[R] a question about glht function

[Achim Zeileis]

On Tue, 26 Jul 2011, Lao Meng wrote:

> Hi all:
> There's a question about glht function.
>
> My data:data_ori,which inclue CD4, GROUP,time.
>
>
> f_GROUP<-factor(data_ori$GROUP)
>
> f_GROUP is a factor of 3 levels(0,1,2,3)
>
>
> result <- lme(sqrt(CD4) ~ f_GROUP*time ,random = ~time|ID,data=data_ori)
>
> glht(result, linfct = mcp(f_GROUP="Tukey") )
> Error in `[.data.frame`(mf, nhypo[checknm]) : undefined columns selected
>
>
> I can't find out the reason for Error.

We can't either based on the information you provide. If I set up random 
data based on your specification, then everything works fine for me in R 
2.13.1 with nlme 3.1-102 and multcomp 1.2-7.

## random data
set.seed(0)
data_ori <- data.frame(
   CD4 = rnorm(100)^2,
   time = runif(100),
   f_GROUP = factor(sample(0:3, 100, replace = TRUE)),
   ID = factor(rep(1:10, each = 10))
)

## model fitting
library("nlme")
result <- lme(sqrt(CD4) ~ f_GROUP * time, random = ~ time | ID,
   data = data_ori)

## multiple comparisons
library("multcomp")
glht(result, linfct = mcp(f_GROUP = "Tukey"))

Everything works ok. glht() just issues an appropriate warning that Tukey 
contrasts of f_GROUP might not be what you want in the presence of 
interactions.

>
> Any help from you are welcome.
>
>
> Many thanks!
>
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