Updating o-b.org: two new R colname tests and graphics output discussion.

org-babel.org

@@ -204,7 +204,7 @@ would then be [[#sandbox][the sandbox]].
 #+end_src
 
 
-* Tasks [32/51]
+* Tasks [33/51]
 ** PROPOSED optional timestamp for output
    Add option to place an (inactive) timestamp at the #+resname, to
    record when that output was generated.
@@ -367,6 +367,52 @@ languages which almost always produce graphical output should set
 results in the buffer.  Then if there is a combination of =silent= and
 =file= =:results= headers we could drop the results to a temp buffer
 and pop open that buffer...
+
+*** Adding to a discussion started in email
+    I'm not deeply wedded to these ideas, just noting them down. I'm
+    probably just thinking of R and haven't really thought about how
+    this fits with the other graphics-generating languages.
+Dan:
+> I used the approach below to get graphical file output
+> today, which is one idea at least. Maybe it could be linked up with
+> your :results file variable. (Or do we need a :results image for R?)
+>
+Eric:
+I don't think we need a special image results variable, but I may be
+missing what the code below accomplishes.  Would the task I added about
+adding org-open-at-point functionality to source code blocks take care
+of this need?
+
+Dan: I'm not sure. I think the ability for a script to generate both
+text and graphical output might be a natural expectation, at least for
+R users.
+
+>
+> Dan
+>
+> #+srcname: cohort-scatter-plots-2d(org_babel_graphical_output_file="cohort-scatter-plots-2d.png")
+> #+begin_src R 
+>   if(exists("org_babel_output_file"))
+>       png(filename=org_babel_graphical_output_file, width=1000, height=1000)
+>   ## plotting code in here
+>   if(exists("org_babel_graphical_output_file")) dev.off()
+> #+end_src
+
+Dan: Yes, the results :file option is nice for dealing with graphical
+output, and that could well be enough. Something based on the scheme
+above would have a couple of points in its favour:
+1. It's easy to switch between output going to on-screen graphics and
+   output going to file: Output will go to screen unless a string variable
+   with a standard name (e.g. ""org_babel_graphical_output_file"")
+   exists in which case it will go to the file indicated by the value
+   of that variable.
+2. The block can return a result / script output, as well as produce
+   graphical output.
+
+In interactive use we might want to allow the user to choose between
+screen and file output. In non-interactive use such as export, it
+would be file output (subject to the :exports directives).
+
 ** TODO =\C-c \C-o= to open results of source block
 by adding a =defadvice= to =org-open-at-point= we can use the common
 =\C-c \C-o= keybinding to open the results of a source-code block.
@@ -386,20 +432,21 @@ there are spaces in the message and scalar otherwise.
 
 [Not any more]
 
-#+begin_src R :var msg=msg-from-python
+#+srcname: msg-from-R(msg=msg-from-python)
+#+begin_src R
 paste(msg, "und R", sep=" ")
 #+end_src
 
 #+resname:
 : org-babel speaks elisp y python und R
 
-#+srcname: msg-from-python
-#+begin_src python :var msg=msg-from-elisp
+#+srcname: msg-from-python(msg=msg-from-elisp)
+#+begin_src python
 msg + " y python"
 #+end_src
 
-#+srcname: msg-from-elisp
-#+begin_src emacs-lisp :var msg="org-babel speaks"
+#+srcname: msg-from-elisp(msg="org-babel speaks")
+#+begin_src emacs-lisp
 (concat msg " elisp")
 #+end_src
 ** STARTED share org-babel [1/4]
@@ -629,23 +676,6 @@ Another example is in the [[*operations%20in%20on%20tables][grades example]].
 *** Current design
     This is covered by the [[file:library-of-babel.org][Library of Babel]], which will contain
     ready-made source blocks designed to carry out useful common tasks.
-** PROPOSED Are we happy with current behaviour regarding vector/scalar output?
-This simple example of multilingual chaining produces vector output if
-there are spaces in the message and scalar otherwise.
-
-#+begin_src R :var msg=msg-from-python
-paste(msg, "und_R", sep="_")
-#+end_src
-
-#+srcname: msg-from-python
-#+begin_src python :var msg=msg-from-elisp
-msg + "_y_python"
-#+end_src
-
-#+srcname: msg-from-elisp
-#+begin_src emacs-lisp :var msg="org-babel_speaks"
-(concat msg "_elisp")
-#+end_src
 
 ** PROPOSED conversion between org-babel and noweb (e.g. .Rnw) format
    I haven't thought about this properly. Just noting it down. What
@@ -723,67 +753,11 @@ for quick tests
 mean(mean(vec))
 #+end_src
 
+#+resname:
 : 2
 
-** DEFERRED re-implement R evaluation using ess-command or ess-execute
-   I don't have any complaints with the current R evaluation code or
-   behaviour, but I think it would be good to use the ESS functions
-   from a political point of view. Plus of course it has the normal
-   benefits of an API (insulates us from any underlying changes etc). [DED]
-
-   I'll look into this.  I believe that I looked at and rejected these
-   functions initially but now I can't remember why.  I agree with
-   your overall point about using API's where available.  I will take
-   a look back at these and either switch to using the ess commands,
-   or at least articulate under this TODO the reasons for using our
-   custom R-interaction commands. [Eric]
-
-   ess-execute
-
-   Lets just replace =org-babel-R-input-command= with =ess-execute=.
-
-   I tried this, and although it works in some situations, I find that
-   =ess-command= will often just hang indefinitely without returning
-   results.  Also =ess-execute= will occasionally hang, and pops up
-   the buffer containing the results of the command's execution, which
-   is undesirable.  For now these functions can not be used.  Maybe
-   someone more familiar with the ESS code can recommend proper usage
-   of =ess-command= or some other lower-level function which could be
-   used in place of [[file:lisp/org-babel-R.el::defun%20org-babel%20R%20input%20command%20command][org-babel-R-input-command]].
-
-*** ess functions
-   
-#+begin_quote ess-command
-(ess-command COM &optional BUF SLEEP NO-PROMPT-CHECK)
-
-Send the ESS process command COM and delete the output
-from the ESS process buffer.  If an optional second argument BUF exists
-save the output in that buffer. BUF is erased before use.
-COM should have a terminating newline.
-Guarantees that the value of .Last.value will be preserved.
-When optional third arg SLEEP is non-nil, `(sleep-for (* a SLEEP))'
-will be used in a few places where `a' is proportional to `ess-cmd-delay'.
-#+end_quote
-
-#+begin_quote ess-execute
-(ess-execute COMMAND &optional INVERT BUFF MESSAGE)
-
-Send a command to the ESS process.
-A newline is automatically added to COMMAND.  Prefix arg (or second arg
-INVERT) means invert the meaning of
-`ess-execute-in-process-buffer'.  If INVERT is 'buffer, output is
-forced to go to the process buffer.  If the output is going to a
-buffer, name it *BUFF*.	 This buffer is erased before use.  Optional
-fourth arg MESSAGE is text to print at the top of the buffer (defaults
-to the command if BUFF is not given.)
-#+end_quote
-
-*** out current setup
 
-    1) The body of the R source code block is wrapped in a function
-    2) The function is called inside of a =write.table= function call
-       writing the results to a table
-    3) The table is read using =org-table-import=
+: 2
 
 ** DEFERRED Rework Interaction with Running Processes [2/5]
 *** DONE robust to errors interrupting execution
@@ -879,6 +853,65 @@ $0
 
