[R] a question about glht function

[Peter Ehlers]

On 2011-07-26 01:13, Achim Zeileis wrote:
>
>
> 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.

Yes, but try this:

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

  f_GROUP<-factor(data_ori$GROUP)
  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

(Note that I changed data_ori$f_GROUP to data_ori$GROUP.)

Peter Ehlers

>
>>
>> Any help from you are welcome.
>>
>>
>> Many thanks!
>>
>> 	[[alternative HTML version deleted]]
>>
>> ______________________________________________
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> ______________________________________________
> R-help at r-project.org 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.