From: Daniele Pizzolli <dan@toel.it>
To: "Charles C. Berry" <ccberry@ucsd.edu>,
Aaron Ecay <aaronecay@gmail.com>,
Andreas Leha <andreas.leha@med.uni-goettingen.de>,
emacs-orgmode@gnu.org, Ista Zahn <istazahn@gmail.com>,
mcg <giepen.m@googlemail.com>
Subject: Re: [PATCH] inline src block results can be removed
Date: Mon, 24 Nov 2014 10:48:40 +0100 [thread overview]
Message-ID: <b52cbe2d2cc2963024c59a80c8c721e0@toel.it> (raw)
In-Reply-To: <87zjbqrapy.fsf@nicolasgoaziou.fr>
On 2014-11-17 00:23, Nicolas Goaziou wrote:
> "Charles C. Berry" writes:
>
>> For now, I'd be willing to make patches that will allow removal of the
>> inline src block results that do *not* involve these header args:
[]
> IMO, we're too much focused on the implementation details. We ought to
> agree on what should be done first. For example, considering
> `org-babel-insert-result' and its RESULT-PARAMS argument, I think the
> following makes sense:
>
> | Param | Example output |
> |---------+-----------------------------------|
> | default | {{{results(42)}}} |
> | file | {{{results(file:something.pdf)}}} |
> | list | |
> | raw | 42 |
> | drawer | |
> | org | {{{results(src_org{...})}}} |
> | html | {{{results(@@html:...@@)}}} |
> | latex | {{{results(@@latex:...@@)}}} |
> | code | {{{results(src_xxx{...})}}} |
>
> Basically, it should be possible to remove any kind of result using
> "results" macro, with the exception of "raw". "list" and "drawer" can
> be ignored since there is no inline equivalent.
[]
> There's no rush, however. Non-removable results from inline source
> blocks have been there for a long time.
Hello all,
I jump into this conversation because in the next months I will try to
write a supplementary information annex using org-mode with Gnu R, so
my idea on what should be done follows...
I guess I will start my project using those patches. Thanks!
A brief review on how how results are presented (or usually
anticipated) inline led me to the following wish list:
* provide some facilities to keep track of the 'unit of measurement'
Few numbers are pure numbers. There is a little value added to the
correctness of the work as a whole if I get the correct number from
babel but I have hard coded the wrong unit of measure in the text.
Please follow the examples.
# Load used languages
#+BEGIN_SRC emacs-lisp
(org-babel-do-load-languages
'org-babel-load-languages
'((emacs-lisp . nil)
(octave . t)
(R . t)))
#+END_SRC
Ideally, I think that reasonable solution would take table like the
following:
#+TBLNAME:speed-1
| speed | speed_unit |
|-------+------------|
| 12 | km/s |
and output by default or through an easy to call syntax:
#+BEGIN_EXAMPLE
12 km/s
#+END_EXAMPLE
I am not aware of any facilities provided by languages like R or
octave to keep track of the unit of measure, If you have some please
share.
A more space wise representation, that add another layer of
indirection would be to have a look-up table like the following:
#+TBLNAME:speed-1-units-lookup
| name | unit |
|--------+------|
| speed | km/s |
| length | km |
| time | s |
But I am not sure that it's worth it, at least for those that are
working with small data sets.
* support for inline rendering of tables
The most complex inline output I think I will need at some point
follows:
#+TBLNAME:data-set-1
#+NAME:data-set-1
| position | item1 | author1 | item2 | author2 | correlation |
|----------+-------+---------+-------+---------+-------------|
| 1 | i1 | a1 | j1 | b1 | c1 |
| 2 | i2 | a2 | j2 | b2 | c2 |
| 3 | i3 | a3 | j3 | b3 | c3 |
#+NAME: block-1
#+BEGIN_SRC R :session :colnames yes :exports none :var
data_set_1=data-set-1
# Just to show that we use R
data_set_2 <- data_set_1
#+END_SRC
#+RESULTS: block-1
| position | item1 | author1 | item2 | author2 | correlation |
|----------+-------+---------+-------+---------+-------------|
| 1 | i1 | a1 | j1 | b1 | c1 |
| 2 | i2 | a2 | j2 | b2 | c2 |
| 3 | i3 | a3 | j3 | b3 | c3 |
And I really like to be easily rendered as an inline string through
some formatting specs e.g.:
#+BEGIN_EXAMPLE
#+PROPERTY: header-args: R :fmt '(%(position)i) “%(item1)s” by
/%(author1)s/ correlate to “%(item2)s” by /%(author2)s/ with a
correlation coefficient of %(correlation).2f'
#+PROPERTY: header-args: R :rowsep (', ', ' and ')
The preliminary results show that: src_R[:session :results
replace]{data_set_2}.
#+END_EXAMPLE
Will be rendered as:
#+BEGIN_org
The preliminary results show that:
(1) “i1” by /a1/ correlate to “j1” by /b1/ with a correlation
coefficient of c1,
(2) “i2” by /a2/ correlate to “j2” by /b2/ with a correlation
coefficient of c2 and
(3) “i3” by /a3/ correlate to “j3” by /b3/ with a correlation
coefficient of c3.
