[R] Package contrast error

From: Ken Nussear <knussear_at_usgs.gov>
Date: Thu, 03 May 2007 10:23:09 -0700


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

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