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* Babel-R TBLFM example
@ 2014-06-25  6:55 Shiyuan
  2014-07-28 13:21 ` Bastien
  0 siblings, 1 reply; 9+ messages in thread
From: Shiyuan @ 2014-06-25  6:55 UTC (permalink / raw)
  To: emacs-orgmode

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Hi all,
    I am looking at the Babel R example in
http://orgmode.org/worg/org-tutorials/org-R/org-R.html

This short example show how to use code block in Org Tables.
The example first makes an org-mode table, which I can follow and reproduce
the result:

#+name: tbl-example-data()
#+begin_src R
runif(n=5, min=0, max=1)
#+end_src

#+RESULTS: tbl-example-data
|  0.118510485393927 |
|  0.742342338664457 |
|  0.438421099446714 |
| 0.0867570964619517 |
|  0.604204315226525 |

Then it defines r source code block and use TBLFM

#+name: R-mean(x)
#+begin_src R
mean(x)
#+end_src

#+RESULTS: R-mean

#+tblname: summaries
| mean   |
|--------|
| #ERROR |
#+TBLFM: @2$1='(sbe "R-mean" (x "tbl-example-data()"))

When I export to html(C-c C-e h o), the  #+TBLFM seems to be ignored and
shows  no effect. When I place my cursor in the table and recalculate the
table formula using C-u C-c C-c in the table. I got an error as shown
above.   In the *Message* buffer, I can see the following messages.
byte-code: Beginning of buffer [8 times]
Re-applying formulas to full table...
Re-applying formula to field: @2$1
Re-applying formulas to full table...(line 1)
Re-applying formula to field: @2$1
Re-applying formulas to 1 lines...done
Re-applying formulas...done [2 times]

Any steps I missed? I am using org mode 8.2.6

Also, I found this tutorial for org-R
http://orgmode.org/worg/org-tutorials/org-R/org-R.html, however, the
org-R-apply function seems no longer available in my org mode 8.2.6. Is
org-R supposed to be deprecated?

Thanks.

Shiyuan

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^ permalink raw reply	[flat|nested] 9+ messages in thread

• * Re: Babel-R TBLFM example
    2014-06-25  6:55 Babel-R TBLFM example Shiyuan
  @ 2014-07-28 13:21 ` Bastien
    2014-07-29  6:15   ` Shiyuan
    0 siblings, 1 reply; 9+ messages in thread
  From: Bastien @ 2014-07-28 13:21 UTC (permalink / raw)
    To: Shiyuan; +Cc: emacs-orgmode
  
  Hi Shiyuan,
  
  Shiyuan <gshy2014@gmail.com> writes:
  
  > Also, I found this tutorial for org-R http://orgmode.org/worg/
  > org-tutorials/org-R/org-R.html, however, the org-R-apply function
  > seems no longer available in my org mode 8.2.6. Is org-R supposed to
  > be deprecated?
  
  No, but it's moving.  Since ob-R.el is perhaps one of the most useful
  Babel library out there, we need to document the changes carefully in
  etc/ORG-NEWS.
  
  -- 
   Bastien
  
  ^ permalink raw reply	[flat|nested] 9+ messages in thread

• • * Re: Babel-R TBLFM example
      2014-07-28 13:21 ` Bastien
    @ 2014-07-29  6:15   ` Shiyuan
      2014-07-29 13:20     ` Bastien
      0 siblings, 1 reply; 9+ messages in thread
    From: Shiyuan @ 2014-07-29  6:15 UTC (permalink / raw)
      To: Bastien; +Cc: emacs-orgmode@gnu.org
    
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    Thanks Bastien. I see ob-R.el from org-mode repos has been updated. So is
    the org-R from git-repos ready to use? Could you suggest  a good place to
    start learning the new org-R? The source file ob-R.el?
    
