org-babel export table from R to LaTeX

org-babel export table from R to LaTeX

[Riccardo Romoli]

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Hi, I work with org-babel and R.
In the R session I create a table that I have to export to LaTeX.
This is the code I use:

#+headers: :results latex
#+begin_src R :session *R* :exports results
.....
  print(xtable(summary(mypca)))
#+end_src

I do not understand why the exported table is delimited by "|":

|% latex table generated in R 2.14.1 by xtable 1.6-0 package |
| % Tue Feb 14 16:21:48 2012 |
| \begin{table}[ht] |
  | \begin{center} |
    | \begin{tabular}{rrrrrrrrrrrrrrrrr} |
      | \hline |
      | & PC1 & PC2 & PC3 & PC4 & PC5 & PC6 & PC7 & PC8 & PC9 & PC10 &
      PC11 & PC12 & PC13 & PC14 & PC15 & PC16 \\ |
      | \hline |
      | Standard deviation & 3.4693 & 2.8113 & 2.5561 & 2.2668 &
      2.0015 & 1.9236 & 1.7287 & 1.6220 & 1.4288 & 1.3456 & 1.2596 &
      1.2195 & 1.1278 & 1.0778 & 0.8390 & 0.0000 \\ |
      | Proportion of Variance & 0.2188 & 0.1437 & 0.1188 & 0.0934 &
      0.0728 & 0.0673 & 0.0543 & 0.0478 & 0.0371 & 0.0329 & 0.0289 &
      0.0270 & 0.0231 & 0.0211 & 0.0128 & 0.0000 \\ |
      | Cumulative Proportion & 0.2188 & 0.3625 & 0.4813 & 0.5747 &
      0.6476 & 0.7149 & 0.7692 & 0.8170 & 0.8541 & 0.8871 & 0.9159 &
      0.9429 & 0.9661 & 0.9872 & 1.0000 & 1.0000 \\ |
      | \hline |
      | \end{tabular} |
    | \end{center} |
  | \end{table} |
| |

Should I change some headers settings??

Best

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Re: org-babel export table from R to LaTeX

[Riccardo Romoli]

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If I set :export latex when I exports to LaTeX I have only the R code, not
the table.

Best

2012/2/14 Christophe Pouzat <christophe.pouzat@gmail.com>

> Riccardo Romoli <ric.romoli@gmail.com> writes:
>
> > Hi, I work with org-babel and R.
> > In the R session I create a table that I have to export to LaTeX.
> > This is the code I use:
> >
> > #+headers: :results latex
> > #+begin_src R :session *R* :exports results
> > .....
> >   print(xtable(summary(mypca)))
> > #+end_src
> >
> > I do not understand why the exported table is delimited by "|":
> >
> > |% latex table generated in R 2.14.1 by xtable 1.6-0 package |
> > | % Tue Feb 14 16:21:48 2012 |
> > | \begin{table}[ht] |
> >   | \begin{center} |
> >     | \begin{tabular}{rrrrrrrrrrrrrrrrr} |
> >       | \hline |
> >       | & PC1 & PC2 & PC3 & PC4 & PC5 & PC6 & PC7 & PC8 & PC9 & PC10 &
> >       PC11 & PC12 & PC13 & PC14 & PC15 & PC16 \\ |
> >       | \hline |
> >       | Standard deviation & 3.4693 & 2.8113 & 2.5561 & 2.2668 &
> >       2.0015 & 1.9236 & 1.7287 & 1.6220 & 1.4288 & 1.3456 & 1.2596 &
> >       1.2195 & 1.1278 & 1.0778 & 0.8390 & 0.0000 \\ |
> >       | Proportion of Variance & 0.2188 & 0.1437 & 0.1188 & 0.0934 &
> >       0.0728 & 0.0673 & 0.0543 & 0.0478 & 0.0371 & 0.0329 & 0.0289 &
> >       0.0270 & 0.0231 & 0.0211 & 0.0128 & 0.0000 \\ |
> >       | Cumulative Proportion & 0.2188 & 0.3625 & 0.4813 & 0.5747 &
> >       0.6476 & 0.7149 & 0.7692 & 0.8170 & 0.8541 & 0.8871 & 0.9159 &
> >       0.9429 & 0.9661 & 0.9872 & 1.0000 & 1.0000 \\ |
> >       | \hline |
> >       | \end{tabular} |
> >     | \end{center} |
> >   | \end{table} |
> > | |
> >
> > Should I change some headers settings??
> >
> > Best
> >
>
> Hi Riccardo,
>
> Try ":exports latex" instead of ":exports results"
>
> Christophe
> --
>
> Most people are not natural-born statisticians. Left to our own
> devices we are not very good at picking out patterns from a sea of
> noisy data. To put it another way, we are all too good at picking out
> non-existent patterns that happen to suit our purposes.
> Bradley Efron & Robert Tibshirani (1993) An Introduction to the Bootstrap
>
> --
>
> Christophe Pouzat
> MAP5 - Mathématiques Appliquées à Paris 5
> CNRS UMR 8145
> 45, rue des Saints-Pères
> 75006 PARIS
> France
>
> tel: +33142863828
> mobile: +33662941034
> web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
>

