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Updating o-b.org: two new R colname tests and graphics output discussion.
This commit is contained in:
Dan Davison
parent
062bc09d84
commit
daf3e210da
234
org-babel.org
234
org-babel.org
@ -204,7 +204,7 @@ would then be [[#sandbox][the sandbox]].
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#+end_src
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* Tasks [32/51]
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* Tasks [33/51]
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** PROPOSED optional timestamp for output
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Add option to place an (inactive) timestamp at the #+resname, to
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record when that output was generated.
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@ -367,6 +367,52 @@ languages which almost always produce graphical output should set
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results in the buffer. Then if there is a combination of =silent= and
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=file= =:results= headers we could drop the results to a temp buffer
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and pop open that buffer...
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*** Adding to a discussion started in email
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I'm not deeply wedded to these ideas, just noting them down. I'm
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probably just thinking of R and haven't really thought about how
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this fits with the other graphics-generating languages.
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Dan:
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> I used the approach below to get graphical file output
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> today, which is one idea at least. Maybe it could be linked up with
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> your :results file variable. (Or do we need a :results image for R?)
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>
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Eric:
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I don't think we need a special image results variable, but I may be
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missing what the code below accomplishes. Would the task I added about
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adding org-open-at-point functionality to source code blocks take care
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of this need?
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Dan: I'm not sure. I think the ability for a script to generate both
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text and graphical output might be a natural expectation, at least for
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R users.
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>
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> Dan
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>
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> #+srcname: cohort-scatter-plots-2d(org_babel_graphical_output_file="cohort-scatter-plots-2d.png")
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> #+begin_src R
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> if(exists("org_babel_output_file"))
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> png(filename=org_babel_graphical_output_file, width=1000, height=1000)
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> ## plotting code in here
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> if(exists("org_babel_graphical_output_file")) dev.off()
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> #+end_src
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Dan: Yes, the results :file option is nice for dealing with graphical
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output, and that could well be enough. Something based on the scheme
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above would have a couple of points in its favour:
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1. It's easy to switch between output going to on-screen graphics and
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output going to file: Output will go to screen unless a string variable
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with a standard name (e.g. ""org_babel_graphical_output_file"")
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exists in which case it will go to the file indicated by the value
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of that variable.
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2. The block can return a result / script output, as well as produce
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graphical output.
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In interactive use we might want to allow the user to choose between
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screen and file output. In non-interactive use such as export, it
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would be file output (subject to the :exports directives).
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** TODO =\C-c \C-o= to open results of source block
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by adding a =defadvice= to =org-open-at-point= we can use the common
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=\C-c \C-o= keybinding to open the results of a source-code block.
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@ -386,20 +432,21 @@ there are spaces in the message and scalar otherwise.
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[Not any more]
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#+begin_src R :var msg=msg-from-python
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#+srcname: msg-from-R(msg=msg-from-python)
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#+begin_src R
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paste(msg, "und R", sep=" ")
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#+end_src
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#+resname:
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: org-babel speaks elisp y python und R
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#+srcname: msg-from-python
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#+begin_src python :var msg=msg-from-elisp
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#+srcname: msg-from-python(msg=msg-from-elisp)
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#+begin_src python
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msg + " y python"
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#+end_src
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#+srcname: msg-from-elisp
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#+begin_src emacs-lisp :var msg="org-babel speaks"
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#+srcname: msg-from-elisp(msg="org-babel speaks")
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#+begin_src emacs-lisp
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(concat msg " elisp")
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#+end_src
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** STARTED share org-babel [1/4]
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@ -629,23 +676,6 @@ Another example is in the [[*operations%20in%20on%20tables][grades example]].
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*** Current design
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This is covered by the [[file:library-of-babel.org][Library of Babel]], which will contain
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ready-made source blocks designed to carry out useful common tasks.
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** PROPOSED Are we happy with current behaviour regarding vector/scalar output?
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This simple example of multilingual chaining produces vector output if
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there are spaces in the message and scalar otherwise.
