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lme to determine if there is a group effect

3 messages · John Sorkin, Bert Gunter, Thierry Onkelinx

#
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
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
The results give information about time, but does not say if the gruops are different
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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#
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:
#
Dear John,

lme() not longer requires a GroupedData object. You can directly use a
data.frame which is easier to specify different models.

You want something like

lme(value ~ time * group, random = ~ time|SS, data = data1)

PS Note that the R-Sig-mixedmodels is more suited for this kind of question.

Best regards,

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2016-08-25 0:46 GMT+02:00 John Sorkin <jsorkin at grecc.umaryland.edu>: