* Out of Order Evaluation
@ 2014-03-20 22:02 Michael Weylandt
2014-03-20 22:13 ` Andreas Leha
2014-03-24 2:06 ` Eric Schulte
0 siblings, 2 replies; 7+ messages in thread
From: Michael Weylandt @ 2014-03-20 22:02 UTC (permalink / raw)
To: emacs-orgmode@gnu.org
Hi,
I want to put a summary of my analysis at the beginning of a document using results calculated at the end of the document. Is this possible?
#=========
#+TITLE: Test
#+AUTHOR: Michael Weylandt
#+PROPERTY: header-args:R :session *__R__* :exports both
* Summary
The mean result was src_R[:exports results]{mean(x)}
* Analysis,
We do some complicated calculations:
#+BEGIN_SRC R
x <- rnorm(5)
#+END_SRC
#=========
Is this possible in a single pass? I've played with #+NAME and <<block()>> but haven't gotten the out-of-order evaluation quite right.
Michael
(Bonus question, is there a way to not have to put ":exports results" in inline blocks?)
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Out of Order Evaluation
2014-03-20 22:02 Out of Order Evaluation Michael Weylandt
@ 2014-03-20 22:13 ` Andreas Leha
2014-03-21 1:34 ` Charles Berry
2014-03-24 2:06 ` Eric Schulte
1 sibling, 1 reply; 7+ messages in thread
From: Andreas Leha @ 2014-03-20 22:13 UTC (permalink / raw)
To: emacs-orgmode
Hi Michael,
Michael Weylandt <michael.weylandt@gmail.com> writes:
> Hi,
>
> I want to put a summary of my analysis at the beginning of a document
> using results calculated at the end of the document. Is this possible?
>
> #=========
> #+TITLE: Test
> #+AUTHOR: Michael Weylandt
> #+PROPERTY: header-args:R :session *__R__* :exports both
>
> * Summary
> The mean result was src_R[:exports results]{mean(x)}
>
> * Analysis,
> We do some complicated calculations:
>
> #+BEGIN_SRC R
> x <- rnorm(5)
> #+END_SRC
> #=========
>
> Is this possible in a single pass? I've played with #+NAME and
> <<block()>> but haven't gotten the out-of-order evaluation quite
> right.
>
> Michael
>
How about something along:
--8<---------------cut here---------------start------------->8---
#+TITLE: Test
#+AUTHOR: Michael Weylandt
#+PROPERTY: header-args:R :session *__R__* :exports both
* Summary
The mean result was src_R[:exports results :var analysisresults=theanalysis()]{mean(unlist(analysisresults))}
* Analysis,
We do some complicated calculations:
#+name: theanalysis
#+BEGIN_SRC R
x <- rnorm(5)
#+END_SRC
--8<---------------cut here---------------end--------------->8---
Regards,
Andreas
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Out of Order Evaluation
2014-03-20 22:13 ` Andreas Leha
@ 2014-03-21 1:34 ` Charles Berry
2014-03-21 8:01 ` Andreas Leha
2014-03-21 18:51 ` Michael Weylandt
0 siblings, 2 replies; 7+ messages in thread
From: Charles Berry @ 2014-03-21 1:34 UTC (permalink / raw)
To: emacs-orgmode
Andreas Leha <andreas.leha <at> med.uni-goettingen.de> writes:
>
> Hi Michael,
>
> Michael Weylandt <michael.weylandt <at> gmail.com> writes:
>
> > Hi,
> >
> > I want to put a summary of my analysis at the beginning of a document
> > using results calculated at the end of the document. Is this possible?
[snip]
> >
> > Is this possible in a single pass?
Not quite. The method suggested by Andreas computes the result twice. If
there is any randomness in the results (as in the example) you will get a
different answer in the summary than when the block is later evaluated.
> > I've played with #+NAME and
> > <<block()>> but haven't gotten the out-of-order evaluation quite
> > right.
You can use
#+results: the-mean
before
#+NAME: the-mean
#+begin_src R
mean(x)
#+end_src
which is after 'theanalysis' block.
And if the format is not pleasing add a filter that reformats the result.
> >
> > Michael
> >
>
> How about something along:
>
> --8<---------------cut here---------------start------------->8---
> #+TITLE: Test
> #+AUTHOR: Michael Weylandt
> #+PROPERTY: header-args:R :session *__R__* :exports both
>
> * Summary
> The mean result was src_R[:exports results :var
analysisresults=theanalysis()]{mean(unlist(analysisresults))}
>
> * Analysis,
> We do some complicated calculations:
>
> #+name: theanalysis
> #+BEGIN_SRC R
> x <- rnorm(5)
> #+END_SRC
> --8<---------------cut here---------------end--------------->8---
It might be better to mark all the blocks in the doc ':eval never'
and ':exports code' or ':exports none' and put blocks before the first
headline that do all the calcs from noweb references, and put the #+results
lines (if you need them) wherever you want them in the doc. Like so:
--8<---------------cut here---------------start------------->8---
#+TITLE: Test
#+AUTHOR: Michael Weylandt
#+PROPERTY: header-args:R :session *__R__* :exports both
#+NAME: master
#+BEGIN_SRC R :noweb yes :results silent :exports results
<<theanalysis>>
#+END_SRC
* Summary
The mean result was src_R[:exports results]{mean(x)}
* Analysis,
We do some complicated calculations:
#+name: theanalysis
#+BEGIN_SRC R :eval never :exports code
x <- rnorm(5)
#+END_SRC
--8<---------------cut here---------------end--------------->8---
IMO, needing ':exports results' for inline src blocks is a bug not a
feature.
HTH,
Chuck
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Out of Order Evaluation
2014-03-21 1:34 ` Charles Berry
@ 2014-03-21 8:01 ` Andreas Leha
2014-03-21 8:15 ` Andreas Leha
2014-03-21 18:51 ` Michael Weylandt
1 sibling, 1 reply; 7+ messages in thread
From: Andreas Leha @ 2014-03-21 8:01 UTC (permalink / raw)
To: emacs-orgmode
Charles Berry <ccberry@ucsd.edu> writes:
> Andreas Leha <andreas.leha <at> med.uni-goettingen.de> writes:
>
>>
>> Hi Michael,
>>
>> Michael Weylandt <michael.weylandt <at> gmail.com> writes:
>>
>> > Hi,
>> >
>> > I want to put a summary of my analysis at the beginning of a document
>> > using results calculated at the end of the document. Is this possible?
>
> [snip]
>
>> >
>> > Is this possible in a single pass?
>
>
> Not quite. The method suggested by Andreas computes the result twice. If
> there is any randomness in the results (as in the example) you will get a
> different answer in the summary than when the block is later evaluated.
>
Well, you could enter the ':cache yes' world here. Although, for me,
that produced more problems than it solved (since there is no tracking
of dependencies among code blocks in :session mode).
My typical workflow now is something 'less literate': My typical
project Org file will look like this:
--8<---------------cut here---------------start------------->8---
* Execution
This is full of #+call: lines. By (my own) convention, this subtree has
to be evaluated before exporting the next subsection.
* Report
This is the report / presentation.
* Analysis
This contains all the code block to be called from the Execution
subtree.
(Plus usually quite a lot of code blocks from dead ends of the
project...)
--8<---------------cut here---------------end--------------->8---
This solves your problem (and is along the lines Charles suggests as
well), but requires more work than just export the document and is,
thus, less literate.
Regards,
Andreas
>> > I've played with #+NAME and
>> > <<block()>> but haven't gotten the out-of-order evaluation quite
>> > right.
>
> You can use
>
> #+results: the-mean
>
> before
>
> #+NAME: the-mean
> #+begin_src R
> mean(x)
> #+end_src
>
> which is after 'theanalysis' block.
>
> And if the format is not pleasing add a filter that reformats the result.
>
>
>> >
>> > Michael
>> >
>>
>> How about something along:
>>
>> --8<---------------cut here---------------start------------->8---
>> #+TITLE: Test
>> #+AUTHOR: Michael Weylandt
>> #+PROPERTY: header-args:R :session *__R__* :exports both
>>
>> * Summary
>> The mean result was src_R[:exports results :var
> analysisresults=theanalysis()]{mean(unlist(analysisresults))}
>>
>> * Analysis,
>> We do some complicated calculations:
>>
>> #+name: theanalysis
>> #+BEGIN_SRC R
>> x <- rnorm(5)
>> #+END_SRC
>> --8<---------------cut here---------------end--------------->8---
>
>
> It might be better to mark all the blocks in the doc ':eval never'
> and ':exports code' or ':exports none' and put blocks before the first
> headline that do all the calcs from noweb references, and put the #+results
> lines (if you need them) wherever you want them in the doc. Like so:
>
>
>
> #+TITLE: Test
> #+AUTHOR: Michael Weylandt
> #+PROPERTY: header-args:R :session *__R__* :exports both
>
>
> #+NAME: master
> #+BEGIN_SRC R :noweb yes :results silent :exports results
> <<theanalysis>>
> #+END_SRC
>
> * Summary
>
>
> The mean result was src_R[:exports results]{mean(x)}
>
> * Analysis,
> We do some complicated calculations:
>
> #+name: theanalysis
> #+BEGIN_SRC R :eval never :exports code
> x <- rnorm(5)
> #+END_SRC
>
>
> IMO, needing ':exports results' for inline src blocks is a bug not a
> feature.
>
> HTH,
>
> Chuck
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Out of Order Evaluation
2014-03-21 8:01 ` Andreas Leha
@ 2014-03-21 8:15 ` Andreas Leha
0 siblings, 0 replies; 7+ messages in thread
From: Andreas Leha @ 2014-03-21 8:15 UTC (permalink / raw)
To: emacs-orgmode
Andreas Leha <andreas.leha@med.uni-goettingen.de> writes:
> Charles Berry <ccberry@ucsd.edu> writes:
>
>> Andreas Leha <andreas.leha <at> med.uni-goettingen.de> writes:
>>
>>>
>>> Hi Michael,
>>>
>>> Michael Weylandt <michael.weylandt <at> gmail.com> writes:
>>>
>>> > Hi,
>>> >
>>> > I want to put a summary of my analysis at the beginning of a document
>>> > using results calculated at the end of the document. Is this possible?
>>
>> [snip]
>>
>>> >
>>> > Is this possible in a single pass?
>>
>>
>> Not quite. The method suggested by Andreas computes the result twice. If
>> there is any randomness in the results (as in the example) you will get a
>> different answer in the summary than when the block is later evaluated.
>>
>
> Well, you could enter the ':cache yes' world here. Although, for me,
> that produced more problems than it solved (since there is no tracking
> of dependencies among code blocks in :session mode).
>
> My typical workflow now is something 'less literate': My typical
> project Org file will look like this:
>
> * Execution
> This is full of #+call: lines. By (my own) convention, this subtree has
> to be evaluated before exporting the next subsection.
>
> * Report
> This is the report / presentation.
>
> * Analysis
> This contains all the code block to be called from the Execution
> subtree.
> (Plus usually quite a lot of code blocks from dead ends of the
> project...)
>
>
> This solves your problem (and is along the lines Charles suggests as
> well), but requires more work than just export the document and is,
> thus, less literate.
I should add here, that working with #+call lines is not too convenient.
These are missing some functionality compared to source blocks. Most
importantly 'C-c C-v v' and 'C-c C-v n' are missing. I wanted to have a
look at those for quite some time, but have not gotten around to do so.
Regards,
Andreas
>
> Regards,
> Andreas
>
>
>
>>> > I've played with #+NAME and
>>> > <<block()>> but haven't gotten the out-of-order evaluation quite
>>> > right.
>>
>> You can use
>>
>> #+results: the-mean
>>
>> before
>>
>> #+NAME: the-mean
>> #+begin_src R
>> mean(x)
>> #+end_src
>>
>> which is after 'theanalysis' block.
>>
>> And if the format is not pleasing add a filter that reformats the result.
>>
>>
>>> >
>>> > Michael
>>> >
>>>
>>> How about something along:
>>>
>>> --8<---------------cut here---------------start------------->8---
>>> #+TITLE: Test
>>> #+AUTHOR: Michael Weylandt
>>> #+PROPERTY: header-args:R :session *__R__* :exports both
>>>
>>> * Summary
>>> The mean result was src_R[:exports results :var
>> analysisresults=theanalysis()]{mean(unlist(analysisresults))}
>>>
>>> * Analysis,
>>> We do some complicated calculations:
>>>
>>> #+name: theanalysis
>>> #+BEGIN_SRC R
>>> x <- rnorm(5)
>>> #+END_SRC
>>> --8<---------------cut here---------------end--------------->8---
>>
>>
>> It might be better to mark all the blocks in the doc ':eval never'
>> and ':exports code' or ':exports none' and put blocks before the first
>> headline that do all the calcs from noweb references, and put the #+results
>> lines (if you need them) wherever you want them in the doc. Like so:
>>
>>
>>
>> #+TITLE: Test
>> #+AUTHOR: Michael Weylandt
>> #+PROPERTY: header-args:R :session *__R__* :exports both
>>
>>
>> #+NAME: master
>> #+BEGIN_SRC R :noweb yes :results silent :exports results
>> <<theanalysis>>
>> #+END_SRC
>>
>> * Summary
>>
>>
>> The mean result was src_R[:exports results]{mean(x)}
>>
>> * Analysis,
>> We do some complicated calculations:
>>
>> #+name: theanalysis
>> #+BEGIN_SRC R :eval never :exports code
>> x <- rnorm(5)
>> #+END_SRC
>>
>>
>> IMO, needing ':exports results' for inline src blocks is a bug not a
>> feature.