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#+begin_src R :var msg=msg-from-python
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paste(msg, "und_R", sep="_")
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#+end_src
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#+srcname: msg-from-python
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#+begin_src python :var msg=msg-from-elisp
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msg + "_y_python"
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#+end_src
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#+srcname: msg-from-elisp
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#+begin_src emacs-lisp :var msg="org-babel_speaks"
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(concat msg "_elisp")
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#+end_src
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** PROPOSED conversion between org-babel and noweb (e.g. .Rnw) format
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I haven't thought about this properly. Just noting it down. What
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@ -723,67 +753,11 @@ for quick tests
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mean(mean(vec))
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#+end_src
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#+resname:
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: 2
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** DEFERRED re-implement R evaluation using ess-command or ess-execute
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I don't have any complaints with the current R evaluation code or
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behaviour, but I think it would be good to use the ESS functions
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from a political point of view. Plus of course it has the normal
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benefits of an API (insulates us from any underlying changes etc). [DED]
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I'll look into this. I believe that I looked at and rejected these
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functions initially but now I can't remember why. I agree with
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your overall point about using API's where available. I will take
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a look back at these and either switch to using the ess commands,
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or at least articulate under this TODO the reasons for using our
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custom R-interaction commands. [Eric]
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ess-execute
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Lets just replace =org-babel-R-input-command= with =ess-execute=.
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I tried this, and although it works in some situations, I find that
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=ess-command= will often just hang indefinitely without returning
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results. Also =ess-execute= will occasionally hang, and pops up
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the buffer containing the results of the command's execution, which
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is undesirable. For now these functions can not be used. Maybe
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someone more familiar with the ESS code can recommend proper usage
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of =ess-command= or some other lower-level function which could be
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used in place of [[file:lisp/org-babel-R.el::defun%20org-babel%20R%20input%20command%20command][org-babel-R-input-command]].
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*** ess functions
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#+begin_quote ess-command
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(ess-command COM &optional BUF SLEEP NO-PROMPT-CHECK)
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Send the ESS process command COM and delete the output
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from the ESS process buffer. If an optional second argument BUF exists
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save the output in that buffer. BUF is erased before use.
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COM should have a terminating newline.
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Guarantees that the value of .Last.value will be preserved.
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When optional third arg SLEEP is non-nil, `(sleep-for (* a SLEEP))'
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will be used in a few places where `a' is proportional to `ess-cmd-delay'.
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#+end_quote
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#+begin_quote ess-execute
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(ess-execute COMMAND &optional INVERT BUFF MESSAGE)
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Send a command to the ESS process.
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A newline is automatically added to COMMAND. Prefix arg (or second arg
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INVERT) means invert the meaning of
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`ess-execute-in-process-buffer'. If INVERT is 'buffer, output is
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forced to go to the process buffer. If the output is going to a
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buffer, name it *BUFF*. This buffer is erased before use. Optional
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fourth arg MESSAGE is text to print at the top of the buffer (defaults
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to the command if BUFF is not given.)
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#+end_quote
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*** out current setup
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1) The body of the R source code block is wrapped in a function
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2) The function is called inside of a =write.table= function call
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writing the results to a table
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3) The table is read using =org-table-import=
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: 2
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** DEFERRED Rework Interaction with Running Processes [2/5]
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*** DONE robust to errors interrupting execution
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@ -879,6 +853,65 @@ $0
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waiting for guidance from those more familiar with yasnippets
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** REJECTED re-implement R evaluation using ess-command or ess-execute
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I don't have any complaints with the current R evaluation code or
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behaviour, but I think it would be good to use the ESS functions
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from a political point of view. Plus of course it has the normal
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benefits of an API (insulates us from any underlying changes etc). [DED]
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I'll look into this. I believe that I looked at and rejected these
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functions initially but now I can't remember why. I agree with
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your overall point about using API's where available. I will take
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a look back at these and either switch to using the ess commands,
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or at least articulate under this TODO the reasons for using our
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custom R-interaction commands. [Eric]
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ess-execute
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Lets just replace =org-babel-R-input-command= with =ess-execute=.
