Re: [Rpy] Repeated measure ANOVA : formula and summary problem

Etienne Gaudrain Tue, 18 Dec 2007 11:39:10 -0800

Hi Toby,

You're right that I can call the R file as many time I want, even if addsome subjects in my experiment. However, I need Python because I makesome treatments on my data before analysing it (e.g. some fittings withnon linear functions...). I could probably make the same directly in R,but I don't know the language enough... (shame on me, bouuuuuh !).However, I also planned to cross the responses of my subjects with somecharacteristics of the auditory signal I presented to them, and forsignal handling, I'm definitely more cumfortable in Scipy than in R.Whatever... the point is that then the number and the names of theparameters I have to include in the analysis varies every time.


This could be solved by making Python function such as:

|def aov(r_instance, formula, data):
   f = open("file.R","rb")
   f.write("""
       library('stats')
       my.summary = function(Res) {
         av <- aov( %s, data=Res)
         summary(av)
       }
       """ % formula
   f.close()
   r_instance.source("file.R")
   r_instance.my_summary(data)|


Then I just have to call:

|aov(r, "score~factor+Error(id_subject/factor)", Res)|

I'll try this. Thanks !

-Etienne






Toby Hocking a écrit :

Hi Etienne,

I don't think you have to make a new R file every time, you just have to make it once and 
call r.source("file.R") every time. Then use your R function with a new 
dataset. This type of data flow works great for me, and I think it is rather the opposite 
of hacking, since you achieve separation of R code and python code to a large extent.

Toby

-----Original Message-----
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Etienne
Gaudrain
Sent: Tuesday, December 18, 2007 11:18 AM
To: RPy help, support and design discussion list
Subject: Re: [Rpy] Repeated measure ANOVA : formula and summary problem


Ok, I guess this should work, thank you very much!

However, it means that I have to make an R file everytime I make adifferent analysis. Of course, I could easily make a Python functionthat create the R file and call it... etc...Maybe I'm a purist, but this juste looks like hacking... isn't it a morestraight forward way to do it ?


Thank you again, your solution definetly solve my issue!!
-Etienne




Toby Hocking a écrit :

Why don't you put your R code in file.R:

library('stats')
my.summary = function(Res) {
  av <- aov( score~factor+Error(id_subject/factor), data=Res)
  summary(av)
}

then from python:

r.source("file.R")
r.my_summary(Res)

???


-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Etienne Gaudrain
Sent: Tuesday, December 18, 2007 10:53 AM
To: rpy-list@lists.sourceforge.net
Subject: [Rpy] Repeated measure ANOVA : formula and summary problem


Hi everyone,

I'm new to RPy, and I came to this terrific module as I was used to make some 
of my analyses in R, and I came to Python in replacement of Matlab. Formerly, I 
manipulated data with Matlab, put it in a MySQL database, and made my stats in 
R via ODBC. I'm now thinking about jumping one step by calling R directly from 
Python with RPy.

The analysis I almost always have to do is a repeated measure ANOVA. The way I 
do this in R is :


# after odbc connection and sql query, Res contains my data

library('stats')
av <- aov( score~factor+Error(id_subject/factor), data=Res)
summary(av)


Now I tried the same in RPy :


# retrieve data from sql query, Res is a dictionnary

r.library('stats')
av = r.aov("score~factor+Error(id_subject/factor)", data=Res)


This fails saying that "Error" isn't defined in the dataframe...
After reading some R doc about GLM, I found that using the R function formula() 
seemed to solve this problem:

av = r.aov(r.formula("score~factor+Error(id_subject/factor)"), data=Res)
r.summary(av)

However, a new problem rose in r.summary(). This function returns something 
that isn't readable, and that does not contain the p values, or anything 
similar. It seems that the r.summary_aov() function might be adequat, but this 
function returns an Error saying that there is a NaN somewhere...

Does anybody have an advice on how to perform the repeated measure ANOVA?
Thanks!
-Etienne


PS : I use Windows XP, Python 2.5.1, Numpy 1.0.3.1 and RPy 1.0.1-Numpy-py2.5 
and R 2.6.1.

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Re: [Rpy] Repeated measure ANOVA : formula and summary problem

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