Hi All,
I've been searching the help archives but haven't found a workable
solution to this problem.
I'm running an lme model with the following call:
>lme.fnl <- lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID)
> anova(lme.fnl)
numDF denDF F-value p-value
(Intercept) 1 168 19255.389 <.0001
S 1 168 5.912 0.0161
Tr 2 116 15.919 <.0001
Yr 1 168 77.837 <.0001
Tr:Yr 2 168 47.584 <.0001
>summary(lme.fnl)
Linear mixed-effects model fit by REML
Data: NULL
AIC BIC logLik
580.6991 613.5399 -281.3496
Random effects:
Formula: ~1 | TID
(Intercept) Residual
StdDev: 0.3697006 0.5316062
Fixed effects: Max ~ S + Tr + Yr + Tr:Yr
Value Std.Error DF t-value p-value
(Intercept) -13.5681 113.2623 168 -0.119793 0.9048
SM 0.2187 0.0957 168 2.284605 0.0236
TrT97 1375.5897 164.0060 116 8.387434 0.0000
TrT98 2890.9462 455.3497 116 6.348848 0.0000
Yr 0.0099 0.0567 168 0.174005 0.8621
TrT97:Yr -0.6883 0.0821 168 -8.384798 0.0000
TrT98:Yr -1.4463 0.2279 168 -6.347310 0.0000
Correlation:
(Intr) SM TrT97 TrT98 Yr TT97:Y
SM 0.067
TrT97 -0.691 -0.049
TrT98 -0.248 -0.001 0.171
Yr -1.000 -0.067 0.691 0.248
TrT97:Yr 0.691 0.048 -1.000 -0.171 -0.691
TrT98:Yr 0.248 0.001 -0.171 -1.000 -0.248 0.171
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.19017911 -0.58108001 -0.04983642 0.57323031 2.39811353
Number of Observations: 291
Number of Groups: 119
I'm specifically interested in differences of in the differences
between my treatment groups (3) and Year (Yr), and importantly in the
interaction. Normally I'm used to running independent contrast
analysis to explore these differences, but I'm not sure how to
extract this information using lme. Can anyone point me in the right
direction?
Thanks
Ken
[[alternative HTML version deleted]]
Andrew Robinson
2007-Apr-30 22:48 UTC
[R] Independent contrasts from lme with interactions
Ken, estimable in the gmodels package will help you. Cheers Andrew On Mon, Apr 30, 2007 at 03:11:57PM -0700, Ken Nussear wrote:> Hi All, > > I've been searching the help archives but haven't found a workable > solution to this problem. > > I'm running an lme model with the following call: > > >lme.fnl <- lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID) > > anova(lme.fnl) > numDF denDF F-value p-value > (Intercept) 1 168 19255.389 <.0001 > S 1 168 5.912 0.0161 > Tr 2 116 15.919 <.0001 > Yr 1 168 77.837 <.0001 > Tr:Yr 2 168 47.584 <.0001 > > > >summary(lme.fnl) > Linear mixed-effects model fit by REML > Data: NULL > AIC BIC logLik > 580.6991 613.5399 -281.3496 > > Random effects: > Formula: ~1 | TID > (Intercept) Residual > StdDev: 0.3697006 0.5316062 > > Fixed effects: Max ~ S + Tr + Yr + Tr:Yr > Value Std.Error DF t-value p-value > (Intercept) -13.5681 113.2623 168 -0.119793 0.9048 > SM 0.2187 0.0957 168 2.284605 0.0236 > TrT97 1375.5897 164.0060 116 8.387434 0.0000 > TrT98 2890.9462 455.3497 116 6.348848 0.0000 > Yr 0.0099 0.0567 168 0.174005 0.8621 > TrT97:Yr -0.6883 0.0821 168 -8.384798 0.0000 > TrT98:Yr -1.4463 0.2279 168 -6.347310 0.0000 > Correlation: > (Intr) SM TrT97 TrT98 Yr TT97:Y > SM 0.067 > TrT97 -0.691 -0.049 > TrT98 -0.248 -0.001 0.171 > Yr -1.000 -0.067 0.691 0.248 > TrT97:Yr 0.691 0.048 -1.000 -0.171 -0.691 > TrT98:Yr 