[R] Package contrast error

[Chuck Cleland]

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]]
> 
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-- 
Chuck Cleland, Ph.D.
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