[R] Problems using allEffects() (package effect)

[Jonas Mandel]

Hello,

Sorry for the lack of clarity, I thought I was clear about the package :
it's the function allEffects from the package effects.

Here is my example again (unfortunately I can't give the data) :
The data concerns effects of 3 treatments on the tumoral volume of mice.

> head(data)
           Id Série Traitement vTum temps Volume
 55656.1 55656     7          3    1     1  14.03
 55805.1 55805     7          3    3     1  59.92
 55829.1 55829     7          3    1     1  15.31
 55806.1 55806     7          3    2     1  28.01
 50725.1 50725     7          3    2     1  34.48
 55737.1 55737     7          3    2     1  43.56

vTum is a factor coding for the qualitative initial volume, from small
to big, temps is the time (integer) in month since beginning of
treatment, and Série is a factor coding for the batch. Data is unbalanced.

I fit a linear model as follows:
> lm1=lm(Volume ~  temps + Traitement:temps + Série , data)

And then I try to use allEffects to compute (and then plot) the effects
of the interaction:
> eff.lm1 <- allEffects(mod=lm1, xlevels=list(temps=c(1:3), Traitement=1:3))

And here is the error I get:
Error in apply(mod.matrix[, components], 1, prod) : index out of range

In the example given in the help page there are factor variables and
numeric variables so I don't think the problem comes from here. Any help
is welcome here.

Cheers,
Jonas


Joris Meys a écrit :
> Please, read the posting guide:
> - provide a minimal example
> - tell us from which package the function is coming
> 
> I guess you used the function allEffects() from the package effects, and did :
> eff.lm1 <- allEffect(lm1)
> 
> Then I guess that there's something wrong with the variables you put
> into the model. Sure they're factor variables and not numeric?
> 
> Cheers
> Joris
> 
> 
> 
> On Thu, Jun 17, 2010 at 6:03 PM, Jonas Mandel <jonas.mandel at curie.fr> wrote:
>> Dear R users,
>>
>> I have some trouble using the allEffects() function to compute and
>> display effect plots for a linear model.
>> My data is quite simple, it concerns effects of 3 treatments on the
>> tumoral volume of mice. vTum codes for the qualitative initial volume,
>> from small to big, temps is the time in month since beginning of
>> treatment, and Série codes for the batch. Data is unbalanced.
>>
>>> head(data)
>>           Id Série Traitement vTum temps Volume
>> 55656.1 55656     7          3    1     1  14.03
>> 55805.1 55805     7          3    3     1  59.92
>> 55829.1 55829     7          3    1     1  15.31
>> 55806.1 55806     7          3    2     1  28.01
>> 50725.1 50725     7          3    2     1  34.48
>> 55737.1 55737     7          3    2     1  43.56
>>
>>
>> The linear model is also quite simple :
>>> lm1=lm(Volume ~  temps + Traitement:temps + Série , data)
>> But when I try to use allEffects() I get this error:
>>> eff.lm1 <- allEffect(mod=lm1,
>> Error in apply(mod.matrix[, components], 1, prod) : index out of range
>>
>> I read the help and the example but I don't understand the reason why it
>> doesn't work. Can you help me ?
>> Thanks
>>
>>
>> --
>> Jonas Mandel
>>
>> ______________________________________________
>> 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.
>>
> 
> 
>