    Shiyuan
    
    
    On Mon, Jul 28, 2014 at 6:21 AM, Bastien <bzg@gnu.org> wrote:
    
    > Hi Shiyuan,
    >
    > Shiyuan <gshy2014@gmail.com> writes:
    >
    > > Also, I found this tutorial for org-R http://orgmode.org/worg/
    > > org-tutorials/org-R/org-R.html, however, the org-R-apply function
    > > seems no longer available in my org mode 8.2.6. Is org-R supposed to
    > > be deprecated?
    >
    > No, but it's moving.  Since ob-R.el is perhaps one of the most useful
    > Babel library out there, we need to document the changes carefully in
    > etc/ORG-NEWS.
    >
    > --
    >  Bastien
    >
    
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    ^ permalink raw reply	[flat|nested] 9+ messages in thread

  • • * Re: Babel-R TBLFM example
        2014-07-29  6:15   ` Shiyuan
      @ 2014-07-29 13:20     ` Bastien
        2014-08-24 23:02       ` Shiyuan
        0 siblings, 1 reply; 9+ messages in thread
      From: Bastien @ 2014-07-29 13:20 UTC (permalink / raw)
        To: Shiyuan; +Cc: emacs-orgmode@gnu.org
      
      Hi Shiyuan,
      
      Shiyuan <gshy2014@gmail.com> writes:
      
      > Thanks Bastien. I see ob-R.el from org-mode repos has been updated.
      > So is the org-R from git-repos ready to use? Could you suggest  a
      > good place to start learning the new org-R? The source file ob-R.el?
      
      The recent committers to ob-R.el we be more in a position to help here
      but yes, reading the source is certainly a good start.
      
      I hope we will have a clear picture of what changed in ob-R.el in 8.3,
      together with updated tutorials.
      
      Best,
      
      -- 
       Bastien
      
      ^ permalink raw reply	[flat|nested] 9+ messages in thread

    • • * Re: Babel-R TBLFM example
          2014-07-29 13:20     ` Bastien
        @ 2014-08-24 23:02       ` Shiyuan
          2014-08-25  7:51         ` Sebastien Vauban
          0 siblings, 1 reply; 9+ messages in thread
        From: Shiyuan @ 2014-08-24 23:02 UTC (permalink / raw)
          To: Bastien; +Cc: emacs-orgmode@gnu.org
        
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        I am looking at a simpler example, the pie-chart example as in this link:
        http://orgmode.org/worg/org-contrib/babel/intro.html#literate-programming
        
        This example(src code attached in the end) first generates a table by a
        shell command and then run a R one-liner which uses the table.  However,
        when the R code is evaluated, I got an error about the object dirs not
        found.  This is what I got in the buffer running R:
        -------------------------------
        options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient',
        show.error.locations=TRUE)
        >
        Error in pie(dirs[, 1], labels = dirs[, 2]) (from
        test-org-babe-meta-programming.org@24170fIx#1) : object 'dirs' not found
        -----------------------------------------------
        
        It looks like that the conversion is wrong.  When I run
        `org-babel-expand-src-block`
        on the R source code, I don't see the R object dirs is expanded to
        anything. I don't understand how the conversion works, and how Babel passes
        the table to R. Any explanation is appreciated. Which function/file should
        I look at? Are there working examples for passing a table to R? Thanks.
        
        Shiyuan
        
        
        ------------------------------
        #+name: directories
        #+begin_src shell :results replace
          cd ~ && du -sc * |grep -v total
        #+end_src
        
        #+RESULTS: directories
        |       8 | #*message*-20140319-231047# |
        | 1168376 | Documents                   |
        | 9952288 | Downloads                   |
        |       8 | xmodmap2~                   |
        
        #+name: directory-pie-chart(dirs = directories)
        #+begin_src R :session R-pie-example :file ~/tmp/dirs.png
          pie(dirs[,1], labels = dirs[,2])
        #+end_src
        
        
        On Tue, Jul 29, 2014 at 6:20 AM, Bastien <bzg@gnu.org> wrote:
        
        > Hi Shiyuan,
        >
        > Shiyuan <gshy2014@gmail.com> writes:
        >
        > > Thanks Bastien. I see ob-R.el from org-mode repos has been updated.
        > > So is the org-R from git-repos ready to use? Could you suggest  a
        > > good place to start learning the new org-R? The source file ob-R.el?
        >
        > The recent committers to ob-R.el we be more in a position to help here
        > but yes, reading the source is certainly a good start.
        >
        > I hope we will have a clear picture of what changed in ob-R.el in 8.3,
        > together with updated tutorials.
        >
        > Best,
        >
        > --
        >  Bastien
        >
        
