[R] glht: Problem with symbolic contrast for factors with number-levels

2011-03-04 Thread Ulrich Halekoh 
Using a factor with  'number'  levels the straightforward 
symbolic formulation of a contrast in 'glht' of
the 'multcomp' package fails.

How can this problem be resolved without having to redefine the factor levels?

Example:
#A is a factor with  'number' levels
#B similar factor with 'letter' levels
dat-data.frame(y=1:4,A=factor(c(1,1,2,2)),
  B=factor(c('e','e','f','f')) )
motA-lm(y~A,data=dat)
motB-lm(y~B,data=dat)
library(multcomp)
#does not work
glht(motA,linfct=mcp(A=c(2 - 1 = 0 )))

#the error message is
# Error in coefs(ex[[3]]) : 
#   cannot interpret expression '1' as linear function

#works
glht(motB,linfct=mcp(B=c(f - e  = 0)))

regards

Ulrich Halekoh
Aarhus University
e-mail: ulrich.hale...@agrsci.dk

I use R.2.12.2, package version of multcomp : 1.2-5

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Re: [R] glht: Problem with symbolic contrast for factors withnumber-levels

2011-03-04 Thread William Dunlap 

 -Original Message-
 From: r-help-boun...@r-project.org 
 [mailto:r-help-boun...@r-project.org] On Behalf Of Ulrich Halekoh
 Sent: Friday, March 04, 2011 11:04 AM
 To: r-help@r-project.org
 Subject: [R] glht: Problem with symbolic contrast for factors 
 withnumber-levels
 
 Using a factor with  'number'  levels the straightforward 
 symbolic formulation of a contrast in 'glht' of
 the 'multcomp' package fails.
 
 How can this problem be resolved without having to redefine 
 the factor levels?
 
 Example:
 #A is a factor with  'number' levels
 #B similar factor with 'letter' levels
 dat-data.frame(y=1:4,A=factor(c(1,1,2,2)),
   B=factor(c('e','e','f','f')) )
 motA-lm(y~A,data=dat)
 motB-lm(y~B,data=dat)
 library(multcomp)
 #does not work
 glht(motA,linfct=mcp(A=c(2 - 1 = 0 )))
 
 #the error message is
 # Error in coefs(ex[[3]]) : 
 #   cannot interpret expression '1' as linear function

Try putting backquotes around the factor levels so
the R parser makes names out of them.

   glht(motA,linfct=mcp(A=c(`2` - `1` = 0 )))
  
   General Linear Hypotheses

  Multiple Comparisons of Means: User-defined Contrasts
  
  
  Linear Hypotheses:
 Estimate
  `2` - `1` == 02

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com 
 
 #works
 glht(motB,linfct=mcp(B=c(f - e  = 0)))
 
 regards
 
 Ulrich Halekoh
 Aarhus University
 e-mail: ulrich.hale...@agrsci.dk
 
 I use R.2.12.2, package version of multcomp : 1.2-5
 
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 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.
 

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Re: [R] glht: Problem with symbolic contrast for factors with number-levels

2011-03-04 Thread Richard M. Heiberger 
Use backquotes

confint(glht(motA,linfct=mcp(A=c(`2` - `1` = 0 




On Fri, Mar 4, 2011 at 2:03 PM, Ulrich Halekoh ulrich.hale...@agrsci.dkwrote:

 Using a factor with  'number'  levels the straightforward
 symbolic formulation of a contrast in 'glht' of
 the 'multcomp' package fails.

 How can this problem be resolved without having to redefine the factor
 levels?

 Example:
 #A is a factor with  'number' levels
 #B similar factor with 'letter' levels
 dat-data.frame(y=1:4,A=factor(c(1,1,2,2)),
  B=factor(c('e','e','f','f')) )
 motA-lm(y~A,data=dat)
 motB-lm(y~B,data=dat)
 library(multcomp)
 #does not work
 glht(motA,linfct=mcp(A=c(2 - 1 = 0 )))

 #the error message is
 # Error in coefs(ex[[3]]) :
 #   cannot interpret expression '1' as linear function

 #works
 glht(motB,linfct=mcp(B=c(f - e  = 0)))

 regards

 Ulrich Halekoh
 Aarhus University
 e-mail: ulrich.hale...@agrsci.dk

 I use R.2.12.2, package version of multcomp : 1.2-5

 __
 R-help@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.htmlhttp://www.r-project.org/posting-guide.html
 and provide commented, minimal, self-contained, reproducible code.


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[R] glht problem

2009-05-19 Thread Stats Wolf 
I am struggling with a simple repeated-measure model:

fit-lme(trait~year * A, random = ~1|subj/year)

A being a factor with three levels. I got have the following results
for  anova(fit):

numDF denDF   F-value p-value
(Intercept) 1   126 2471.4720  .0001
year   2060   10.4126  .0001
A 2   126   23.0721  .0001
year:A40   1261.6499  0.0193

Now I try to use glht for A, but fail:

Linear Hypotheses:
  Estimate Std. Error z value p value
A2 - A1 == 0  0.25   1.10   0.227   0.972
A3 - A1 == 0 1.001.10   0.909   0.634
A3 - A2 == 0  0.75   1.10   0.682   0.774
(Adjusted p values reported -- single-step method)

Warning message:
In mcp2matrix(model, linfct = linfct) :
  covariate interactions found -- default contrast might be inappropriate


What can be going on with this?

many thanks in advance,
Wolf

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