#+END_org
For languages that does not support tables with headers we can stick
with the positional formatting:
#+NAME: block-2
#+BEGIN_SRC octave :session :colnames yes :exports none :var
data_set_1=data-set-1
ans = data_set_1;
#+END_SRC
# TODO: figure out why this does not work
#+RESULTS: block-2
: iii123aaa123jjj123bbb123ccc123
#+BEGIN_EXAMPLE
#+PROPERTY: header-args: octave :fmt '(%i) “%s” by /%s/ correlate to
“%s” by /%s/ with a correlation coefficient of %.2f'
#+PROPERTY: header-args: octave :rowsep (', ', ' and ')
The preliminary results show that: src_octave[:session :results
replace)]{ans}.
#+END_EXAMPLE
#+BEGIN_org
The preliminary results show that:
(1) “i1” by /a1/ correlate to “j1” by /b1/ with a correlation
coefficient of c1,
(2) “i2” by /a2/ correlate to “j2” by /b2/ with a correlation
coefficient of c2 and
(3) “i3” by /a3/ correlate to “j3” by /b3/ with a correlation
coefficient of c3.
#+END_org
* support for humanization
A minor point would be supporting some humanization of the numbers
using extended format placeholder to support:
- number-as-word or number-as-cardinal :: 1 -> one
- number-as-ordinal :: 2 -> second
- number-as-pretty-fraction :: 2.3333 -> 2 + 1/3
- number-as-word-fraction :: 2.3333 -> two and one third
- number-as-natural-size :: 1000000 -> 1.0 MB
- number-as-natural-size-binary :: 1000000 -> 976.6 KiB
* auto formatting standard test result
It would be nice to simplify the insertion of the result of standard
test like Chi-square by taking the =R= result and rewrite in a
sentence form:
#+BEGIN_org
\Chi-squared = 0.214, d.f. = 1, p-value < 0.05
#+END_org
But this is really lower priority because it will need a lot work to
keep track of language and test specific parameters.
* Conclusion
I really like to hear your feedback on those points. Maybe am I
taking the avoidance of cute and paste point of the reproducible
research too far?
Best,
Daniele
next prev parent reply other threads:[~2014-11-24 9:49 UTC|newest]
Thread overview: 35+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-11-12 0:49 [PATCH] inline src block results can be removed Charles C. Berry
2014-11-12 1:10 ` Andreas Leha
2014-11-12 6:58 ` Charles C. Berry
2014-11-12 19:34 ` Aaron Ecay
2014-11-12 23:47 ` Charles C. Berry
2014-11-13 17:48 ` Nicolas Goaziou
2014-11-13 19:06 ` Andreas Leha
2014-11-14 17:43 ` Charles C. Berry
2014-11-14 20:39 ` Nicolas Goaziou
2014-11-14 23:04 ` Aaron Ecay
2014-11-16 0:10 ` Nicolas Goaziou
2014-11-15 20:22 ` Charles C. Berry
2014-11-16 23:23 ` Nicolas Goaziou
2014-11-24 9:48 ` Daniele Pizzolli [this message]
2014-11-24 10:18 ` Andreas Leha
2015-01-13 0:48 ` New patches WAS " Charles C. Berry
2015-01-16 22:41 ` Nicolas Goaziou
2015-01-19 3:22 ` Charles C. Berry
2015-01-19 17:53 ` Nicolas Goaziou
2015-01-19 19:31 ` Charles C. Berry
2015-01-20 23:30 ` Nicolas Goaziou
2015-01-22 3:07 ` Charles C. Berry
2015-01-22 23:08 ` Nicolas Goaziou
2015-01-24 22:47 ` Charles C. Berry
2015-01-25 1:14 ` Aaron Ecay
2015-01-25 5:01 ` Charles C. Berry
2015-01-29 20:31 ` Charles C. Berry
2015-01-17 3:22 ` Aaron Ecay
2015-01-17 22:20 ` Nicolas Goaziou
2015-01-18 19:13 ` Aaron Ecay
2015-01-18 22:34 ` Nicolas Goaziou
2015-01-18 22:55 ` Aaron Ecay
-- strict thread matches above, loose matches on Subject: below --
2014-11-24 11:12 Daniele Pizzolli
2014-11-25 8:04 ` Daniele Pizzolli
2014-11-25 9:52 ` Andreas Leha
Reply instructions:
You may reply publicly to this message via plain-text email
using any one of the following methods:
* Save the following mbox file, import it into your mail client,
and reply-to-all from there: mbox
Avoid top-posting and favor interleaved quoting:
https://en.wikipedia.org/wiki/Posting_style#Interleaved_style
List information: https://www.orgmode.org/
* Reply using the --to, --cc, and --in-reply-to
switches of git-send-email(1):
git send-email \
--in-reply-to=b52cbe2d2cc2963024c59a80c8c721e0@toel.it \
--to=dan@toel.it \
--cc=aaronecay@gmail.com \
--cc=andreas.leha@med.uni-goettingen.de \
--cc=ccberry@ucsd.edu \
--cc=emacs-orgmode@gnu.org \
--cc=giepen.m@googlemail.com \
--cc=istazahn@gmail.com \
/path/to/YOUR_REPLY
https://kernel.org/pub/software/scm/git/docs/git-send-email.html
* If your mail client supports setting the In-Reply-To header
via mailto: links, try the mailto: link
Be sure your reply has a Subject: header at the top and a blank line
before the message body.
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/emacs/org-mode.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).