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Re: org-babel export table from R to LaTeX

[Christophe Pouzat]

Sorry,

Checking foo.org (http://orgmode.org/w/?p=worg.git;a=blob_plain;f=org-contrib/babel/examples/foo.org;hb=HEAD) I got the correct way to do it:

#+begin_src R :results output latex :exports results
  library(xtable)
  xtable(foo, caption = "ANOVA Table", label = "tab:one",
      digits = c(0, 0, 2, 0, 2, 3, 3))
#+end_src

Does it solve your problem?

Christophe

Riccardo Romoli <ric.romoli@gmail.com> writes:

> If I set :export latex when I exports to LaTeX I have only the R code, not the
> table.
>
> Best
>
> 2012/2/14 Christophe Pouzat <christophe.pouzat@gmail.com>
>
>     Riccardo Romoli <ric.romoli@gmail.com> writes:
>
>     > Hi, I work with org-babel and R.
>     > In the R session I create a table that I have to export to LaTeX.
>     > This is the code I use:
>     >
>     > #+headers: :results latex
>     > #+begin_src R :session *R* :exports results
>     > .....
>     >   print(xtable(summary(mypca)))
>     > #+end_src
>     >
>     > I do not understand why the exported table is delimited by "|":
>     >
>     > |% latex table generated in R 2.14.1 by xtable 1.6-0 package |
>     > | % Tue Feb 14 16:21:48 2012 |
>     > | \begin{table}[ht] |
>     >   | \begin{center} |
>     >     | \begin{tabular}{rrrrrrrrrrrrrrrrr} |
>     >       | \hline |
>     >       | & PC1 & PC2 & PC3 & PC4 & PC5 & PC6 & PC7 & PC8 & PC9 & PC10 &
>     >       PC11 & PC12 & PC13 & PC14 & PC15 & PC16 \\ |
>     >       | \hline |
>     >       | Standard deviation & 3.4693 & 2.8113 & 2.5561 & 2.2668 &
>     >       2.0015 & 1.9236 & 1.7287 & 1.6220 & 1.4288 & 1.3456 & 1.2596 &
>     >       1.2195 & 1.1278 & 1.0778 & 0.8390 & 0.0000 \\ |
>     >       | Proportion of Variance & 0.2188 & 0.1437 & 0.1188 & 0.0934 &
>     >       0.0728 & 0.0673 & 0.0543 & 0.0478 & 0.0371 & 0.0329 & 0.0289 &
>     >       0.0270 & 0.0231 & 0.0211 & 0.0128 & 0.0000 \\ |
>     >       | Cumulative Proportion & 0.2188 & 0.3625 & 0.4813 & 0.5747 &
>     >       0.6476 & 0.7149 & 0.7692 & 0.8170 & 0.8541 & 0.8871 & 0.9159 &
>     >       0.9429 & 0.9661 & 0.9872 & 1.0000 & 1.0000 \\ |
>     >       | \hline |
>     >       | \end{tabular} |
>     >     | \end{center} |
>     >   | \end{table} |
>     > | |
>     >
>     > Should I change some headers settings??
>     >
>     > Best
>     >
>
>     Hi Riccardo,
>
>     Try ":exports latex" instead of ":exports results"
>
>     Christophe
>     --
>
>     Most people are not natural-born statisticians. Left to our own
>     devices we are not very good at picking out patterns from a sea of
>     noisy data. To put it another way, we are all too good at picking out
>     non-existent patterns that happen to suit our purposes.
>     Bradley Efron & Robert Tibshirani (1993) An Introduction to the Bootstrap
>
>     --
>
>     Christophe Pouzat
>     MAP5 - Mathématiques Appliquées à Paris 5
>     CNRS UMR 8145
>     45, rue des Saints-Pères
>     75006 PARIS
>     France
>
>     tel: +33142863828
>     mobile: +33662941034
>     web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
>
>