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        ^ permalink raw reply	[flat|nested] 9+ messages in thread

      • • * Re: Babel-R TBLFM example
            2014-08-24 23:02       ` Shiyuan
          @ 2014-08-25  7:51         ` Sebastien Vauban
            2014-08-26  6:18           ` Shiyuan
            0 siblings, 1 reply; 9+ messages in thread
          From: Sebastien Vauban @ 2014-08-25  7:51 UTC (permalink / raw)
            To: emacs-orgmode-mXXj517/zsQ
          
          Shiyuan wrote:
          > I am looking at a simpler example, the pie-chart example as in this link:
          > http://orgmode.org/worg/org-contrib/babel/intro.html#literate-programming
          >
          > This example(src code attached in the end) first generates a table by a
          > shell command and then run a R one-liner which uses the table.  However,
          > when the R code is evaluated, I got an error about the object dirs not
          > found.  This is what I got in the buffer running R:
          > -------------------------------
          > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient',
          > show.error.locations=TRUE)
          >>
          > Error in pie(dirs[, 1], labels = dirs[, 2]) (from
          > test-org-babe-meta-programming.org@24170fIx#1) : object 'dirs' not found
          > -----------------------------------------------
          >
          > It looks like that the conversion is wrong.  When I run
          > `org-babel-expand-src-block`
          > on the R source code, I don't see the R object dirs is expanded to
          > anything. I don't understand how the conversion works, and how Babel passes
          > the table to R. Any explanation is appreciated. Which function/file should
          > I look at? Are there working examples for passing a table to R? Thanks.
          >
          > #+name: directories
          > #+begin_src shell :results replace
          >   cd ~ && du -sc * |grep -v total
          > #+end_src
          >
          > #+RESULTS: directories
          > |       8 | #*message*-20140319-231047# |
          > | 1168376 | Documents                   |
          > | 9952288 | Downloads                   |
          > |       8 | xmodmap2~                   |
          >
          > #+name: directory-pie-chart(dirs = directories)
          > #+begin_src R :session R-pie-example :file ~/tmp/dirs.png
          >   pie(dirs[,1], labels = dirs[,2])
          > #+end_src
          
          AFAICT, the arguments to code blocks may not be defined and set in the
          `name' line anymore: this must be done on the `begin_src' line.
          
          So, the following should work:
          
            #+name: directory-pie-chart
            #+begin_src R :var dirs=directories :session R-pie-example :file ~/tmp/dirs.png
              pie(dirs[,1], labels = dirs[,2])
            #+end_src
          
          Best regards,
            Seb
          
          -- 
          Sebastien Vauban
          
          ^ permalink raw reply	[flat|nested] 9+ messages in thread

        • • * Re: Babel-R TBLFM example
              2014-08-25  7:51         ` Sebastien Vauban
            @ 2014-08-26  6:18           ` Shiyuan
              2014-08-26  6:57             ` Thomas S. Dye
              0 siblings, 1 reply; 9+ messages in thread
            From: Shiyuan @ 2014-08-26  6:18 UTC (permalink / raw)
              Cc: emacs-orgmode@gnu.org
            
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            Yes, it works. Thanks, Sebastien.
            
            Shiyuan
            
            
            On Mon, Aug 25, 2014 at 12:51 AM, Sebastien Vauban <sva-news@mygooglest.com>
            wrote:
            
