Re: R code not producing expected results

From: "Charles C. Berry" <cberry@tajo.ucsd.edu>
To: "Blanchette, Marco" <MAB@stowers.org>
Cc: "emacs-orgmode@gnu.org" <emacs-orgmode@gnu.org>
Subject: Re: R code not producing expected results
Date: Thu, 12 Aug 2010 23:57:20 -0700	[thread overview]
Message-ID: <Pine.LNX.4.64.1008122300280.7685@tajo.ucsd.edu> (raw)
In-Reply-To: <C88A3527.16634%mab@stowers.org>

On Thu, 12 Aug 2010, Blanchette, Marco wrote:

> Dear all,
>

> Sorry if this is something totally obvious but I am learning to use
   org-mode for my everyday work with R. I just installed the latest
   stable release of org-mode (v7.01g) on top of GNU Emacs 23.1.50.1
   (x86_64-apple-darwin10.2.0, NS apple-appkit-1038.25). I also
   installed the CRAN ascii package v0.7 on top of R v2.11.1. I am
   currently working on a MacBook pro with Snow Leopard 10.6.4

>

> Early on today, while reading the org-babel intro, I was able to run
   the following example but somehow, later tonight, it started to
   break and I spent the last few hours scratching my head to
   understand what change and why it now suddenly break. Your help will
   be greatly appreciated as I am discovering that org-mode in
   collaboration with org-babel have great potential to help us create
   more readable report of our daily analysis, as long as I can get
   through these early hurdles.

The code you say is "straight from ...org-babel-doc-R.php" is not quite.

Note all the header args:

 	#+begin_src R :results output code :session ascii

Also note that ascii() does not return an object of class "matrix" or 
"data.frame". Try str(ascii( < all the rest > )).

With :results value (the default) you will get a different outcome as
you saw below.

'value' tries to be smart about what it does with .Last.value, but "ascii" 
objects are a bit too tricky for it.

'output' on the other hand is pretty simple on the elisp side and 
relies on R's print() to get the dispatch for the print method right.

If you want to use ':results value' you will need to form a data.frame 
from ascii() yourself, rather than rely on as.data.frame to find a method 
to do the conversion. Or you will need to write a method for 
as.data.frame.ascii.

HTH,

Chuck

>
> Here is the org buffer that now breaks:
>
> * Two examples of R code that worked when I started the tutorial but suddenly started to fail...
>
> ** some R code that should generate a nice table
> #+BEGIN_SRC R
>  library(ascii)
>  options(asciiType="org")
>
>  d <- as.data.frame(replicate(4,rnorm(100)))
>
>  ascii(cor(d),include.rownames=T, include.colnames=T,header=T)
> #+END_SRC
>
> ** Some code straight from [[http://orgmode.org/worg/org-contrib/babel/languages/org-babel-doc-R.php][org-babel]]
> #+BEGIN_SRC R
> library(ascii)
> options(asciiType="org")
> ascii(summary(table(1:4, 1:4)))
> #+END_SRC
>
>
> With the following error recover from the *Org-Babel Error* buffer
>
> Loading required package: proto
> Error in as.data.frame.default(x[[i]], optional = TRUE) :
>  cannot coerce class 'c("ascii", "proto", "environment")' into a data.frame
> Calls: write.table ... data.frame -> as.data.frame -> as.data.frame.default
> Execution halted
>
> Thanks for the helps.
> --
> Marco Blanchette, Ph.D.
> Assistant Investigator
> Stowers Institute for Medical Research
> 1000 East 50th St.
>
> Kansas City, MO 64110
>
> Tel: 816-926-4071
> Cell: 816-726-8419
> Fax: 816-926-2018
>
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Charles C. Berry                            (858) 534-2098
                                             Dept of Family/Preventive Medicine
E mailto:cberry@tajo.ucsd.edu	            UC San Diego
http://famprevmed.ucsd.edu/faculty/cberry/  La Jolla, San Diego 92093-0901