-- 

Most people are not natural-born statisticians. Left to our own
devices we are not very good at picking out patterns from a sea of
noisy data. To put it another way, we are all too good at picking out
non-existent patterns that happen to suit our purposes.
Bradley Efron & Robert Tibshirani (1993) An Introduction to the Bootstrap

--

Christophe Pouzat
MAP5 - Mathématiques Appliquées à Paris 5
CNRS UMR 8145
45, rue des Saints-Pères
75006 PARIS
France

tel: +33142863828
mobile: +33662941034
web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html

Re: org-babel export table from R to LaTeX

[Andreas Leha]

Christophe Pouzat <christophe.pouzat@gmail.com> writes:

> Sorry,
>
> Checking foo.org
> (http://orgmode.org/w/?p=worg.git;a=blob_plain;f=org-contrib/babel/examples/foo.org;hb=HEAD)
> I got the correct way to do it:
>
> #+begin_src R :results output latex :exports results
>   library(xtable)
>   xtable(foo, caption = "ANOVA Table", label = "tab:one",
>       digits = c(0, 0, 2, 0, 2, 3, 3))
> #+end_src
>
> Does it solve your problem?
>
> Christophe
>
> Riccardo Romoli <ric.romoli@gmail.com> writes:
>
>> If I set :export latex when I exports to LaTeX I have only the R code, not the
>> table.
>>
>> Best
>>
>> 2012/2/14 Christophe Pouzat <christophe.pouzat@gmail.com>
>>
>>     Riccardo Romoli <ric.romoli@gmail.com> writes:
>>
>>     > Hi, I work with org-babel and R.
>>     > In the R session I create a table that I have to export to LaTeX.
>>     > This is the code I use:
>>     >
>>     > #+headers: :results latex
>>     > #+begin_src R :session *R* :exports results
>>     > .....
>>     >   print(xtable(summary(mypca)))
>>     > #+end_src
>>     >
>>     > I do not understand why the exported table is delimited by "|":
>>     >
>>     > |% latex table generated in R 2.14.1 by xtable 1.6-0 package |
>>     > | % Tue Feb 14 16:21:48 2012 |
>>     > | \begin{table}[ht] |
>>     >   | \begin{center} |
>>     >     | \begin{tabular}{rrrrrrrrrrrrrrrrr} |
>>     >       | \hline |
>>     >       | & PC1 & PC2 & PC3 & PC4 & PC5 & PC6 & PC7 & PC8 & PC9 & PC10 &
>>     >       PC11 & PC12 & PC13 & PC14 & PC15 & PC16 \\ |
>>     >       | \hline |
>>     >       | Standard deviation & 3.4693 & 2.8113 & 2.5561 & 2.2668 &
>>     >       2.0015 & 1.9236 & 1.7287 & 1.6220 & 1.4288 & 1.3456 & 1.2596 &
>>     >       1.2195 & 1.1278 & 1.0778 & 0.8390 & 0.0000 \\ |
>>     >       | Proportion of Variance & 0.2188 & 0.1437 & 0.1188 & 0.0934 &
>>     >       0.0728 & 0.0673 & 0.0543 & 0.0478 & 0.0371 & 0.0329 & 0.0289 &
>>     >       0.0270 & 0.0231 & 0.0211 & 0.0128 & 0.0000 \\ |
>>     >       | Cumulative Proportion & 0.2188 & 0.3625 & 0.4813 & 0.5747 &
>>     >       0.6476 & 0.7149 & 0.7692 & 0.8170 & 0.8541 & 0.8871 & 0.9159 &
>>     >       0.9429 & 0.9661 & 0.9872 & 1.0000 & 1.0000 \\ |
>>     >       | \hline |
>>     >       | \end{tabular} |
>>     >     | \end{center} |
>>     >   | \end{table} |
>>     > | |
>>     >
>>     > Should I change some headers settings??
>>     >
>>     > Best
>>     >
>>
>>     Hi Riccardo,
>>
>>     Try ":exports latex" instead of ":exports results"
>>
>>     Christophe
>>     --
>>
>>     Most people are not natural-born statisticians. Left to our own
>>     devices we are not very good at picking out patterns from a sea of
>>     noisy data. To put it another way, we are all too good at picking out
>>     non-existent patterns that happen to suit our purposes.
>>     Bradley Efron & Robert Tibshirani (1993) An Introduction to the Bootstrap
>>
>>     --
>>
>>     Christophe Pouzat
>>     MAP5 - Mathématiques Appliquées à Paris 5
>>     CNRS UMR 8145
>>     45, rue des Saints-Pères
>>     75006 PARIS
>>     France
>>
>>     tel: +33142863828
>>     mobile: +33662941034
>>     web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
>>
>>

