* import R data frame into org-mode table
@ 2013-07-16 15:19 Rob Stewart
2013-07-17 22:09 ` Andreas Leha
2013-07-17 22:48 ` Thomas S. Dye
0 siblings, 2 replies; 10+ messages in thread
From: Rob Stewart @ 2013-07-16 15:19 UTC (permalink / raw)
To: emacs-orgmode
I have an R script that generates a data frame, that I export to a CSV
file. The data looks something like this:
"","Variant","Xaxis","N","mean","sd","se"
"1","line1",10,5,111.11,9.33,3.11
"1","line1",20,5,112.11,9.13,3.14
"1","line1",30,5,113.11,9.43,3.10
"1","line2",10,5,101.11,8.33,2.11
"1","line2",20,5,100.11,8.13,2.12
"1","line2",30,5,108.11,8.03,2.10
I have an ongoing org-mode document in which I'd like to report this
data. I'd like to add a table that looks something like this:
| Variant | X Axis | Y Axis | N | Mean | Standard Deviation |
Standard Error |
|----------------------------------------------------------------------------|
The data will change frequently over the coming months. I'd like
org-mode to auto-magically read a CSV file, to construct my org-table
on-the-fly. I'd hoping to avoid copying and pasting results each time.
Is there some org-mode or emacs+ESS magic I can use to populate my
empty table, with source data from my CSV file?
--
Rob
^ permalink raw reply [flat|nested] 10+ messages in thread* Re: import R data frame into org-mode table 2013-07-16 15:19 import R data frame into org-mode table Rob Stewart @ 2013-07-17 22:09 ` Andreas Leha 2013-07-29 14:42 ` Rob Stewart 2013-07-17 22:48 ` Thomas S. Dye 1 sibling, 1 reply; 10+ messages in thread From: Andreas Leha @ 2013-07-17 22:09 UTC (permalink / raw) To: emacs-orgmode Rob Stewart <robstewart57@gmail.com> writes: > I have an R script that generates a data frame, that I export to a CSV > file. The data looks something like this: > > "","Variant","Xaxis","N","mean","sd","se" > "1","line1",10,5,111.11,9.33,3.11 > "1","line1",20,5,112.11,9.13,3.14 > "1","line1",30,5,113.11,9.43,3.10 > "1","line2",10,5,101.11,8.33,2.11 > "1","line2",20,5,100.11,8.13,2.12 > "1","line2",30,5,108.11,8.03,2.10 > > I have an ongoing org-mode document in which I'd like to report this > data. I'd like to add a table that looks something like this: > > | Variant | X Axis | Y Axis | N | Mean | Standard Deviation | > Standard Error | > |----------------------------------------------------------------------------| > > The data will change frequently over the coming months. I'd like > org-mode to auto-magically read a CSV file, to construct my org-table > on-the-fly. I'd hoping to avoid copying and pasting results each time. > > Is there some org-mode or emacs+ESS magic I can use to populate my > empty table, with source data from my CSV file? > > -- > Rob Definitely there is: --8<---------------cut here---------------start------------->8--- #+begin_src R :results table :colnames yes read.csv('test.csv') #+end_src #+results: | X | Variant | Xaxis | N | mean | sd | se | |---+---------+-------+---+--------+------+------| | 1 | line1 | 10 | 5 | 111.11 | 9.33 | 3.11 | | 1 | line1 | 20 | 5 | 112.11 | 9.13 | 3.14 | | 1 | line1 | 30 | 5 | 113.11 | 9.43 | 3.1 | | 1 | line2 | 10 | 5 | 101.11 | 8.33 | 2.11 | | 1 | line2 | 20 | 5 | 100.11 | 8.13 | 2.12 | | 1 | line2 | 30 | 5 | 108.11 | 8.03 | 2.1 | --8<---------------cut here---------------end--------------->8--- Regards, Andreas ^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: import R data frame into org-mode table 2013-07-17 22:09 ` Andreas Leha @ 2013-07-29 14:42 ` Rob Stewart 2013-07-29 15:35 ` Cook, Malcolm 0 siblings, 1 reply; 10+ messages in thread From: Rob Stewart @ 2013-07-29 14:42 UTC (permalink / raw) To: Andreas Leha; +Cc: emacs-orgmode Hi Andreas, On 17 July 2013 23:09, Andreas Leha <andreas.leha@med.uni-goettingen.de> wrote: > Definitely there is: > > --8<---------------cut here---------------start------------->8--- > #+begin_src R :results table :colnames yes > read.csv('test.csv') > #+end_src > > #+results: > | X | Variant | Xaxis | N | mean | sd | se | > |---+---------+-------+---+--------+------+------| > | 1 | line1 | 10 | 5 | 111.11 | 9.33 | 3.11 | > | 1 | line1 | 20 | 5 | 112.11 | 9.13 | 3.14 | > | 1 | line1 | 30 | 5 | 113.11 | 9.43 | 3.1 | > | 1 | line2 | 10 | 5 | 101.11 | 8.33 | 2.11 | > | 1 | line2 | 20 | 5 | 100.11 | 8.13 | 2.12 | > | 1 | line2 | 30 | 5 | 108.11 | 8.03 | 2.1 | > > --8<---------------cut here---------------end--------------->8--- Great. I've gone ahead and done this. There are two additional requirements: 1) My table needs a caption. Will #+CAPTION: just above the #+BEGIN_SRC just work? Even better, a label, allowing me to also cross reference it. 2) My table is too long for 1 page. It spans multiple pages vertically. According to this StackOverflow answer http://stackoverflow.com/a/2896850/1526266 , I should instead use longtable, not tabular. Is there a way to coerce your above snippet to use longtable, instead of tabular which is the default. Thanks! -- Rob ^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: import R data frame into org-mode table 2013-07-29 14:42 ` Rob Stewart @ 2013-07-29 15:35 ` Cook, Malcolm 2013-07-29 16:03 ` John Hendy 0 siblings, 1 reply; 10+ messages in thread From: Cook, Malcolm @ 2013-07-29 15:35 UTC (permalink / raw) To: 'Rob Stewart', 'Andreas Leha' Cc: 'emacs-orgmode@gnu.org' >Hi Andreas, > >On 17 July 2013 23:09, Andreas Leha <andreas.leha@med.uni-goettingen.de> wrote: > >> Definitely there is: >> >> --8<---------------cut here---------------start------------->8--- >> #+begin_src R :results table :colnames yes >> read.csv('test.csv') >> #+end_src >> >> #+results: >> | X | Variant | Xaxis | N | mean | sd | se | >> |---+---------+-------+---+--------+------+------| >> | 1 | line1 | 10 | 5 | 111.11 | 9.33 | 3.11 | >> | 1 | line1 | 20 | 5 | 112.11 | 9.13 | 3.14 | >> | 1 | line1 | 30 | 5 | 113.11 | 9.43 | 3.1 | >> | 1 | line2 | 10 | 5 | 101.11 | 8.33 | 2.11 | >> | 1 | line2 | 20 | 5 | 100.11 | 8.13 | 2.12 | >> | 1 | line2 | 30 | 5 | 108.11 | 8.03 | 2.1 | >> >> --8<---------------cut here---------------end--------------->8--- > >Great. I've gone ahead and done this. There are two additional requirements: >1) My table needs a caption. Will #+CAPTION: just above the >#+BEGIN_SRC just work? Yes > Even better, a label, allowing me to also cross >reference it. >2) My table is too long for 1 page. It spans multiple pages >vertically. According to this StackOverflow answer >http://stackoverflow.com/a/2896850/1526266 , I should instead use >longtable, not tabular. Is there a way to coerce your above snippet to >use longtable, instead of tabular which is the default. > Looks like your answer is here: http://orgmode.org/manual/Tables-in-LaTeX-export.html >Thanks! > >-- >Rob ^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: import R data frame into org-mode table 2013-07-29 15:35 ` Cook, Malcolm @ 2013-07-29 16:03 ` John Hendy 2013-07-29 17:11 ` Nick Dokos 2013-07-29 20:17 ` Cook, Malcolm 0 siblings, 2 replies; 10+ messages in thread From: John Hendy @ 2013-07-29 16:03 UTC (permalink / raw) To: Cook, Malcolm; +Cc: Rob Stewart, emacs-orgmode@gnu.org, Andreas Leha On Mon, Jul 29, 2013 at 10:35 AM, Cook, Malcolm <MEC@stowers.org> wrote: >>Hi Andreas, > > > >On 17 July 2013 23:09, Andreas Leha <andreas.leha@med.uni-goettingen.de> wrote: > > > >> Definitely there is: > >> > >> --8<---------------cut here---------------start------------->8--- > >> #+begin_src R :results table :colnames yes > >> read.csv('test.csv') > >> #+end_src > >> > >> #+results: > >> | X | Variant | Xaxis | N | mean | sd | se | > >> |---+---------+-------+---+--------+------+------| > >> | 1 | line1 | 10 | 5 | 111.11 | 9.33 | 3.11 | > >> | 1 | line1 | 20 | 5 | 112.11 | 9.13 | 3.14 | > >> | 1 | line1 | 30 | 5 | 113.11 | 9.43 | 3.1 | > >> | 1 | line2 | 10 | 5 | 101.11 | 8.33 | 2.11 | > >> | 1 | line2 | 20 | 5 | 100.11 | 8.13 | 2.12 | > >> | 1 | line2 | 30 | 5 | 108.11 | 8.03 | 2.1 | > >> > >> --8<---------------cut here---------------end--------------->8--- > > > >Great. I've gone ahead and done this. There are two additional requirements: > >1) My table needs a caption. Will #+CAPTION: just above the > >#+BEGIN_SRC just work? > > Yes > >> Even better, a label, allowing me to also cross > >reference it. > >2) My table is too long for 1 page. It spans multiple pages > >vertically. According to this StackOverflow answer > >http://stackoverflow.com/a/2896850/1526266 , I should instead use > >longtable, not tabular. Is there a way to coerce your above snippet to > >use longtable, instead of tabular which is the default. > > > > Looks like your answer is here: http://orgmode.org/manual/Tables-in-LaTeX-export.html Sort of. Depends on the Org-mode version, and someone will have to chime in on the updated status of various parts of the manual. For 8+, I believe the syntax is different: #+attr_latex: :environment longtable Also, there have been many threads in the past about how to add #+attr_latex lines to results output (mostly graphics/files) successfully. If you simply take the above and add =#+attr_latex: stuff= above the =#+results= line, babel won't recognize it and will just create a new results block. If those on this email are already well aware of this... my apologies for being redundant, but it causes enough confusion that I figured I'd leave another bread crumb trail :) Here's an example of a time that came up on the list: - http://lists.gnu.org/archive/html/emacs-orgmode/2012-07/msg00237.html You need to use any attributes (that includes #+begin/end_center, and any #+attr_backend lines) *in combination with* a named source block. So the full solution should look something like this: #+name: export-table #+begin_src R :results table :colnames yes read.csv('test.csv') #+end_src #+RESULTS: export-table #+attr_latex: :environment longtable | | | I see above that =:results output org= was used. There was some discussion about this for use with the new exporter as I wasn't getting great results: - https://lists.gnu.org/archive/html/emacs-orgmode/2013-03/msg01582.html - http://www.mail-archive.com/emacs-orgmode@gnu.org/msg69748.html If it's working for you, don't worry about it. If not, you may find some help in those threads. I've taken to using the ascii package for output org-mode tables from R. - http://orgmode.org/worg/org-contrib/babel/examples/ascii.html Works great for me. Good luck! John > > >Thanks! > > > >-- > >Rob > > ^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: import R data frame into org-mode table 2013-07-29 16:03 ` John Hendy @ 2013-07-29 17:11 ` Nick Dokos 2013-07-29 20:17 ` Cook, Malcolm 1 sibling, 0 replies; 10+ messages in thread From: Nick Dokos @ 2013-07-29 17:11 UTC (permalink / raw) To: emacs-orgmode John Hendy <jw.hendy@gmail.com> writes: > On Mon, Jul 29, 2013 at 10:35 AM, Cook, Malcolm <MEC@stowers.org> wrote: >>>Hi Andreas, >> > >> >On 17 July 2013 23:09, Andreas Leha <andreas.leha@med.uni-goettingen.de> wrote: >> > >> >> Definitely there is: >> >> >> >> --8<---------------cut here---------------start------------->8--- >> >> #+begin_src R :results table :colnames yes >> >> read.csv('test.csv') >> >> #+end_src >> >> >> >> #+results: >> >> | X | Variant | Xaxis | N | mean | sd | se | >> >> |---+---------+-------+---+--------+------+------| >> >> | 1 | line1 | 10 | 5 | 111.11 | 9.33 | 3.11 | >> >> | 1 | line1 | 20 | 5 | 112.11 | 9.13 | 3.14 | >> >> | 1 | line1 | 30 | 5 | 113.11 | 9.43 | 3.1 | >> >> | 1 | line2 | 10 | 5 | 101.11 | 8.33 | 2.11 | >> >> | 1 | line2 | 20 | 5 | 100.11 | 8.13 | 2.12 | >> >> | 1 | line2 | 30 | 5 | 108.11 | 8.03 | 2.1 | >> >> >> >> --8<---------------cut here---------------end--------------->8--- >> > >> >Great. I've gone ahead and done this. There are two additional requirements: >> >1) My table needs a caption. Will #+CAPTION: just above the >> >#+BEGIN_SRC just work? >> >> Yes I don't think so: the caption is a property of the table, not of the code block, so putting it before the code block does not work (at least in my limited 8.x tests). You have to put it before the table - see example below. >> >>> Even better, a label, allowing me to also cross >> >reference it. >> >2) My table is too long for 1 page. It spans multiple pages >> >vertically. According to this StackOverflow answer >> >http://stackoverflow.com/a/2896850/1526266 , I should instead use >> >longtable, not tabular. Is there a way to coerce your above snippet to >> >use longtable, instead of tabular which is the default. >> > >> >> Looks like your answer is here: http://orgmode.org/manual/Tables-in-LaTeX-export.html > > Sort of. Depends on the Org-mode version, and someone will have to > chime in on the updated status of various parts of the manual. For 8+, > I believe the syntax is different: > > #+attr_latex: :environment longtable > > Also, there have been many threads in the past about how to add > #+attr_latex lines to results output (mostly graphics/files) > successfully. If you simply take the above and add =#+attr_latex: > stuff= above the =#+results= line, babel won't recognize it and will > just create a new results block. If those on this email are already > well aware of this... my apologies for being redundant, but it causes > enough confusion that I figured I'd leave another bread crumb trail :) > Here's an example of a time that came up on the list: > - http://lists.gnu.org/archive/html/emacs-orgmode/2012-07/msg00237.html > This is no longer the case: Eric S. fixed this a couple of months ago, so that even an unlabeled #+RESULTS block will get the recomputed results without creating a new block. The following exports fine to latex/pdf with current org: --8<---------------cut here---------------start------------->8--- * foo #+begin_src R :results table :colnames yes :exports results read.csv('test.csv') #+end_src #+NAME: foo #+CAPTION: My table #+ATTR_LATEX: :environment longtable #+RESULTS: | X | Variant | Xaxis | N | mean | sd | se | |---+---------+-------+---+--------+------+------| | 1 | line1 | 10 | 5 | 111.11 | 9.33 | 3.11 | | 1 | line1 | 20 | 5 | 112.11 | 9.13 | 3.14 | | 1 | line1 | 30 | 5 | 113.11 | 9.43 | 3.1 | | 1 | line2 | 10 | 5 | 101.11 | 8.33 | 2.11 | | 1 | line2 | 20 | 5 | 100.11 | 8.13 | 2.12 | | 1 | line2 | 30 | 5 | 108.11 | 8.03 | 2.1 | * bar See Table \ref{foo}. --8<---------------cut here---------------end--------------->8--- even satisfying the OP's desire for labeling the table so that the xref will work (although there may be better methods to xref: I haven't kept up with the recent discussions on the ML). Of course, naming the code block should still be considered best practice IMO. -- Nick ^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: import R data frame into org-mode table 2013-07-29 16:03 ` John Hendy 2013-07-29 17:11 ` Nick Dokos @ 2013-07-29 20:17 ` Cook, Malcolm 2013-07-29 21:40 ` Nick Dokos 1 sibling, 1 reply; 10+ messages in thread From: Cook, Malcolm @ 2013-07-29 20:17 UTC (permalink / raw) To: 