 waiting for guidance from those more familiar with yasnippets
 
+** REJECTED re-implement R evaluation using ess-command or ess-execute
+   I don't have any complaints with the current R evaluation code or
+   behaviour, but I think it would be good to use the ESS functions
+   from a political point of view. Plus of course it has the normal
+   benefits of an API (insulates us from any underlying changes etc). [DED]
+
+   I'll look into this.  I believe that I looked at and rejected these
+   functions initially but now I can't remember why.  I agree with
+   your overall point about using API's where available.  I will take
+   a look back at these and either switch to using the ess commands,
+   or at least articulate under this TODO the reasons for using our
+   custom R-interaction commands. [Eric]
+
+   ess-execute
+
+   Lets just replace =org-babel-R-input-command= with =ess-execute=.
+
+   I tried this, and although it works in some situations, I find that
+   =ess-command= will often just hang indefinitely without returning
+   results.  Also =ess-execute= will occasionally hang, and pops up
+   the buffer containing the results of the command's execution, which
+   is undesirable.  For now these functions can not be used.  Maybe
+   someone more familiar with the ESS code can recommend proper usage
+   of =ess-command= or some other lower-level function which could be
+   used in place of [[file:lisp/org-babel-R.el::defun%20org-babel%20R%20input%20command%20command][org-babel-R-input-command]].
+
+*** ess functions
+   
+#+begin_quote ess-command
+(ess-command COM &optional BUF SLEEP NO-PROMPT-CHECK)
+
+Send the ESS process command COM and delete the output
+from the ESS process buffer.  If an optional second argument BUF exists
+save the output in that buffer. BUF is erased before use.
+COM should have a terminating newline.
+Guarantees that the value of .Last.value will be preserved.
+When optional third arg SLEEP is non-nil, `(sleep-for (* a SLEEP))'
+will be used in a few places where `a' is proportional to `ess-cmd-delay'.
+#+end_quote
+
+#+begin_quote ess-execute
+(ess-execute COMMAND &optional INVERT BUFF MESSAGE)
+
+Send a command to the ESS process.
+A newline is automatically added to COMMAND.  Prefix arg (or second arg
+INVERT) means invert the meaning of
+`ess-execute-in-process-buffer'.  If INVERT is 'buffer, output is
+forced to go to the process buffer.  If the output is going to a
+buffer, name it *BUFF*.	 This buffer is erased before use.  Optional
+fourth arg MESSAGE is text to print at the top of the buffer (defaults
+to the command if BUFF is not given.)
+#+end_quote
+
+*** out current setup
+
+    1) The body of the R source code block is wrapped in a function
+    2) The function is called inside of a =write.table= function call
+       writing the results to a table
+    3) The table is read using =org-table-import=
 ** DONE use example block for large amounts of stdout output?
    We're currently `examplizing' with : at the beginning of the line,
    but should larger amounts of output be in a
@@ -2642,6 +2675,8 @@ of these tests may fail.
 | ruby                    | table-ruby                 |     |       1-2-3 |       1-2-3 | pass |
 | python                  | table-python               |     |           5 |           5 | pass |
 | R                       | table-R                    |     |         3.5 |         3.5 | pass |
+| R: col names in R       | table-R-colnames           |     |          -3 |          -3 | pass |
+| R: col names in org     | table-R-colnames-org       |     |         169 |         169 | pass |
 |-------------------------+----------------------------+-----+-------------+-------------+------|
 | source block references |                            |     |             |             | pass |
 |-------------------------+----------------------------+-----+-------------+-------------+------|
@@ -2675,7 +2710,8 @@ of these tests may fail.
 #+TBLFM: $5='(if (= (length $3) 1) (progn (message (format "running %S" '(sbe $2 (n $3)))) (sbe $2 (n $3))) (sbe $2))::$6='(if (string= $4 $5) "pass" (format "expected %S but was %S" $4 $5))
 #+TBLFM: $5=""::$6=""
 
-The second line (followed by replacing '[]' with '') can be used to blank out the table results, in the absence of a better method.
+The second TBLFM line (followed by replacing '[]' with '') can be used
+to blank out the table results, in the absence of a better method.
 
 ** basic tests
 
@@ -2721,6 +2757,12 @@ b + 4
 | 1 | 2 | 3 |
 | 4 | 5 | 6 |
 
+#+tblname: test-table-colnames
+| var1 | var2 | var3 |
+|------+------+------|
+|    1 |   22 |   13 |
+|   41 |   55 |   67 |
+
 #+srcname: table-elisp
 #+begin_src emacs-lisp :results silent :var table=test-table
 (length (car table))
@@ -2738,12 +2780,34 @@ table.first.join("-")
 table[1][1]
 #+end_src
 
-
-#+srcname: table-R
-#+begin_src R :var table=test-table
+#+srcname: table-R(table=test-table)
+#+begin_src R
 mean(mean(table))
 #+end_src
 
+#+srcname: table-R-colnames(table=test-table-colnames)
+#+begin_src R :results silent
+sum(table$var2 - table$var3)
+#+end_src
+
+#+srcname: R-square(x=default-name-doesnt-exist)
+#+begin_src R :colnames t
+x^2
+#+end_src
+
+This should return 169. The fact that R is able to use the column name
+to index the data frame (x$var3) proves that a table with column names
+(a header row) has been recognised as input for the R-square function
+block, and that the R-square block has output an elisp table with
+column names, and that the colnames have again been recognised when
+creating the R variables in this block.
+#+srcname: table-R-colnames-org(x = R-square(x=test-table-colnames))
+#+begin_src R
+x$var3[1]
+#+end_src
+
+
+
 
 ** references