Trying to use contrast to look at differences within an lme
lme.fnl.REML <- lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID,
method = "REML")
I have three levels of Tr I'm trying to contrast among different
years (R, T97, T98), years = 1997-1999, so I'm interested in
contrasts of the interaction term.
> anova(lme.fnl.REML)
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.REML)
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
>
When I try to get the contrast I get one of two errors each time.
Trying for a paired contrast...
tst <- contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R"), b=list
(Yr=levels(Yr, Tr="T97")))
Error in gendata.default(fit = list(modelStruct = list(reStruct = list
( :
not enough factors
Trying to include the other factor to make R happy....
> tst <- contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R"),
b=list
(Yr=levels(Yr, Tr="T97")), c=list(Yr=levels(Yr, Tr="T98"))
+ )
Error in contrastCalc(fit, ...) : argument 4 matches multiple formal
arguments
Can anyone help with the syntax here?
Thanks
Ken
[[alternative HTML version deleted]]
Ken Nussear wrote:> Trying to use contrast to look at differences within an lme > > lme.fnl.REML <- lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID, > method = "REML") > > I have three levels of Tr I'm trying to contrast among different > years (R, T97, T98), years = 1997-1999, so I'm interested in > contrasts of the interaction term. > > > anova(lme.fnl.REML) > 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.REML) > 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 > > > > When I try to get the contrast I get one of two errors each time. > > Trying for a paired contrast... > > tst <- contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R"), b=list > (Yr=levels(Yr, Tr="T97"))) > Error in gendata.default(fit = list(modelStruct = list(reStruct = list > ( : > not enough factors > > Trying to include the other factor to make R happy.... > > > tst <- contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R"), b=list > (Yr=levels(Yr, Tr="T97")), c=list(Yr=levels(Yr, Tr="T98")) > + ) > Error in contrastCalc(fit, ...) : argument 4 matches multiple formal > arguments > > Can anyone help with the syntax here?I believe you need to include one or more values S at which to contrast the treatments in each of the lists. So you might try something like this: contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R", S="M"), b=list(Yr=levels(Yr), Tr="T97", S="M")) or contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R", S=levels(S)), b=list(Yr=levels(Yr), Tr="T97", S=levels(S)))> 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.-- Chuck Cleland, Ph.D. NDRI, Inc. 71 West 23rd Street, 8th floor New York, NY 10010 tel: (212) 845-4495 (Tu, Th) tel: (732) 512-0171 (M, W, F) fax: (917) 438-0894
Ken,> lme.fnl.REML <- lme(Max ~ S + Tr + Yr + Tr:Yr, random = ~1 |TID, > method = "REML") >You have three variables in the model: S, Tr and Yr.> tst <- contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R"), b=list > (Yr=levels(Yr, Tr="T97"))) > Error in gendata.default(fit = list(modelStruct = list(reStruct = list> ( : > not enough factors >I think that you need to specify a value for S in the lists for a and b. Also, I think that there is a typo: b=list(Yr=levels(Yr), Tr="T97") instead of b=list(Yr=levels(Yr, Tr="T97"))> Trying to include the other factor to make R happy.... > > > tst <- contrast(lme.fnl.REML, a=list(Yr=levels(Yr), Tr="R"), b=list > (Yr=levels(Yr, Tr="T97")), c=list(Yr=levels(Yr, Tr="T98")) > + ) > Error in contrastCalc(fit, ...) : argument 4 matches multiple formal > argumentsMax ---------------------------------------------------------------------- LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}