'John Hendy' Cc: 'Rob Stewart', 'emacs-orgmode@gnu.org', 'Andreas Leha' >-----Original Message----- >From: John Hendy [mailto:jw.hendy@gmail.com] >Sent: Monday, July 29, 2013 11:03 AM >To: Cook, Malcolm >Cc: Rob Stewart; Andreas Leha; emacs-orgmode@gnu.org >Subject: Re: [O] import R data frame into org-mode table > >On Mon, Jul 29, 2013 at 10:35 AM, Cook, Malcolm <MEC@stowers.org> wrote: >>>Hi Andreas, >> > >> >On 17 July 2013 23:09, Andreas Leha <andreas.leha@med.uni-goettingen.de> wrote: >> > >> >> Definitely there is: >> >> >> >> --8<---------------cut here---------------start------------->8--- >> >> #+begin_src R :results table :colnames yes >> >> read.csv('test.csv') >> >> #+end_src >> >> >> >> #+results: >> >> | X | Variant | Xaxis | N | mean | sd | se | >> >> |---+---------+-------+---+--------+------+------| >> >> | 1 | line1 | 10 | 5 | 111.11 | 9.33 | 3.11 | >> >> | 1 | line1 | 20 | 5 | 112.11 | 9.13 | 3.14 | >> >> | 1 | line1 | 30 | 5 | 113.11 | 9.43 | 3.1 | >> >> | 1 | line2 | 10 | 5 | 101.11 | 8.33 | 2.11 | >> >> | 1 | line2 | 20 | 5 | 100.11 | 8.13 | 2.12 | >> >> | 1 | line2 | 30 | 5 | 108.11 | 8.03 | 2.1 | >> >> >> >> --8<---------------cut here---------------end--------------->8--- >> > >> >Great. I've gone ahead and done this. There are two additional requirements: >> >1) My table needs a caption. Will #+CAPTION: just above the >> >#+BEGIN_SRC just work? >> >> Yes >> >>> Even better, a label, allowing me to also cross >> >reference it. >> >2) My table is too long for 1 page. It spans multiple pages >> >vertically. According to this StackOverflow answer >> >http://stackoverflow.com/a/2896850/1526266 , I should instead use >> >longtable, not tabular. Is there a way to coerce your above snippet to >> >use longtable, instead of tabular which is the default. >> > >> >> Looks like your answer is here: http://orgmode.org/manual/Tables-in-LaTeX-export.html > >Sort of. Depends on the Org-mode version, and someone will have to >chime in on the updated status of various parts of the manual. For 8+, >I believe the syntax is different: > >#+attr_latex: :environment longtable > >Also, there have been many threads in the past about how to add >#+attr_latex lines to results output (mostly graphics/files) >successfully. If you simply take the above and add =#+attr_latex: >stuff= above the =#+results= line, babel won't recognize it and will >just create a new results block. If those on this email are already >well aware of this... my apologies for being redundant, but it causes >enough confusion that I figured I'd leave another bread crumb trail :) >Here's an example of a time that came up on the list: >- http://lists.gnu.org/archive/html/emacs-orgmode/2012-07/msg00237.html > >You need to use any attributes (that includes #+begin/end_center, and >any #+attr_backend lines) *in combination with* a named source block. >So the full solution should look something like this: > >#+name: export-table >#+begin_src R :results table :colnames yes >read.csv('test.csv') >#+end_src > >#+RESULTS: export-table >#+attr_latex: :environment longtable >| | | [Cook, Malcolm] Indeed, thanks, and, my worked out example follows using emacs 2.18.9 and org-mode version 8.0.6 #+LATEX: \listoftables #+LaTeX_HEADER: \usepackage{longtable} #+name: longtabletest #+CAPTION: test of longtable caption #+begin_src R :results value :colnames yes data.frame(num=1:260,alpha=rep(LETTERS,10)) #+end_src #+RESULTS: #+attr_latex: :environment longtable | num | alpha | |-----+-------| | 1 | A | | 2 | B | ... ~Malcolm > >I see above that =:results output org= was used. There was some >discussion about this for use with the new exporter as I wasn't >getting great results: >- https://lists.gnu.org/archive/html/emacs-orgmode/2013-03/msg01582.html >- http://www.mail-archive.com/emacs-orgmode@gnu.org/msg69748.html > >If it's working for you, don't worry about it. If not, you may find >some help in those threads. I've taken to using the ascii package for >output org-mode tables from R. >- http://orgmode.org/worg/org-contrib/babel/examples/ascii.html > >Works great for me. > > >Good luck! >John > > >> >> >Thanks! >> > >> >-- >> >Rob >> >> ^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: import R data frame into org-mode table 2013-07-29 20:17 ` Cook, Malcolm @ 2013-07-29 21:40 ` Nick Dokos 2013-07-30 17:59 ` Cook, Malcolm 0 siblings, 1 reply; 10+ messages in thread From: Nick Dokos @ 2013-07-29 21:40 UTC (permalink / raw) To: emacs-orgmode "Cook, Malcolm" <MEC@stowers.org> writes: > > Indeed, thanks, and, my worked out example follows using emacs 2.18.9 and org-mode version 8.0.6 > 2.18.9? > #+LATEX: \listoftables > #+LaTeX_HEADER: \usepackage{longtable} > #+name: longtabletest > #+CAPTION: test of longtable caption > #+begin_src R :results value :colnames yes > data.frame(num=1:260,alpha=rep(LETTERS,10)) > #+end_src > > #+RESULTS: > #+attr_latex: :environment longtable > | num | alpha | > |-----+-------| > | 1 | A | > | 2 | B | > ... Does this really produce a table caption for you when you export to latex? And does the attr_latex line stay there at the top of the table when the code block is evaluated? For me, the answers are "no" and "no". I have to rewrite it as follows in order for it to work: > #+begin_src R :results value :colnames yes > data.frame(num=1:260,alpha=rep(LETTERS,10)) > #+end_src > > #+CAPTION: test of longtable caption > #+attr_latex: :environment longtable > #+RESULTS: > | num | alpha | > |-----+-------| > | 1 | A | > | 2 | B | -- Nick ^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: import R data frame into org-mode table 2013-07-29 21:40 ` Nick Dokos @ 2013-07-30 17:59 ` Cook, Malcolm 0 siblings, 0 replies; 10+ messages in thread From: Cook, Malcolm @ 2013-07-30 17:59 UTC (permalink / raw) To: 'Nick Dokos', 'emacs-orgmode@gnu.org' >> >> Indeed, thanks, and, my worked out example follows using emacs 2.18.9 and org-mode version 8.0.6 >> > >2.18.9? oops, that was the GTK_ Version number. My emacs is 24.3.1. >> #+LATEX: \listoftables >> #+LaTeX_HEADER: \usepackage{longtable} >> #+name: longtabletest >> #+CAPTION: test of longtable caption >> #+begin_src R :results value :colnames yes >> data.frame(num=1:260,alpha=rep(LETTERS,10)) >> #+end_src >> >> #+RESULTS: >> #+attr_latex: :environment longtable >> | num | alpha | >> |-----+-------| >> | 1 | A | >> | 2 | B | >> ... > >Does this really produce a table caption for you when you export to >latex? > And does the attr_latex line stay there at the top of the table >when the code block is evaluated? Yes and Yes. At least, I swear it worked in my hands yesterday, but today the answer is No and No. !! I can't explain what has changed. > For me, the answers are "no" and >"no". > I have to rewrite it as follows in order for it to work: > >> #+begin_src R :results value :colnames yes >> data.frame(num=1:260,alpha=rep(LETTERS,10)) >> #+end_src >> >> #+CAPTION: test of longtable caption >> #+attr_latex: :environment longtable >> #+RESULTS: >> | num | alpha | >> |-----+-------| >> | 1 | A | >> | 2 | B | In my hands, both the #+CAPTION and the #+att_latex as you place them are deleted upon source block evaluation. Are you sure your placement works for you? Summary: In my hands today, there is no placement of them that both survives source block re-evaluation and works. And, they can both be placed immediately above or below the #+RESULTS: line and are respected on export. (However, another funny interaction, the caption of the longtable has multiple entries, one for each page, in my #+LATEX: \listoftables ) Hmmmm.... > >-- >Nick > > ^ permalink raw reply [flat|nested] 10+ messages in thread
