* Babel-R TBLFM example @ 2014-06-25 6:55 Shiyuan 2014-07-28 13:21 ` Bastien 0 siblings, 1 reply; 9+ messages in thread From: Shiyuan @ 2014-06-25 6:55 UTC (permalink / raw To: emacs-orgmode [-- Attachment #1: Type: text/plain, Size: 1544 bytes --] Hi all, I am looking at the Babel R example in http://orgmode.org/worg/org-tutorials/org-R/org-R.html This short example show how to use code block in Org Tables. The example first makes an org-mode table, which I can follow and reproduce the result: #+name: tbl-example-data() #+begin_src R runif(n=5, min=0, max=1) #+end_src #+RESULTS: tbl-example-data | 0.118510485393927 | | 0.742342338664457 | | 0.438421099446714 | | 0.0867570964619517 | | 0.604204315226525 | Then it defines r source code block and use TBLFM #+name: R-mean(x) #+begin_src R mean(x) #+end_src #+RESULTS: R-mean #+tblname: summaries | mean | |--------| | #ERROR | #+TBLFM: @2$1='(sbe "R-mean" (x "tbl-example-data()")) When I export to html(C-c C-e h o), the #+TBLFM seems to be ignored and shows no effect. When I place my cursor in the table and recalculate the table formula using C-u C-c C-c in the table. I got an error as shown above. In the *Message* buffer, I can see the following messages. byte-code: Beginning of buffer [8 times] Re-applying formulas to full table... Re-applying formula to field: @2$1 Re-applying formulas to full table...(line 1) Re-applying formula to field: @2$1 Re-applying formulas to 1 lines...done Re-applying formulas...done [2 times] Any steps I missed? I am using org mode 8.2.6 Also, I found this tutorial for org-R http://orgmode.org/worg/org-tutorials/org-R/org-R.html, however, the org-R-apply function seems no longer available in my org mode 8.2.6. Is org-R supposed to be deprecated? Thanks. Shiyuan [-- Attachment #2: Type: text/html, Size: 2379 bytes --] ^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Babel-R TBLFM example 2014-06-25 6:55 Babel-R TBLFM example Shiyuan @ 2014-07-28 13:21 ` Bastien 2014-07-29 6:15 ` Shiyuan 0 siblings, 1 reply; 9+ messages in thread From: Bastien @ 2014-07-28 13:21 UTC (permalink / raw To: Shiyuan; +Cc: emacs-orgmode Hi Shiyuan, Shiyuan <gshy2014@gmail.com> writes: > Also, I found this tutorial for org-R http://orgmode.org/worg/ > org-tutorials/org-R/org-R.html, however, the org-R-apply function > seems no longer available in my org mode 8.2.6. Is org-R supposed to > be deprecated? No, but it's moving. Since ob-R.el is perhaps one of the most useful Babel library out there, we need to document the changes carefully in etc/ORG-NEWS. -- Bastien ^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Babel-R TBLFM example 2014-07-28 13:21 ` Bastien @ 2014-07-29 6:15 ` Shiyuan 2014-07-29 13:20 ` Bastien 0 siblings, 1 reply; 9+ messages in thread From: Shiyuan @ 2014-07-29 6:15 UTC (permalink / raw To: Bastien; +Cc: emacs-orgmode@gnu.org [-- Attachment #1: Type: text/plain, Size: 745 bytes --] Thanks Bastien. I see ob-R.el from org-mode repos has been updated. So is the org-R from git-repos ready to use? Could you suggest a good place to start learning the new org-R? The source file ob-R.el? Shiyuan On Mon, Jul 28, 2014 at 6:21 AM, Bastien <bzg@gnu.org> wrote: > Hi Shiyuan, > > Shiyuan <gshy2014@gmail.com> writes: > > > Also, I found this tutorial for org-R http://orgmode.org/worg/ > > org-tutorials/org-R/org-R.html, however, the org-R-apply function > > seems no longer available in my org mode 8.2.6. Is org-R supposed to > > be deprecated? > > No, but it's moving. Since ob-R.el is perhaps one of the most useful > Babel library out there, we need to document the changes carefully in > etc/ORG-NEWS. > > -- > Bastien > [-- Attachment #2: Type: text/html, Size: 1311 bytes --] ^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Babel-R TBLFM example 2014-07-29 6:15 ` Shiyuan @ 2014-07-29 13:20 ` Bastien 2014-08-24 23:02 ` Shiyuan 0 siblings, 1 reply; 9+ messages in thread From: Bastien @ 2014-07-29 13:20 UTC (permalink / raw To: Shiyuan; +Cc: emacs-orgmode@gnu.org Hi Shiyuan, Shiyuan <gshy2014@gmail.com> writes: > Thanks Bastien. I see ob-R.el from org-mode repos has been updated. > So is the org-R from git-repos ready to use? Could you suggest a > good place to start learning the new org-R? The source file ob-R.el? The recent committers to ob-R.el we be more in a position to help here but yes, reading the source is certainly a good start. I hope we will have a clear picture of what changed in ob-R.el in 8.3, together with updated tutorials. Best, -- Bastien ^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Babel-R TBLFM example 2014-07-29 