>>
>> HTH,
>>
>> Chuck
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Out of Order Evaluation
2014-03-21 1:34 ` Charles Berry
2014-03-21 8:01 ` Andreas Leha
@ 2014-03-21 18:51 ` Michael Weylandt
1 sibling, 0 replies; 7+ messages in thread
From: Michael Weylandt @ 2014-03-21 18:51 UTC (permalink / raw)
To: Charles Berry; +Cc: emacs-orgmode@gnu.org
On Mar 20, 2014, at 21:34, Charles Berry <ccberry@ucsd.edu> wrote:
> Andreas Leha <andreas.leha <at> med.uni-goettingen.de> writes:
>
>>
>> Hi Michael,
>>
>> Michael Weylandt <michael.weylandt <at> gmail.com> writes:
>>
>>> Hi,
>>>
>>> I want to put a summary of my analysis at the beginning of a document
>>> using results calculated at the end of the document. Is this possible?
>
> [snip]
>
>>>
>>> Is this possible in a single pass?
>
>
> Not quite. The method suggested by Andreas computes the result twice. If
> there is any randomness in the results (as in the example) you will get a
> different answer in the summary than when the block is later evaluated.
>
>>> I've played with #+NAME and
>>> <<block()>> but haven't gotten the out-of-order evaluation quite
>>> right.
>
> You can use
>
> #+results: the-mean
>
> before
>
> #+NAME: the-mean
> #+begin_src R
> mean(x)
> #+end_src
>
> which is after 'theanalysis' block.
>
> And if the format is not pleasing add a filter that reformats the results
Great. The named result block is just what I needed.
>
> IMO, needing ':exports results' for inline src blocks is a bug not a
> feature.
>
Agreed, particularly in light of Eric's comments at
http://lists.gnu.org/archive/html/emacs-orgmode/2014-03/msg00285.html
There's the variable org-babel-inline-header-args, but it seems using
#+PROPERTY: header-args :exports both
overrules/breaks it
Would org want something like
#+PROPERTY: inline-header-args :exports results
Or just 'hard-code' :exports results for all inline blocks?
^ permalink raw reply [flat|nested] 7+ messages in thread
* Re: Out of Order Evaluation
2014-03-20 22:02 Out of Order Evaluation Michael Weylandt
2014-03-20 22:13 ` Andreas Leha
@ 2014-03-24 2:06 ` Eric Schulte
1 sibling, 0 replies; 7+ messages in thread
From: Eric Schulte @ 2014-03-24 2:06 UTC (permalink / raw)
To: Michael Weylandt; +Cc: emacs-orgmode@gnu.org
Michael Weylandt <michael.weylandt@gmail.com> writes:
> Hi,
>
> I want to put a summary of my analysis at the beginning of a document
> using results calculated at the end of the document. Is this possible?
>
Yes, simply place the calculation in a subtree marked with :noexport at
the top of the document.
Best,
>
> #=========
> #+TITLE: Test
> #+AUTHOR: Michael Weylandt
> #+PROPERTY: header-args:R :session *__R__* :exports both
>
> * Summary
> The mean result was src_R[:exports results]{mean(x)}
>
> * Analysis,
> We do some complicated calculations:
>
> #+BEGIN_SRC R
> x <- rnorm(5)
> #+END_SRC
> #=========
>
> Is this possible in a single pass? I've played with #+NAME and
> <<block()>> but haven't gotten the out-of-order evaluation quite
> right.
>
> Michael
>
> (Bonus question, is there a way to not have to put ":exports results" in inline blocks?)
--
Eric Schulte
https://cs.unm.edu/~eschulte
PGP: 0x614CA05D
^ permalink raw reply [flat|nested] 7+ messages in thread
end of thread, other threads:[~2014-03-24 2:08 UTC | newest]
Thread overview: 7+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2014-03-20 22:02 Out of Order Evaluation Michael Weylandt
2014-03-20 22:13 ` Andreas Leha
2014-03-21 1:34 ` Charles Berry
2014-03-21 8:01 ` Andreas Leha
2014-03-21 8:15 ` Andreas Leha
2014-03-21 18:51 ` Michael Weylandt
2014-03-24 2:06 ` Eric Schulte
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