On Tue, 26 Jul 2011, Peter Ehlers wrote:
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.)
Thanks for pointing this out. So the workaround seems to be to simply put
f_GROUP into data_ori.
The source of the problem is that because "nlme" does not provide a
model.frame() method for "lme" objects, "multcomp" brings its own
unexported multcomp:::model.frame.lme() which simply extracts $data.
However, this is not always the model.frame - as in this example. It would
probably be safer to modify the $call and reevaluate the model frame as
lme() itself does.
Peter Ehlers
Any help from you are welcome.
Many thanks!
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and provide commented, minimal, self-contained, reproducible code.
