[R] trouble with model.tables SE means

[David Winsemius]

On Dec 22, 2009, at 8:52 PM, Jon Prince wrote:

>
>
> David Winsemius wrote:
>>
>>
>> On Dec 22, 2009, at 5:19 PM, Jon Prince wrote:
>>>
>>> David Winsemius wrote:
>>>>
>>>> On Dec 22, 2009, at 4:22 PM, Jon Prince wrote:
>>>>
>>>>> Hi, I'm new to R, with some experience with Matlab and SPSS.  
>>>>> I've figured out how to run my repeated measures anova and am  
>>>>> getting the right numbers for my effects (comparing with results  
>>>>> from other software), but am having trouble with the  
>>>>> model.tables function. Specifically, using:
>>>>>
>>>>> prints the means, but then won't do the SE values, instead giving:
>>>>>
>>>>> Warning message:
>>>>> In model.tables.aovlist(fm, "means", se = TRUE) :
>>>>> SEs for type 'means' are not yet implemented"
>>>>>
>>>>> Asking for SEs for "effects" works fine, but that's not what I  
>>>>> want. I searched the help for this issue and one other person  
>>>>> has had this problem last year (http://markmail.org/message/k5yxxqcfiihvzvtp?q=list:r-project+model%2Etables 
>>>>> ), but the person helping them was unable to replicate it,  
>>>>> inferring that it was an out-of-date version. My version is:
>>>>>
>>>>> R version 2.10.1 (2009-12-14)
>>>>>
>>>>> I only downloaded it the other day, and therefore cannot have an  
>>>>> outdated version. How can I fix this error and get my SE values?  
>>>>> Apologies if I have not provided sufficient information, and  
>>>>> thanks in advance for your help.
>>>>
>>>> When I look at the output of the first model.tables call copied  
>>>> from the help page, I see a list element that holds "se" values.  
>>>> Try:
>>>>
>>>> model.tables(fm,"means",se=TRUE)$se
>>>>
>>>
>>> Thanks for the rapid reply! Unfortunately adding the $se returns  
>>> NULL, and repeats the same warning message ("...not yet  
>>> implemented"). If you're not experiencing the issue, is it  
>>> possible for me to replace the relevant code/source file with what  
>>> you have (or would that require recompiling)? Could this be an OS  
>>> issue? I'm running Mac OSX 10.6.2.
>>>
>>> By the way, I "replied all" on this message, but let me know if  
>>> that is not the preferred convention. Cheers,
>>
>> Reply all. That way people can correct my mistakes and general  
>> cluelessness. I'm running MacOSX 10.5.8 so it would seem less  
>> likely that is the explanation.
>>
>> 1) Did you run the example in the help pages?
>>
>> 2) When I look at :
>>
>> > methods(model.tables)
>> [1] model.tables.aov*     model.tables.aovlist*
>>
>> ... I see both an "aov" method and an "aovlist" method. Is it  
>> possible that there is something about the object that you are  
>> working on that makes it an aovlist at thus invokes a different  
>> function than what the help page invokes?
>>
>> The code would not require complination... it's available with  
>> getAnywhere() and I do not see any calls to compiled or .Internal  
>> subroutines. Tell me what happens with the above questions first.
>>
>
> Sorry for the delayed response, I've been trying to work out the  
> discrepancy between my data and the example data in terms of getting  
> the SE means.
>
> 1.) Upon trying the example, it appears to work on my machine (i.e.,  
> I get the SE means). Since then I've been spending my time trying to  
> figure out why it doesn't do the same for my data. I can't figure it  
> out.
>
> 2.) Given my lack of experience, it is quite possible that I've  
> loused up an object somewhere, but I don't know how to track that  
> down. I have put my code below, and can send the data file too if  
> you're willing to take a look. Both the p and t factors have three  
> levels, combined factorially. There are four replications of each p- 
> t combination, and the rating data vary from 1 to 7.
>
> ##load data
>   rate_data<-read.table("/Users/jonprince/Desktop/ 
> attend_pitch_3p3t.txt")
> ##set factors
>   p<-factor(rate_data$V3)
>   t<-factor(rate_data$V2)
>   subject<-factor(rate_data$V1)
> ##set data
>   rate<-rate_data$V4
> ##run anova
>   fm<-aov(rate ~ p*t + Error(subject/(p*t)),rate_data)

But, but, but, ... none of those objects (p,t,subject, rate) are part  
of rate_data!

> ##get summary
>   summary(fm)
> ##tables
>   model.tables(fm,"means",se=TRUE)

Without more information, I would be flailing around, and even then I  
am not particularly experienced with the aov framework. My guess is  
that you will get better advice on the R-mixed-models-SIG. I would  
offer more information to that group, at a minimum the output of str  
on rate_data (once you actually create the variables IN rate_data.)

-- 
David
>
> Thanks again, I really appreciate the help.
>
> Jon
>
>
> -- 
> Jon Prince
> Postdoctoral Research Associate
>
>

David Winsemius, MD
Heritage Laboratories
West Hartford, CT