John:  I think you want the output from coef(fitRIRT).   The 
ranef(fitRIRT) will give you the subject specific random effect deviations 
from the fixed effects means.  The coef(fitRIRT) will give you the 
combination of the fixed effect means with the subject specific random 
effect deviations and, thus, in the scale you are expecting.

Brian

Brian S. Cade, PhD

U. S. Geological Survey
Fort Collins Science Center
2150 Centre Ave., Bldg. C
Fort Collins, CO  80526-8818

email:  brian_cade@usgs.gov
tel:  970 226-9326



From:
"John Sorkin" <jsorkin@grecc.umaryland.edu>
To:
<r-help@r-project.org>, "Kenneth Frost" <kfrost@wisc.edu>
Date:
12/04/2012 09:10 AM
Subject:
Re: [R] lme: subject-specific slopes.
Sent by:
r-help-bounces@r-project.org



Ken,
Thank you for your help. ranef(fitRIRT) does not give me what I expect. 
The subject-specific slopes, and subject-specific intercepts are not 
anywhere close to what I would expect them to be; the mean of the 
subject-specfic values should be close to those reported by 
summary(fitRIRT) and they are not. As you will see by examining the 
material below, the subject-specific slopes are off by many order of 
magnitude. The intercepts are also far from the value reported in 
summary(fitRIRT). Do you have any thoughts?
Thanks,
John
 
> fitRIRT <- lme(echogen~time,random=~ 
1+time|subject,data=repeatdata,na.action=na.omit)> summary(fitRIRT)Linear 
mixed-effects model fit by REML
 Data: repeatdata 
      AIC      BIC    logLik
  495.097 507.2491 -241.5485

Random effects:
 Formula: ~1 + time | subject
 Structure: General positive-definite, Log-Cholesky parametrization
            StdDev       Corr 
(Intercept) 1.917511e+01 (Intr)
time        2.032276e-04 0 
Residual    1.044601e+01 

Fixed effects: echogen ~ time 
               Value Std.Error DF   t-value p-value
(Intercept) 64.54864  4.258235 32 15.158543  0.0000
time         0.35795  0.227080 32  1.576307  0.1248
 Correlation: 
     (Intr)
time -0.242

Standardized Within-Group Residuals:
        Min          Q1         Med          Q3         Max 
-1.61362755 -0.52710871  0.02948008  0.41793322  1.77340082 

Number of Observations: 58
Number of Groups: 25 > ranef(fitRIRT)   (Intercept)          time
1    -3.278112  2.221016e-09
2   -35.400618  4.314995e-08
3    11.493110 -6.797543e-09
4   -16.209586 -7.070834e-08
5     3.585227 -2.389705e-08
6     1.614320 -1.967700e-09
7     8.346905  5.827094e-08
8    30.917812 -3.768584e-08
9    -0.394101 -9.158251e-09
10    4.437509 -4.057971e-08
11   31.956597 -2.126275e-08
12   41.567402 -4.853942e-08
13  -10.723993  1.307152e-08
14   -4.554837  5.551908e-09
15   -4.554501  4.815086e-08
16   13.296985 -3.743967e-08
17   -8.255439  1.733238e-08
18  -21.317239  2.203885e-08
19  -13.480159  2.194016e-08
20  -13.044766  2.269168e-08
21   11.639198 -1.418706e-08
22  -27.457388 -1.154099e-08
23    2.194001 -5.509119e-09
24   -3.992646  7.682188e-08
25    1.614320 -1.967700e-09
 
 


 
 
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
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)>>> 
Kenneth Frost <kfrost@wisc.edu> 12/4/2012 10:44 AM >>>
I think this might be close to what you want. ranef(fitRIRT)

On 12/04/12, John Sorkin  wrote:
> I am running a random intercept random slope regression:
> 
> fitRIRT <- lme(echogen~time,random=~ 
1+time|subject,data=repeatdata,na.action=na.omit)
> summary(fitRIRT)
> 
> I would like to get the subject-specific slopes, i.e. the slope that the 
model computes for each subject. If I have 10-subjects I should have 
10-slopes. I don't see the slope when I look at the items listed in 
> names(summary(fitRIRT)
> nor when I look at the items listed in 
> names(fitRIRT)
> 
> Thanks 
> John
> 
> 
> 
> 
> 
> 
> John David Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology
> 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)
> Confidentiality Statement:
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> 
> 
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--
Kenneth Frost
Graduate Research Assistant - Dept. of Plant Pathology
University of Wisconsin - Madison
Lab: (608) 262-9914
Mobile: (608) 556-9637
kfrost@wisc.edu


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