R help - Apr 2006 - TukeyHSDs function (pgirmess package)

Dear R-help,
 
I have been trying to use the TukeyHSDs function in the "pgirmess"
package to quickly extract all
significant pairwise comparisons in an aov object. However, it seems
that this function isn't working
as intended when only the two last populations means being tested are
significant.
 
An example of this can be seen below:
 
>numbers<-c(464,482,453,434,495,487) 
>group<-gl(3,2,label=c("A","B","C"))
>testobject<-aov(numbers~group)
>result<-TukeyHSD(testobject,conf.level=0.95)
>error<-TukeyHSDs(result)
>error$group[,1]
Error in error$group[, 1] : incorrect number of dimensions
 
To illustrate the "normal" function, the data set below can be used.
 
>numbers<-c(845,829,682, 689,581,495)
 
Is there something wrong with this function? Or is there a better way
to extract significant comparisons
from a tukey test?
 
Cheers,
Rune
-------------------------------------------
Rune Vejen Petersen, M.Sc.Eng.
Statens Serum Institute
Dept. of Infectious Disease Immunology
Artillerivej 5, 81/344
DK-2300 Copenhagen

	[[alternative HTML version deleted]]

Rune Vejen Petersen wrote:
> Dear R-help,
>  
> I have been trying to use the TukeyHSDs function in the
"pgirmess"
> package to quickly extract all
> significant pairwise comparisons in an aov object. However, it seems
> that this function isn't working
> as intended when only the two last populations means being tested are
> significant.
>  
> An example of this can be seen below:
>  
> 
>>numbers<-c(464,482,453,434,495,487) 
>>group<-gl(3,2,label=c("A","B","C"))
>>testobject<-aov(numbers~group)
>>result<-TukeyHSD(testobject,conf.level=0.95)
>>error<-TukeyHSDs(result)
>>error$group[,1]
> 
> Error in error$group[, 1] : incorrect number of dimensions
>  
> To illustrate the "normal" function, the data set below can be
used.
>  
> 
>>numbers<-c(845,829,682, 689,581,495)
> 
>  
> Is there something wrong with this function? Or is there a better way
> to extract significant comparisons
> from a tukey test?
It looks like the line

   res[[1]] <- x[y, ]

in TukeyHSDs() should be replaced with

   res[[1]] <- x[y, , drop = FALSE]


Peter Ehlers
>  
> Cheers,
> Rune
> -------------------------------------------
> Rune Vejen Petersen, M.Sc.Eng.
> Statens Serum Institute
> Dept. of Infectious Disease Immunology
> Artillerivej 5, 81/344
> DK-2300 Copenhagen
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html

Sorry to have been so poorly reactive. I have been abroad for ten days 
and then bogged down with administration for the week when back, so 
totally unproductive!!!

The bug is now fixed in the last release of pgirmess (1.2.6) on its way 
to CRAN and also available on the pgirmess web site 
(http://perso.wanadoo.fr/giraudoux/SiteGiraudoux.html).

Kind regards,

Patrick