is *not* a (random) grouping variable; it's a fixed effect covariate.
2. so I believe your groupedData call should be:

GD<- groupedData(value~time|SS,data=data1,outer = group)

Of course, as you did not give us your data in a convenient form, I
can't check. Please let us know if this is wrong, however, as I don't
want to mislead others down the primrose path.


Cheers,
Bert

Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Wed, Aug 24, 2016 at 3:46 PM, John Sorkin
<jsorkin at grecc.umaryland.edu> wrote:
> I apologize for sending this message again. The last time I sent it, the subject line was not correct. I have corrected the subject line.
>
> I am trying to run a repeated measures analysis of data in which each subject (identified by SS) has 3 observations at three different times (0, 3, and 6). There are two groups of subjects (identified by group). I want to know if the response differs in the two groups. I have tried to used lme. Lme tell me if there is a time effect, but does not tell me if there is a group effect. Once I get this to work I will want to know if there is a significant group*time effect. Can someone tell me how to get an estimate for group. Once I get that, I believe getting an estimate for group*time should be straight forward. The code I have tired to use follows.
> Thank you,
> John
>
>> # This is my data
>> data1
>    SS group time     value baseline
> 1   1  Cont    0  9.000000 9.000000
> 2   2  Cont    0  3.000000 3.000000
> 3   3  Cont    0  8.000000 8.000000
> 4   4  Inte    0  5.690702 5.690702
> 5   5  Inte    0  7.409493 7.409493
> 6   6  Inte    0  7.428018 7.428018
> 7   1  Cont    3 13.713148 9.000000
> 8   2  Cont    3  9.841107 3.000000
> 9   3  Cont    3 12.843236 8.000000
> 10  4  Inte    3  9.300899 5.690702
> 11  5  Inte    3 10.936389 7.409493
> 12  6  Inte    3 12.358499 7.428018
> 13  1  Cont    6 18.952390 9.000000
> 14  2  Cont    6 15.091527 3.000000
> 15  3  Cont    6 17.578812 8.000000
> 16  4  Inte    6 12.325499 5.690702
> 17  5  Inte    6 15.486513 7.409493
> 18  6  Inte    6 18.284965 7.428018
>> # Create a grouped data object. SS identifies each subject
>> # group indentifies group, intervention or control.
>> GD<- groupedData(value~time|SS/group,data=data1,FUN=mean)
>> # Fit the model.
>> fit1 <- lme(GD)
>> cat("The results give information about time, but does not say if the gruops are different\n")
> The results give information about time, but does not say if the gruops are different
>> summary(fit1)
> Linear mixed-effects model fit by REML
>  Data: GD
>        AIC      BIC    logLik
>   74.59447 81.54777 -28.29724
>
> Random effects:
>  Formula: ~time | SS
>  Structure: General positive-definite
>             StdDev    Corr
> (Intercept) 1.3875111 (Intr)
> time        0.2208046 -0.243
>
>  Formula: ~time | group %in% SS
>  Structure: General positive-definite
>             StdDev    Corr
> (Intercept) 1.3875115 (Intr)
> time        0.2208051 -0.243
> Residual    0.3800788
>
> Fixed effects: value ~ time
>                Value Std.Error DF   t-value p-value
> (Intercept) 6.747442 0.8135067 11  8.294268       0
> time        1.588653 0.1326242 11 11.978601       0
>  Correlation:
>      (Intr)
> time -0.268
>
> Standardized Within-Group Residuals:
>         Min          Q1         Med          Q3         Max
> -1.11412947 -0.44986535  0.08034174  0.34615610  1.29943887
>
> Number of Observations: 18
> Number of Groups:
>            SS group %in% SS
>             6             6
>
>
>
>>
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>
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