Re: [Org-Babel] and R... non-numeric cells

From: Neil Hepburn <nhepburn@ualberta.ca>
To: "Sébastien Vauban" <wxhgmqzgwmuf@spammotel.com>
Cc: emacs-orgmode@gnu.org
Subject: Re: [Org-Babel] and R... non-numeric cells
Date: Thu, 12 Aug 2010 09:30:27 -0600	[thread overview]
Message-ID: <C3B8658F-315A-479F-BFFC-3637516BDEAA@ualberta.ca> (raw)
In-Reply-To: <871va3hnvj.fsf@mundaneum.com>

I have had a similar problem and I traced it back to the presence of horizontal lines in the source table. The two ways that I have dealt with the problem are to either not have horizontal lines in the table or use some R stuff to clean things up. For example, suppose that I have the following table

#+TBLNAME: mytbl
|column1|column2|
|------------|-----------|
|  45         |    34      |
|  77         |    56      |

when I send that to R, it will treat everything as character due to the horizontal line.  The following R snippet will clean it up and recast everything as numeric.

#+BEGIN_SRC R :var tbl=mytbl
names(tbl) <- tbl[1,]  #renames the variables from V1, V2 etc to what they should be
tbl <- tb[-1,] #gets rid of the first row that had the errant variable names
for (i in 1:ncol(tbl)){
tbl[,i] <- as.numeric(tbl[,i])
} # the for-loop goes through each column and recasts it as a numeric variable instead of character.
#+END_SRC

of course, if you have a column of text in the first column (or any column for that matter) you need to adjust your for-loop accordingly.

I hope this helps.

-Neil

On 2010-08-12, at 9:06 AM, Sébastien Vauban wrote:

> Hello,
> 
> For a report I'm writing, I've been helped by a colleague of mine (let's call
> him Albert) for the R graphics generation.
> 
> Here's an extract of my doc:
> 
> --8<---------------cut here---------------start------------->8---
> #+TBLNAME: investissement-2010-2013
> #+ATTR_LaTeX: align=lSSSS
> |                        | \s{Année 2010} | \s{Année 2011} | \s{Année 2012} | \s{Année 2013} |
> |------------------------+----------------+----------------+----------------+----------------|
> | RFO                    |     2596376.30 |     1500000.00 |      500000.00 |      500000.00 |
> | RFO réseau structurant |     3804467.00 |     6534066.00 |     3804467.00 |           0.00 |
> | Équipements            |     1000000.00 |      150000.00 |       50000.00 |       50000.00 |
> |------------------------+----------------+----------------+----------------+----------------|
> | Total (HTVA)           |     7400843.30 |     8184066.00 |     4354467.00 |      550000.00 |
> #+TBLFM: @5$2=vsum(@-I..@-II);%.2f::@5$3=vsum(@-I..@-II);%.2f::@5$4=vsum(@-I..@-II);%.2f::@5$5=vsum(@-I..@-II);%.2f
> 
> whose graphical representation is:
> 
> #+srcname: barplot-investment(ptable = investissement-2010-2013)
> #+begin_src R :file 1-01-investissement-2010-2013.png :exports none :session
> source("mcplot.R", local=TRUE)
> ## select the last row only, exclude first column, scale: unit = 1M
> alldata <- as.matrix(ptable[2:4, -1]) / 1000000
> axisLabels <- c("Année", "Montant HTVA (M€)")
> mcStackedBarplot(alldata, "Investissements", c(2010:2013), ptable[-nrow(ptable),1], legend.location="topright")
> #+end_src
> --8<---------------cut here---------------end--------------->8---
> 
> That works perfectly for him (on Ubuntu 9.04, R 2.7.1, Emacs 22.2.1, Org 6.35)
> 
> Not for me... on Ubuntu 10.04, R 2.10.1, Emacs 23.1.1, Org 7.01, ESS 5.10: I
> get the message
> 
>    *Error in as.matrix(ptable[2:4, -1])/1e+06 :
>     non-numeric argument to binary operator*
> 
> As 1M is numeric, the non-numeric operand must be
> =as.matrix(ptable[2:4, -1])=... Verification:
> 
> --8<---------------cut here---------------start------------->8---
>> ptable
>                      V1              V2              V3              V4
> 1                        \\s{Année 2010} \\s{Année 2011} \\s{Année 2012}
> 2                    RFO       2596376.3       1500000.0        500000.0
> 3 RFO réseau structurant       3804467.0       6534066.0       3804467.0
> 4            Équipements       1000000.0        150000.0         50000.0
> 5           Total (HTVA)       7400843.3       8184066.0       4354467.0
>               V5
> 1 \\s{Année 2013}
> 2        500000.0
> 3             0.0
> 4         50000.0
> 5        550000.0
> 
>> as.matrix(ptable[2:4, -1])
>  V2          V3          V4          V5        
> 2 "2596376.3" "1500000.0" "500000.0"  "500000.0"
> 3 "3804467.0" "6534066.0" "3804467.0" "0.0"     
> 4 "1000000.0" "150000.0"  "50000.0"   "50000.0" 
> --8<---------------cut here---------------end--------------->8---
> 
> The numerics are written between double quotes... Why!?
> 
> I had temporarily patched the above problem in my document by updating the line
> with the assignment:
> 
> --8<---------------cut here---------------start------------->8---
> #+srcname: barplot-investment-sva(ptable = investissement-2010-2013)
> #+begin_src R :file 1-01-investissement-sva-2010-2013.png :exports none :session
> source("mcplot.R", local=TRUE)
> ## select the last row only, exclude first column, scale: unit = 1M
> alldata <- matrix(as.numeric(as.matrix(ptable[2:4, -1])), nrow=3, ncol=4) / 1000000
> axisLabels <- c("Année", "Montant HTVA (M€)")
> mcStackedBarplot(alldata, "Investissements", c(2010:2013), ptable[2:4,1], legend.location="topright")
> #+end_src
> --8<---------------cut here---------------end--------------->8---
> 
> and I even just noticed that, instead of complexifying the expression, I can
> simplify it, in my case, as my =ptable= is numeric already:
> 
> --8<---------------cut here---------------start------------->8---
>> ptable[2:4, -1]
>         V2        V3        V4       V5
> 2 2596376.3 1500000.0  500000.0 500000.0
> 3 3804467.0 6534066.0 3804467.0      0.0
> 4 1000000.0  150000.0   50000.0  50000.0
> --8<---------------cut here---------------end--------------->8---
> 
> But I still don't understand what is reponsible of a different treatment of
> string and numerics between our 2 machines.
> 
> Any idea?
> 
> Best regards,
>  Seb
> 
> -- 
> Sébastien Vauban
> 
> 
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=============================================
Neil Hepburn, Lecturer in Economics
Department of Social Sciences, Augustana Faculty
University of Alberta
4901-46 Avenue
Camrose, Alberta  T4V 2R3

Phone (780) 679-1588
email nhepburn@ualberta.ca

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