13:20 ` Bastien @ 2014-08-24 23:02 ` Shiyuan 2014-08-25 7:51 ` Sebastien Vauban 0 siblings, 1 reply; 9+ messages in thread From: Shiyuan @ 2014-08-24 23:02 UTC (permalink / raw To: Bastien; +Cc: emacs-orgmode@gnu.org [-- Attachment #1: Type: text/plain, Size: 2188 bytes --] I am looking at a simpler example, the pie-chart example as in this link: http://orgmode.org/worg/org-contrib/babel/intro.html#literate-programming This example(src code attached in the end) first generates a table by a shell command and then run a R one-liner which uses the table. However, when the R code is evaluated, I got an error about the object dirs not found. This is what I got in the buffer running R: ------------------------------- options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', show.error.locations=TRUE) > Error in pie(dirs[, 1], labels = dirs[, 2]) (from test-org-babe-meta-programming.org@24170fIx#1) : object 'dirs' not found ----------------------------------------------- It looks like that the conversion is wrong. When I run `org-babel-expand-src-block` on the R source code, I don't see the R object dirs is expanded to anything. I don't understand how the conversion works, and how Babel passes the table to R. Any explanation is appreciated. Which function/file should I look at? Are there working examples for passing a table to R? Thanks. Shiyuan ------------------------------ #+name: directories #+begin_src shell :results replace cd ~ && du -sc * |grep -v total #+end_src #+RESULTS: directories | 8 | #*message*-20140319-231047# | | 1168376 | Documents | | 9952288 | Downloads | | 8 | xmodmap2~ | #+name: directory-pie-chart(dirs = directories) #+begin_src R :session R-pie-example :file ~/tmp/dirs.png pie(dirs[,1], labels = dirs[,2]) #+end_src On Tue, Jul 29, 2014 at 6:20 AM, Bastien <bzg@gnu.org> wrote: > Hi Shiyuan, > > Shiyuan <gshy2014@gmail.com> writes: > > > Thanks Bastien. I see ob-R.el from org-mode repos has been updated. > > So is the org-R from git-repos ready to use? Could you suggest a > > good place to start learning the new org-R? The source file ob-R.el? > > The recent committers to ob-R.el we be more in a position to help here > but yes, reading the source is certainly a good start. > > I hope we will have a clear picture of what changed in ob-R.el in 8.3, > together with updated tutorials. > > Best, > > -- > Bastien > [-- Attachment #2: Type: text/html, Size: 3478 bytes --] ^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Babel-R TBLFM example 2014-08-24 23:02 ` Shiyuan @ 2014-08-25 7:51 ` Sebastien Vauban 2014-08-26 6:18 ` Shiyuan 0 siblings, 1 reply; 9+ messages in thread From: Sebastien Vauban @ 2014-08-25 7:51 UTC (permalink / raw To: emacs-orgmode-mXXj517/zsQ Shiyuan wrote: > I am looking at a simpler example, the pie-chart example as in this link: > http://orgmode.org/worg/org-contrib/babel/intro.html#literate-programming > > This example(src code attached in the end) first generates a table by a > shell command and then run a R one-liner which uses the table. However, > when the R code is evaluated, I got an error about the object dirs not > found. This is what I got in the buffer running R: > ------------------------------- > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', > show.error.locations=TRUE) >> > Error in pie(dirs[, 1], labels = dirs[, 2]) (from > test-org-babe-meta-programming.org@24170fIx#1) : object 'dirs' not found > ----------------------------------------------- > > It looks like that the conversion is wrong. When I run > `org-babel-expand-src-block` > on the R source code, I don't see the R object dirs is expanded to > anything. I don't understand how the conversion works, and how Babel passes > the table to R. Any explanation is appreciated. Which function/file should > I look at? Are there working examples for passing a table to R? Thanks. > > #+name: directories > #+begin_src shell :results replace > cd ~ && du -sc * |grep -v total > #+end_src > > #+RESULTS: directories > | 8 | #*message*-20140319-231047# | > | 1168376 | Documents | > | 9952288 | Downloads | > | 8 | xmodmap2~ | > > #+name: directory-pie-chart(dirs = directories) > #+begin_src R :session R-pie-example :file ~/tmp/dirs.png > pie(dirs[,1], labels = dirs[,2]) > #+end_src AFAICT, the arguments to code blocks may not be defined and set in the `name' line anymore: this must be done on the `begin_src' line. So, the following should work: #+name: directory-pie-chart #+begin_src R :var dirs=directories :session R-pie-example :file ~/tmp/dirs.png pie(dirs[,1], labels = dirs[,2]) #+end_src Best