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I tried this, and although it works in some situations, I find that
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=ess-command= will often just hang indefinitely without returning
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results. Also =ess-execute= will occasionally hang, and pops up
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the buffer containing the results of the command's execution, which
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is undesirable. For now these functions can not be used. Maybe
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someone more familiar with the ESS code can recommend proper usage
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of =ess-command= or some other lower-level function which could be
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used in place of [[file:lisp/org-babel-R.el::defun%20org-babel%20R%20input%20command%20command][org-babel-R-input-command]].
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*** ess functions
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#+begin_quote ess-command
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(ess-command COM &optional BUF SLEEP NO-PROMPT-CHECK)
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Send the ESS process command COM and delete the output
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from the ESS process buffer. If an optional second argument BUF exists
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save the output in that buffer. BUF is erased before use.
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COM should have a terminating newline.
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Guarantees that the value of .Last.value will be preserved.
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When optional third arg SLEEP is non-nil, `(sleep-for (* a SLEEP))'
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will be used in a few places where `a' is proportional to `ess-cmd-delay'.
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#+end_quote
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#+begin_quote ess-execute
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(ess-execute COMMAND &optional INVERT BUFF MESSAGE)
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Send a command to the ESS process.
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A newline is automatically added to COMMAND. Prefix arg (or second arg
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INVERT) means invert the meaning of
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`ess-execute-in-process-buffer'. If INVERT is 'buffer, output is
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forced to go to the process buffer. If the output is going to a
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buffer, name it *BUFF*. This buffer is erased before use. Optional
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fourth arg MESSAGE is text to print at the top of the buffer (defaults
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to the command if BUFF is not given.)
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#+end_quote
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*** out current setup
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1) The body of the R source code block is wrapped in a function
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2) The function is called inside of a =write.table= function call
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writing the results to a table
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3) The table is read using =org-table-import=
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** DONE use example block for large amounts of stdout output?
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We're currently `examplizing' with : at the beginning of the line,
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but should larger amounts of output be in a
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@ -2642,6 +2675,8 @@ of these tests may fail.
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| ruby | table-ruby | | 1-2-3 | 1-2-3 | pass |
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| python | table-python | | 5 | 5 | pass |
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| R | table-R | | 3.5 | 3.5 | pass |
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| R: col names in R | table-R-colnames | | -3 | -3 | pass |
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| R: col names in org | table-R-colnames-org | | 169 | 169 | pass |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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| source block references | | | | | pass |
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|-------------------------+----------------------------+-----+-------------+-------------+------|
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@ -2675,7 +2710,8 @@ of these tests may fail.
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#+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))
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#+TBLFM: $5=""::$6=""
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The second line (followed by replacing '[]' with '') can be used to blank out the table results, in the absence of a better method.
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The second TBLFM line (followed by replacing '[]' with '') can be used
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to blank out the table results, in the absence of a better method.
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** basic tests
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@ -2721,6 +2757,12 @@ b + 4
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| 1 | 2 | 3 |
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| 4 | 5 | 6 |
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#+tblname: test-table-colnames
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| var1 | var2 | var3 |
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|------+------+------|
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| 1 | 22 | 13 |
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| 41 | 55 | 67 |
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#+srcname: table-elisp
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#+begin_src emacs-lisp :results silent :var table=test-table
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(length (car table))
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@ -2738,12 +2780,34 @@ table.first.join("-")
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table[1][1]
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#+end_src
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#+srcname: table-R
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#+begin_src R :var table=test-table
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#+srcname: table-R(table=test-table)
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#+begin_src R
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mean(mean(table))
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#+end_src
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#+srcname: table-R-colnames(table=test-table-colnames)
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#+begin_src R :results silent
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sum(table$var2 - table$var3)
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#+end_src
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#+srcname: R-square(x=default-name-doesnt-exist)
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#+begin_src R :colnames t
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x^2
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#+end_src
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This should return 169. The fact that R is able to use the column name
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to index the data frame (x$var3) proves that a table with column names
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(a header row) has been recognised as input for the R-square function
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block, and that the R-square block has output an elisp table with
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column names, and that the colnames have again been recognised when
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creating the R variables in this block.
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#+srcname: table-R-colnames-org(x = R-square(x=test-table-colnames))
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#+begin_src R
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x$var3[1]
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#+end_src
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** references
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