* org-mode R using xtable produces strange output
@ 2018-03-19 23:44 Brian Shine
2018-03-20 16:47 ` Berry, Charles
0 siblings, 1 reply; 3+ messages in thread
From: Brian Shine @ 2018-03-19 23:44 UTC (permalink / raw)
To: Liste-emacs-orgmode@gnu.org; +Cc: Brian Shine
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I am using xtable to produce summary tables of linear models, specifying the output as latex. If I just run the code in R, I get the correct output. However, the latex output in the org document contains a lot of “|”s. I think this is because the header of the table contains some code to make “p > |t|”, where the vertical lines are to indicate “absolute value of t”. My guess is that when the output is written to the results section, org interprets the “|” signs as an org-table and tries to be helpful by adding more of them to make up the correct number of columns. If I switch off the latex output, and write the xtable to a small .tex file, using xtable.print and then include the file after the code block, the table appears correctly.
I’m using emacs 25.2.
Here’s an example:
Best wishes,
Brian
[-- Attachment #2: xtableeg.org --]
[-- Type: application/octet-stream, Size: 1409 bytes --]
#+BEGIN_SRC R :session :exports results :results latex
library(xtable)
examp <- data.frame(x = 1:10, y = 10:1)
print.xtable(xtable(summary(glm(y ~ x, data = examp))))
#+END_SRC
#+RESULTS:
#+BEGIN_EXPORT latex
| % latex table generated in R 3.4.4 by xtable 1.8-2 package | | |
| % Mon Mar 19 23:41:04 2018 | | |
| \begin{table}[ht] | | |
| \centering | | |
| \begin{tabular}{rrrrr} | | |
| \hline | | |
| & Estimate & Std. Error & t value & Pr($>$$ | $t$ | $) \\ |
| \hline | | |
| (Intercept) & 11.0000 & 0.0000 & 10932581685367508.00 & 0.0000 \\ | | |
| x & -1.0000 & 0.0000 & -6166807764706701.00 & 0.0000 \\ | | |
| \hline | | |
| \end{tabular} | | |
| \end{table} | | |
| | | |
#+END_EXPORT
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^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: org-mode R using xtable produces strange output
2018-03-19 23:44 org-mode R using xtable produces strange output Brian Shine
@ 2018-03-20 16:47 ` Berry, Charles
2018-03-20 22:40 ` Brian Shine
0 siblings, 1 reply; 3+ messages in thread
From: Berry, Charles @ 2018-03-20 16:47 UTC (permalink / raw)
To: Brian Shine; +Cc: Liste-emacs-orgmode@gnu.org
> On Mar 19, 2018, at 4:44 PM, Brian Shine <brianshine@mac.com> wrote:
>
> I am using xtable to produce summary tables of linear models, specifying the output as latex. If I just run the code in R, I get the correct output. However, the latex output in the org document contains a lot of “|”s. I think this is because the header of the table contains some code to make “p > |t|”, where the vertical lines are to indicate “absolute value of t”. My guess is that when the output is written to the results section, org interprets the “|” signs as an org-table and tries to be helpful by adding more of them to make up the correct number of columns.
See
(info "(org) results")
and note the difference between `:results output' and `:results value' (the default).
Since you want the printed version of the R object, you should use
`:results output latex'
to pass the printed output to the org #+Results or
`:results raw :wrap export latex'
to pass the unadorned value. In your use case they seem to produce the same #+Results.
HTH,
Chuck
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: org-mode R using xtable produces strange output
2018-03-20 16:47 ` Berry, Charles
@ 2018-03-20 22:40 ` Brian Shine
0 siblings, 0 replies; 3+ messages in thread
From: Brian Shine @ 2018-03-20 22:40 UTC (permalink / raw)
To: Berry, Charles; +Cc: Liste-emacs-orgmode@gnu.org, Brian Shine
Brilliant! Thank you so much.
Best wishes,
Brian
> On 20 Mar 2018, at 16:47, Berry, Charles <ccberry@ucsd.edu> wrote:
>
>
>
>> On Mar 19, 2018, at 4:44 PM, Brian Shine <brianshine@mac.com> wrote:
>>
>> I am using xtable to produce summary tables of linear models, specifying the output as latex. If I just run the code in R, I get the correct output. However, the latex output in the org document contains a lot of “|”s. I think this is because the header of the table contains some code to make “p > |t|”, where the vertical lines are to indicate “absolute value of t”. My guess is that when the output is written to the results section, org interprets the “|” signs as an org-table and tries to be helpful by adding more of them to make up the correct number of columns.
>
>
> See
>
> (info "(org) results")
>
> and note the difference between `:results output' and `:results value' (the default).
>
> Since you want the printed version of the R object, you should use
>
> `:results output latex'
>
> to pass the printed output to the org #+Results or
>
> `:results raw :wrap export latex'
>
> to pass the unadorned value. In your use case they seem to produce the same #+Results.
>
> HTH,
>
> Chuck
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2018-03-19 23:44 org-mode R using xtable produces strange output Brian Shine
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