* Re: import R data frame into org-mode table 2013-07-16 15:19 import R data frame into org-mode table Rob Stewart 2013-07-17 22:09 ` Andreas Leha @ 2013-07-17 22:48 ` Thomas S. Dye 1 sibling, 0 replies; 10+ messages in thread From: Thomas S. Dye @ 2013-07-17 22:48 UTC (permalink / raw) To: Rob Stewart; +Cc: emacs-orgmode Rob Stewart <robstewart57@gmail.com> writes: > I have an R script that generates a data frame, that I export to a CSV > file. The data looks something like this: > > "","Variant","Xaxis","N","mean","sd","se" > "1","line1",10,5,111.11,9.33,3.11 > "1","line1",20,5,112.11,9.13,3.14 > "1","line1",30,5,113.11,9.43,3.10 > "1","line2",10,5,101.11,8.33,2.11 > "1","line2",20,5,100.11,8.13,2.12 > "1","line2",30,5,108.11,8.03,2.10 > > I have an ongoing org-mode document in which I'd like to report this > data. I'd like to add a table that looks something like this: > > | Variant | X Axis | Y Axis | N | Mean | Standard Deviation | > Standard Error | > |----------------------------------------------------------------------------| > > The data will change frequently over the coming months. I'd like > org-mode to auto-magically read a CSV file, to construct my org-table > on-the-fly. I'd hoping to avoid copying and pasting results each time. > > Is there some org-mode or emacs+ESS magic I can use to populate my > empty table, with source data from my CSV file? > > -- > Rob Hi Rob, Andreas' post answers your specific question. In your situation, I typically don't run through a csv file, but just write the R script so the data frame is returned to the Org mode buffer as the result of the source code block. As for the translation of column heads, see the ascii package for R, which has a print() routine that recognizes Org mode as a type of output, and which has facilities for formatting column names. Here is an example from some work in progress that uses a session: #+property: exports results #+property: colnames yes #+property: session *adzes* #+name: lda-mid-z #+header: :results output org #+begin_src R y <- edxrf[edxrf$lab=='UH-Hilo',] fit <- lda(as.factor(site) ~ rb_ppm + sr_ppm + y_ppm + zr_ppm + nb_ppm, data=y, na.action="na.omit", CV=TRUE) adzes <- y$site=='unknown' cap <- "Assignment of unknowns to sources" z <- ascii(cbind(BPBM=y$bpbm[adzes],round(fit$posterior[adzes,],2)),header=T,include.colnames=T,caption=cap) print(z,type="org") rm(y,fit,adzes,cap,z) #+end_src #+RESULTS: lda-mid-z #+BEGIN_ORG #+CAPTION: Assignment of unknowns to sources | BPBM | Haleakala | Kilauea | Mauna Kea | Nu`u | Pololu | Waiahole | unknown | |---------------------------+-----------+---------+-----------+------+--------+----------+---------| | 1985.134.01 adze | 0 | 0.1 | 0 | 0 | 0 | 0.64 | 0.27 | | 50-HA-1349-G-5 adze | 0 | 0.85 | 0 | 0 | 0 | 0 | 0.14 | | 50-HA-900-P24-1 microadze | 0 | 0 | 1 | 0 | 0 | 0 | 0 | ... hth, Tom -- Thomas S. Dye http://www.tsdye.com ^ permalink raw reply [flat|nested] 10+ messages in thread
end of thread, other threads:[~2013-07-30 18:00 UTC | newest] Thread overview: 10+ messages (download: mbox.gz follow: Atom feed -- links below jump to the message on this page -- 2013-07-16 15:19 import R data frame into org-mode table Rob Stewart 2013-07-17 22:09 ` Andreas Leha 2013-07-29 14:42 ` Rob Stewart 2013-07-29 15:35 ` Cook, Malcolm 2013-07-29 16:03 ` John Hendy 2013-07-29 17:11 ` Nick Dokos 2013-07-29 20:17 ` Cook, Malcolm 2013-07-29 21:40 ` Nick Dokos 2013-07-30 17:59 ` Cook, Malcolm 2013-07-17 22:48 ` Thomas S. Dye
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