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 a
different analysis. Of course, I could easily make a Python function
that create the R file and call it... etc...
Maybe I'm a purist, but this juste looks like hacking... isn't it a more
straight 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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