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_c...@usgs.gov
tel: 970 226-9326
From:
"John Sorkin" <jsor...@grecc.umaryland.edu>
To:
<r-help@r-project.org>, "Kenneth Frost" <kfr...@wisc.edu>
Date:
12/04/2012 09:10 AM
Subject:
Re: [R] lme: subject-specific slopes.
Sent by:
r-help-boun...@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 <kfr...@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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--
Kenneth Frost
Graduate Research Assistant - Dept. of Plant Pathology
University of Wisconsin - Madison
Lab: (608) 262-9914
Mobile: (608) 556-9637
kfr...@wisc.edu
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