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lme for between-within anova

1 message · William Simpson

Original
William Simpson
# 
I have the following between-within anova:
aovn1 <- aov(amplitude ~ stereo*site*stimulus +
Error(subject/(site*stimulus)), stereon1)

This works fine. BUT I need to do Tukey HSD multiple comparisons, and
the aov() approach won't work. So I am trying the method posted on
r-help:
lmen1 <- lme(amplitude ~ stereo*site*stimulus, random =
~1|subject/(site*stimulus), stereon1)

This doesn't work:
Error in getGroups.data.frame(dataMix, groups) :
        Invalid formula for groups

Please tell me what to do to get the lme() fit to work.

After I get lmen1, I will do:
anova(lmen1)

summary(lmen1)
summary(glht(lmen1, linfct=mcp(V="Tukey")))

Please tell me if that sounds right.

Thanks very much for any help!

Bill

============= This is the example I am following (with modifications
for my expt design)
You want to use lme() in package nlme, then glht() in the multcomp
package.  This will give you multiplicity adjusted p-values and
confidence intervals.

## Example
require(MASS)         ## for oats data set
require(nlme)         ## for lme()
require(multcomp)  ## for multiple comparison stuff

Aov.mod <- aov(Y ~ N + V + Error(B/V), data = oats)
Lme.mod <- lme(Y ~ N + V, random = ~1 | B/V, data = oats)

summary(Aov.mod)
anova(Lme.mod)

summary(Lme.mod)
summary(glht(Lme.mod, linfct=mcp(V="Tukey")))