* Passing a variable into an R source block.
@ 2021-05-28 15:52 Roger Mason
2021-05-28 17:30 ` Berry, Charles via General discussions about Org-mode.
2021-05-28 19:29 ` William Denton
0 siblings, 2 replies; 4+ messages in thread
From: Roger Mason @ 2021-05-28 15:52 UTC (permalink / raw)
To: emacs-orgmode
Hello,
I have an SQL source block that returns this:
#+RESULTS: query
| date | jid | te | rgkmax | time | elapsed |
|-----------------+-------+----------------------------------+--------+----------+-------------------------------|
| 20210528-053900 | 647_1 | 20210528-053900 1 -1333.58106425 | 7 | 01:00:00 | Job Wall-clock time: 00:03:16 |
| 20210528-053900 | 647_1 | 20210528-053900 2 -1333.25006295 | 7 | 01:00:00 | Job Wall-clock time: 00:03:16 |
| 20210528-053900 | 647_1 | 20210528-053900 3 -1332.40596663 | 7 | 01:00:00 | Job Wall-clock time: 00:03:16 |
| 20210528-053900 | 647_1 | 20210528-053900 4 -1327.18802970 | 7 | 01:00:00 | Job Wall-clock time: 00:03:16 |
| 20210528-053900 | 647_1 | 20210528-053900 5 -1320.63944318 | 7 | 01:00:00 | Job Wall-clock time: 00:03:16 |
I would like to pass this into R for further processing. At the moment
I have this:
#+begin_src R :session :colnames yes :var data=query
r <- data.frame($data)
t <- data.frame( str_split_fixed(r$te, " ", 3) )
colnames(t) <- c('date','cycle','energy')
df <- data.frame(r$date,r$jid,t$cycle,t$energy,r$x,r$time,r$elapsed)
# colnames(df) <- c('date','jid','cycle','energy','time','elapsed')
# df <- transmute(df,date,jid,cycle,energy,time,elapsed = str_remove(elapsed,"Job Wall-clock time: "))
# tail(filter(df,jid == '$jid'),1)$energy
#+end_src
and the output is:
/tmp/unknown!4fCXoM:20:17: unexpected '$'
19: })
20: r <- data.frame($
I presume that is because R uses '$' to select a column from a data
frame.
I tried quoting like this:
r <- data.frame("$data")
but the output is then:
#+RESULTS:
| t.cycle | t.energy |
|---------+----------|
whereas I was expecting 7 columns of data from data frame 'df'.
I don't know if this is an org problem or an R problem, but if someone
can cast light on it, please do.
Thanks,
Roger
GNU Emacs 27.2 (build 1, amd64-portbld-freebsd11.4, X toolkit, cairo
version 1.16.0, Xaw3d scroll bars)
Org mode version 9.2.3 (release_9.2.3-390-gfb5091 @ /home/rmason/.emacs.d/org-git/lisp/)
^ permalink raw reply [flat|nested] 4+ messages in thread* Re: Passing a variable into an R source block.
2021-05-28 15:52 Passing a variable into an R source block Roger Mason
@ 2021-05-28 17:30 ` Berry, Charles via General discussions about Org-mode.
2021-05-29 14:13 ` Roger Mason
2021-05-28 19:29 ` William Denton
1 sibling, 1 reply; 4+ messages in thread
From: Berry, Charles via General discussions about Org-mode. @ 2021-05-28 17:30 UTC (permalink / raw)
To: Roger Mason; +Cc: emacs-orgmode@gnu.org
> On May 28, 2021, at 8:52 AM, Roger Mason <rmason@mun.ca> wrote:
>
> Hello,
>
> I have an SQL source block that returns this:
>
> #+RESULTS: query
>
>
[snip]
> I would like to pass this into R for further processing. At the moment
> I have this:
>
> #+begin_src R :session :colnames yes :var data=query
> r <- data.frame($data)
[snip]
data.frame($data) is not valid R syntax. If you are new to R doing some tutorials will help.
I suggest you use C-c C-v C-v (org-babel-expand-src-block) to see what the R code is and debug the result given in the the *Org Babel Preview...* buffer.
HTH,
Chuck
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: Passing a variable into an R source block.
2021-05-28 17:30 ` Berry, Charles via General discussions about Org-mode.
@ 2021-05-29 14:13 ` Roger Mason
0 siblings, 0 replies; 4+ messages in thread
From: Roger Mason @ 2021-05-29 14:13 UTC (permalink / raw)
To: emacs-orgmode@gnu.org
Hello Charles & William,
Berry, Charles writes:
> data.frame($data) is not valid R syntax. If you are new to R doing some tutorials will help.
>
> I suggest you use C-c C-v C-v (org-babel-expand-src-block) to see what the R code is and debug the result given in the the *Org Babel Preview...* buffer.
You are correct, my R skills are _very_ rusty. I did not know of
org-babel-expand-src-block, thanks for the pointer. Very useful.
William Denton writes:
> The Org table is passed in to R as a data.frame, so all you need is this at the
> start (with stringr loaded in previously):
Thanks William, that got me going in the right direction.
Roger
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: Passing a variable into an R source block.
2021-05-28 15:52 Passing a variable into an R source block Roger Mason
2021-05-28 17:30 ` Berry, Charles via General discussions about Org-mode.
@ 2021-05-28 19:29 ` William Denton
1 sibling, 0 replies; 4+ messages in thread
From: William Denton @ 2021-05-28 19:29 UTC (permalink / raw)
To: Roger Mason; +Cc: emacs-orgmode
The Org table is passed in to R as a data.frame, so all you need is this at the
start (with stringr loaded in previously):
#+begin_src R :session :colnames yes :var data=query
t <- str_split_fixed(data$te, " ", 3)
colnames(t) <- c('date','cycle','energy')
t
#+end_src
#+RESULTS:
| date | cycle | energy |
|-----------------+-------+----------------|
| 20210528-053900 | 1 | -1333.58106425 |
| 20210528-053900 | 2 | -1333.25006295 |
| 20210528-053900 | 3 | -1332.40596663 |
| 20210528-053900 | 4 | -1327.1880297 |
| 20210528-053900 | 5 | -1320.63944318 |
Bill
--
William Denton
https://www.miskatonic.org/
Librarian, artist and licensed private investigator.
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2021-05-29 14:14 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2021-05-28 15:52 Passing a variable into an R source block Roger Mason
2021-05-28 17:30 ` Berry, Charles via General discussions about Org-mode.
2021-05-29 14:13 ` Roger Mason
2021-05-28 19:29 ` William Denton
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).