            > Shiyuan wrote:
            > > I am looking at a simpler example, the pie-chart example as in this link:
            > >
            > http://orgmode.org/worg/org-contrib/babel/intro.html#literate-programming
            > >
            > > This example(src code attached in the end) first generates a table by a
            > > shell command and then run a R one-liner which uses the table.  However,
            > > when the R code is evaluated, I got an error about the object dirs not
            > > found.  This is what I got in the buffer running R:
            > > -------------------------------
            > > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient',
            > > show.error.locations=TRUE)
            > >>
            > > Error in pie(dirs[, 1], labels = dirs[, 2]) (from
            > > test-org-babe-meta-programming.org@24170fIx#1) : object 'dirs' not found
            > > -----------------------------------------------
            > >
            > > It looks like that the conversion is wrong.  When I run
            > > `org-babel-expand-src-block`
            > > on the R source code, I don't see the R object dirs is expanded to
            > > anything. I don't understand how the conversion works, and how Babel
            > passes
            > > the table to R. Any explanation is appreciated. Which function/file
            > should
            > > I look at? Are there working examples for passing a table to R? Thanks.
            > >
            > > #+name: directories
            > > #+begin_src shell :results replace
            > >   cd ~ && du -sc * |grep -v total
            > > #+end_src
            > >
            > > #+RESULTS: directories
            > > |       8 | #*message*-20140319-231047# |
            > > | 1168376 | Documents                   |
            > > | 9952288 | Downloads                   |
            > > |       8 | xmodmap2~                   |
            > >
            > > #+name: directory-pie-chart(dirs = directories)
            > > #+begin_src R :session R-pie-example :file ~/tmp/dirs.png
            > >   pie(dirs[,1], labels = dirs[,2])
            > > #+end_src
            >
            > AFAICT, the arguments to code blocks may not be defined and set in the
            > `name' line anymore: this must be done on the `begin_src' line.
            >
            > So, the following should work:
            >
            >   #+name: directory-pie-chart
            >   #+begin_src R :var dirs=directories :session R-pie-example :file
            > ~/tmp/dirs.png
            >     pie(dirs[,1], labels = dirs[,2])
            >   #+end_src
            >
            > Best regards,
            >   Seb
            >
            > --
            > Sebastien Vauban
            >
            >
            >
            
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            ^ permalink raw reply	[flat|nested] 9+ messages in thread

          • • * Re: Babel-R TBLFM example
                2014-08-26  6:18           ` Shiyuan
              @ 2014-08-26  6:57             ` Thomas S. Dye
                2014-08-26  7:23               ` Sebastien Vauban
                0 siblings, 1 reply; 9+ messages in thread
              From: Thomas S. Dye @ 2014-08-26  6:57 UTC (permalink / raw)
                To: Shiyuan; +Cc: emacs-orgmode@gnu.org
              
              Aloha all,
              
              >> AFAICT, the arguments to code blocks may not be defined and set in the
              >> `name' line anymore: this must be done on the `begin_src' line.
              
              or, on a separate #+header: line.
              
              All the best,
              Tom
              
              -- 
              Thomas S. Dye
              http://www.tsdye.com
              
              ^ permalink raw reply	[flat|nested] 9+ messages in thread

            • • * Re: Babel-R TBLFM example
                  2014-08-26  6:57             ` Thomas S. Dye
                @ 2014-08-26  7:23               ` Sebastien Vauban
                  0 siblings, 0 replies; 9+ messages in thread
                From: Sebastien Vauban @ 2014-08-26  7:23 UTC (permalink / raw)
                  To: emacs-orgmode-mXXj517/zsQ
                
                Thomas S. Dye wrote:
                > Aloha all,
                >
                >>> AFAICT, the arguments to code blocks may not be defined and set in the
                >>> `name' line anymore: this must be done on the `begin_src' line.
                >
                > or, on a separate #+header: line.
                
                Indeed.  I tend to forget to use that; thanks for mentioning it!
                
                Best regards,
                  Seb
                
                -- 
                Sebastien Vauban
                
                ^ permalink raw reply	[flat|nested] 9+ messages in thread

end of thread, other threads:[~2014-08-26  7:23 UTC | newest]

Thread overview: 9+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2014-06-25  6:55 Babel-R TBLFM example Shiyuan
2014-07-28 13:21 ` Bastien
2014-07-29  6:15   ` Shiyuan
2014-07-29 13:20     ` Bastien
2014-08-24 23:02       ` Shiyuan
2014-08-25  7:51         ` Sebastien Vauban
2014-08-26  6:18           ` Shiyuan
2014-08-26  6:57             ` Thomas S. Dye
2014-08-26  7:23               ` Sebastien Vauban

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