R help - Apr 2009 - broken example: lme() + multcomp() Tukey on repeated measures design

I am trying to do Tukey HSD comparisons on a repeated measures expt.
I found the following example on r-help and quoted approvingly elsewhere.
It is broken. Can anyone please tell me how to get it to work?

I am using R 2.4.1.
> require(MASS) ## for oats data set
> require(nlme) ## for lme()
> require(multcomp) ## for multiple comparison stuff
> Aov.mod <- aov(Y ~ N + V + Error(B/V), data = oats)
> Lme.mod <- lme(Y ~ N + V, random = ~1 | B/V, data = oats)
> summary(Aov.mod)
> anova(Lme.mod)
> summary(Lme.mod)
> summary(glht(Lme.mod, linfct=mcp(V="Tukey")))
Error in eval(expr, envir, enclos) : object "Y" not found
Error in factor_contrasts(model) : no 'model.matrix' method for
'model' found!

It all went ok until the last line, where the actual Tukey multiple
comparisons was requested.

Thanks very much for any help!

Bill

William Simpson <william.a.simpson <at> gmail.com> writes:
> 
> I am trying to do Tukey HSD comparisons on a repeated measures expt.
> I found the following example on r-help and quoted approvingly elsewhere.
> It is broken. Can anyone please tell me how to get it to work?
> 
> I am using R 2.4.1. 
That's the problem. Not the R-Version, but the likelihood that the
multcomp package was not updated also, and lme definitively not
in early version.s



other attached packages:
[1] multcomp_1.0-7 mvtnorm_0.9-5  nlme_3.1-90    MASS_7.2-46   

> glht(Lme.mod, linfct=mcp(V="Tukey"))
         General Linear Hypotheses

Multiple Comparisons of Means: Tukey Contrasts


Linear Hypotheses:
                              Estimate
Marvellous - Golden.rain == 0    5.292
Victory - Golden.rain == 0      -6.875
Victory - Marvellous == 0      -12.167



Dieter

On Apr 21, 2009, at 10:12 AM, William Simpson wrote:
> I am trying to do Tukey HSD comparisons on a repeated measures expt.
> I found the following example on r-help and quoted approvingly  
> elsewhere.
> It is broken. Can anyone please tell me how to get it to work?
>
> I am using R 2.4.1.
How many years have you had that version without
updating?
>
>
>> require(MASS) ## for oats data set
>> require(nlme) ## for lme()
>> require(multcomp) ## for multiple comparison stuff
>> Aov.mod <- aov(Y ~ N + V + Error(B/V), data = oats)
>> Lme.mod <- lme(Y ~ N + V, random = ~1 | B/V, data = oats)
>> summary(Aov.mod)
>> anova(Lme.mod)
>> summary(Lme.mod)
>> summary(glht(Lme.mod, linfct=mcp(V="Tukey")))
> Error in eval(expr, envir, enclos) : object "Y" not found
> Error in factor_contrasts(model) : no 'model.matrix' method for  
> 'model' found!
It is not broken when run in version 2.8.1.


David Winsemius, MD
Heritage Laboratories
West Hartford, CT

Thanks for the helpful replies.
I will try updating R and see how it goes.

MASS, nlme, multcomp are all the most recent.

Bill

On Tue, Apr 21, 2009 at 3:12 PM, William Simpson
<william.a.simpson at gmail.com> wrote:
> I am trying to do Tukey HSD comparisons on a repeated measures expt.
> I found the following example on r-help and quoted approvingly elsewhere.
> It is broken. Can anyone please tell me how to get it to work?
>
> I am using R 2.4.1.
>
>> require(MASS) ## for oats data set
>> require(nlme) ## for lme()
>> require(multcomp) ## for multiple comparison stuff
>> Aov.mod <- aov(Y ~ N + V + Error(B/V), data = oats)
>> Lme.mod <- lme(Y ~ N + V, random = ~1 | B/V, data = oats)
>> summary(Aov.mod)
>> anova(Lme.mod)
>> summary(Lme.mod)
>> summary(glht(Lme.mod, linfct=mcp(V="Tukey")))
> Error in eval(expr, envir, enclos) : object "Y" not found
> Error in factor_contrasts(model) : no 'model.matrix' method for
'model' found!
>
> It all went ok until the last line, where the actual Tukey multiple
> comparisons was requested.
>
> Thanks very much for any help!
>
> Bill
>