Hi Riccardo,

additionally, if you do not want to get too tightly bound to LaTeX, check
out the ascii-package, e.g.

#+begin_src R :results output org wrap :exports results
  library(ascii)

  ## from the lm help page:
  ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
  trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
  group <- gl(2,10,20, labels=c("Ctl","Trt"))
  weight <- c(ctl, trt)
  lm.D9 <- lm(weight ~ group)
  lm.D90 <- lm(weight ~ group - 1) # omitting intercept

  print(ascii(anova(lm.D9)), type="org")
#+end_src


Cheers,
Andreas

Re: org-babel export table from R to LaTeX

[Riccardo Romoli]

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Thanks for your suggestion, I solved the problem using:

#+headers: :results output latex
#+begin_src R :session *R* :exports results
...
print(xtable(summary(mypca)))
#+end_src

Regards
Riccardo




2012/2/14 Andreas Leha <andreas.leha@med.uni-goettingen.de>

> Christophe Pouzat <christophe.pouzat@gmail.com> writes:
>
> > Sorry,
> >
> > Checking foo.org
> > (
> http://orgmode.org/w/?p=worg.git;a=blob_plain;f=org-contrib/babel/examples/foo.org;hb=HEAD
> )
> > I got the correct way to do it:
> >
> > #+begin_src R :results output latex :exports results
> >   library(xtable)
> >   xtable(foo, caption = "ANOVA Table", label = "tab:one",
> >       digits = c(0, 0, 2, 0, 2, 3, 3))
> > #+end_src
> >
> > Does it solve your problem?
> >
> > Christophe
> >
> > Riccardo Romoli <ric.romoli@gmail.com> writes:
> >
> >> If I set :export latex when I exports to LaTeX I have only the R code,
> not the
> >> table.
> >>
> >> Best
> >>
> >> 2012/2/14 Christophe Pouzat <christophe.pouzat@gmail.com>
> >>
> >>     Riccardo Romoli <ric.romoli@gmail.com> writes:
> >>
> >>     > Hi, I work with org-babel and R.
> >>     > In the R session I create a table that I have to export to LaTeX.
> >>     > This is the code I use:
> >>     >
> >>     > #+headers: :results latex
> >>     > #+begin_src R :session *R* :exports results
> >>     > .....
> >>     >   print(xtable(summary(mypca)))
> >>     > #+end_src
> >>     >
> >>     > I do not understand why the exported table is delimited by "|":
> >>     >
> >>     > |% latex table generated in R 2.14.1 by xtable 1.6-0 package |
> >>     > | % Tue Feb 14 16:21:48 2012 |
> >>     > | \begin{table}[ht] |
> >>     >   | \begin{center} |
> >>     >     | \begin{tabular}{rrrrrrrrrrrrrrrrr} |
> >>     >       | \hline |
