Re: R code not producing expected results

From: "Thomas S. Dye" <tsd@tsdye.com>
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 20:23:14 -1000	[thread overview]
Message-ID: <F665859D-CF1F-4DBD-8EAA-EB84EA000D48@tsdye.com> (raw)
In-Reply-To: <C88A3527.16634%mab@stowers.org>

Aloha Marco,

Here is the code behind the Worg page:

#+begin_src R :results output org
   library(ascii)
   options(asciiType="org")
   ascii(summary(table(1:4, 1:4)))
#+end_src

This works here.

The key seems to be the header argument :results output

#+BEGIN_SRC R :results output
  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

#+results:
#+begin_example

    Welcome to R!

|----+------+-------+-------+-------+
|    | V1   | V2    | V3    | V4    |
|----+------+-------+-------+-------+
| V1 | 1.00 | 0.09  | 0.09  | 0.13  |
| V2 | 0.09 | 1.00  | -0.00 | -0.13 |
| V3 | 0.09 | -0.00 | 1.00  | 0.18  |
| V4 | 0.13 | -0.13 | 0.18  | 1.00  |
|----+------+-------+-------+-------+
#+end_example

With it added to your other example, it does indeed generate a nice  
table.

I think you are absolutely right about org-mode's babel capabilities  
helping with your R work.  I can't imagine a better environment for  
working in R.

Good luck with your work.

All the best,
Tom

On Aug 12, 2010, at 6:32 PM, 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.
>
> 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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