regards, Seb -- Sebastien Vauban ^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Babel-R TBLFM example 2014-08-25 7:51 ` Sebastien Vauban @ 2014-08-26 6:18 ` Shiyuan 2014-08-26 6:57 ` Thomas S. Dye 0 siblings, 1 reply; 9+ messages in thread From: Shiyuan @ 2014-08-26 6:18 UTC (permalink / raw Cc: emacs-orgmode@gnu.org [-- Attachment #1: Type: text/plain, Size: 2240 bytes --] Yes, it works. Thanks, Sebastien. Shiyuan On Mon, Aug 25, 2014 at 12:51 AM, Sebastien Vauban <sva-news@mygooglest.com> wrote: > Shiyuan wrote: > > I am looking at a simpler example, the pie-chart example as in this link: > > > http://orgmode.org/worg/org-contrib/babel/intro.html#literate-programming > > > > This example(src code attached in the end) first generates a table by a > > shell command and then run a R one-liner which uses the table. However, > > when the R code is evaluated, I got an error about the object dirs not > > found. This is what I got in the buffer running R: > > ------------------------------- > > options(STERM='iESS', str.dendrogram.last="'", editor='emacsclient', > > show.error.locations=TRUE) > >> > > Error in pie(dirs[, 1], labels = dirs[, 2]) (from > > test-org-babe-meta-programming.org@24170fIx#1) : object 'dirs' not found > > ----------------------------------------------- > > > > It looks like that the conversion is wrong. When I run > > `org-babel-expand-src-block` > > on the R source code, I don't see the R object dirs is expanded to > > anything. I don't understand how the conversion works, and how Babel > passes > > the table to R. Any explanation is appreciated. Which function/file > should > > I look at? Are there working examples for passing a table to R? Thanks. > > > > #+name: directories > > #+begin_src shell :results replace > > cd ~ && du -sc * |grep -v total > > #+end_src > > > > #+RESULTS: directories > > | 8 | #*message*-20140319-231047# | > > | 1168376 | Documents | > > | 9952288 | Downloads | > > | 8 | xmodmap2~ | > > > > #+name: directory-pie-chart(dirs = directories) > > #+begin_src R :session R-pie-example :file ~/tmp/dirs.png > > pie(dirs[,1], labels = dirs[,2]) > > #+end_src > > AFAICT, the arguments to code blocks may not be defined and set in the > `name' line anymore: this must be done on the `begin_src' line. > > So, the following should work: > > #+name: directory-pie-chart > #+begin_src R :var dirs=directories :session R-pie-example :file > ~/tmp/dirs.png > pie(dirs[,1], labels = dirs[,2]) > #+end_src > > Best regards, > Seb > > -- > Sebastien Vauban > > > [-- Attachment #2: Type: text/html, Size: 3184 bytes --] ^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Babel-R TBLFM example 2014-08-26 6:18 ` Shiyuan @ 2014-08-26 6:57 ` Thomas S. Dye 2014-08-26 7:23 ` Sebastien Vauban 0 siblings, 1 reply; 9+ messages in thread From: Thomas S. Dye @ 2014-08-26 6:57 UTC (permalink / raw To: Shiyuan; +Cc: emacs-orgmode@gnu.org Aloha all, >> AFAICT, the arguments to code blocks may not be defined and set in the >> `name' line anymore: this must be done on the `begin_src' line. or, on a separate #+header: line. All the best, Tom -- Thomas S. Dye http://www.tsdye.com ^ permalink raw reply [flat|nested] 9+ messages in thread
* Re: Babel-R TBLFM example 2014-08-26 6:57 ` Thomas S. Dye @ 2014-08-26 7:23 ` Sebastien Vauban 0 siblings, 0 replies; 9+ messages in thread From: Sebastien Vauban @ 2014-08-26 7:23 UTC (permalink / raw To: emacs-orgmode-mXXj517/zsQ Thomas S. Dye wrote: > Aloha all, > >>> AFAICT, the arguments to code blocks may not be defined and set in the >>> `name' line anymore: this must be done on the `begin_src' line. > > or, on a separate #+header: line. Indeed. I tend to forget to use that; thanks for mentioning it! Best regards, Seb -- Sebastien Vauban ^ permalink raw reply [flat|nested] 9+ messages in thread
end of thread, other threads:[~2014-08-26 7:23 UTC | newest] Thread overview: 9+ messages (download: mbox.gz follow: Atom feed -- links below jump to the message on this page -- 2014-06-25 6:55 Babel-R TBLFM example Shiyuan 2014-07-28 13:21 ` Bastien 2014-07-29 6:15 ` Shiyuan 2014-07-29 13:20 ` Bastien 2014-08-24 23:02 ` Shiyuan 2014-08-25 7:51 ` Sebastien Vauban 2014-08-26 6:18 ` Shiyuan 2014-08-26 6:57 ` Thomas S. Dye 2014-08-26 7:23 ` Sebastien Vauban
Code repositories for project(s) associated with this external index https://git.savannah.gnu.org/cgit/emacs.git https://git.savannah.gnu.org/cgit/emacs/org-mode.git This is an external index of several public inboxes, see mirroring instructions on how to clone and mirror all data and code used by this external index.