0.248 0.001 -0.171 -1.000 -0.248 0.171 > > Standardized Within-Group Residuals: > Min Q1 Med Q3 Max > -2.19017911 -0.58108001 -0.04983642 0.57323031 2.39811353 > > Number of Observations: 291 > Number of Groups: 119 > > > > I'm specifically interested in differences of in the differences > between my treatment groups (3) and Year (Yr), and importantly in the > interaction. Normally I'm used to running independent contrast > analysis to explore these differences, but I'm not sure how to > extract this information using lme. Can anyone point me in the right > direction? > > Thanks > > Ken > > > > > > > [[alternative HTML version deleted]] > > ______________________________________________ > 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.-- Andrew Robinson Department of Mathematics and Statistics Tel: +61-3-8344-9763 University of Melbourne, VIC 3010 Australia Fax: +61-3-8344-4599 http://www.ms.unimelb.edu.au/~andrewpr http://blogs.mbs.edu/fishing-in-the-bay/
Ken,
Take a look at the just released contrast package.
Max
-----Original Message-----
From: r-help-bounces at stat.math.ethz.ch
[mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Ken Nussear
Sent: Monday, April 30, 2007 6:12 PM
To: r-help at stat.math.ethz.ch
Subject: [R] Independent contrasts from lme with interactions
Hi All,
I've been searching the help archives but haven't found a workable
solution to this problem.
I'm running an lme model with the following call:
>lme.fnl <- lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID)
> anova(lme.fnl)
numDF denDF F-value p-value
(Intercept) 1 168 19255.389 <.0001
S 1 168 5.912 0.0161
Tr 2 116 15.919 <.0001
Yr 1 168 77.837 <.0001
Tr:Yr 2 168 47.584 <.0001
>summary(lme.fnl)
Linear mixed-effects model fit by REML
Data: NULL
AIC BIC logLik
580.6991 613.5399 -281.3496
Random effects:
Formula: ~1 | TID
(Intercept) Residual
StdDev: 0.3697006 0.5316062
Fixed effects: Max ~ S + Tr + Yr + Tr:Yr
Value Std.Error DF t-value p-value
(Intercept) -13.5681 113.2623 168 -0.119793 0.9048
SM 0.2187 0.0957 168 2.284605 0.0236
TrT97 1375.5897 164.0060 116 8.387434 0.0000
TrT98 2890.9462 455.3497 116 6.348848 0.0000
Yr 0.0099 0.0567 168 0.174005 0.8621
TrT97:Yr -0.6883 0.0821 168 -8.384798 0.0000
TrT98:Yr -1.4463 0.2279 168 -6.347310 0.0000
Correlation:
(Intr) SM TrT97 TrT98 Yr TT97:Y
SM 0.067
TrT97 -0.691 -0.049
TrT98 -0.248 -0.001 0.171
Yr -1.000 -0.067 0.691 0.248
TrT97:Yr 0.691 0.048 -1.000 -0.171 -0.691
TrT98:Yr 0.248 0.001 -0.171 -1.000 -0.248 0.171
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-2.19017911 -0.58108001 -0.04983642 0.57323031 2.39811353
Number of Observations: 291
Number of Groups: 119
I'm specifically interested in differences of in the differences
between my treatment groups (3) and Year (Yr), and importantly in the
interaction. Normally I'm used to running independent contrast
analysis to explore these differences, but I'm not sure how to
extract this information using lme. Can anyone point me in the right
direction?
Thanks
Ken
[[alternative HTML version deleted]]
______________________________________________
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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