> >>     >       | & PC1 & PC2 & PC3 & PC4 & PC5 & PC6 & PC7 & PC8 & PC9 &
> PC10 &
> >>     >       PC11 & PC12 & PC13 & PC14 & PC15 & PC16 \\ |
> >>     >       | \hline |
> >>     >       | Standard deviation & 3.4693 & 2.8113 & 2.5561 & 2.2668 &
> >>     >       2.0015 & 1.9236 & 1.7287 & 1.6220 & 1.4288 & 1.3456 &
> 1.2596 &
> >>     >       1.2195 & 1.1278 & 1.0778 & 0.8390 & 0.0000 \\ |
> >>     >       | Proportion of Variance & 0.2188 & 0.1437 & 0.1188 &
> 0.0934 &
> >>     >       0.0728 & 0.0673 & 0.0543 & 0.0478 & 0.0371 & 0.0329 &
> 0.0289 &
> >>     >       0.0270 & 0.0231 & 0.0211 & 0.0128 & 0.0000 \\ |
> >>     >       | Cumulative Proportion & 0.2188 & 0.3625 & 0.4813 & 0.5747
> &
> >>     >       0.6476 & 0.7149 & 0.7692 & 0.8170 & 0.8541 & 0.8871 &
> 0.9159 &
> >>     >       0.9429 & 0.9661 & 0.9872 & 1.0000 & 1.0000 \\ |
> >>     >       | \hline |
> >>     >       | \end{tabular} |
> >>     >     | \end{center} |
> >>     >   | \end{table} |
> >>     > | |
> >>     >
> >>     > Should I change some headers settings??
> >>     >
> >>     > Best
> >>     >
> >>
> >>     Hi Riccardo,
> >>
> >>     Try ":exports latex" instead of ":exports results"
> >>
> >>     Christophe
> >>     --
> >>
> >>     Most people are not natural-born statisticians. Left to our own
> >>     devices we are not very good at picking out patterns from a sea of
> >>     noisy data. To put it another way, we are all too good at picking
> out
> >>     non-existent patterns that happen to suit our purposes.
> >>     Bradley Efron & Robert Tibshirani (1993) An Introduction to the
> Bootstrap
> >>
> >>     --
> >>
> >>     Christophe Pouzat
> >>     MAP5 - Mathématiques Appliquées à Paris 5
> >>     CNRS UMR 8145
> >>     45, rue des Saints-Pères
> >>     75006 PARIS
> >>     France
> >>
> >>     tel: +33142863828
> >>     mobile: +33662941034
> >>     web: http://www.biomedicale.univ-paris5.fr/physcerv/C_Pouzat.html
> >>
> >>
>
> Hi Riccardo,
>
> additionally, if you do not want to get too tightly bound to LaTeX, check
> out the ascii-package, e.g.
>
> #+begin_src R :results output org wrap :exports results
>  library(ascii)
>
>  ## from the lm help page:
>  ctl <- c(4.17,5.58,5.18,6.11,4.50,4.61,5.17,4.53,5.33,5.14)
>  trt <- c(4.81,4.17,4.41,3.59,5.87,3.83,6.03,4.89,4.32,4.69)
>  group <- gl(2,10,20, labels=c("Ctl","Trt"))
>  weight <- c(ctl, trt)
>  lm.D9 <- lm(weight ~ group)
>  lm.D90 <- lm(weight ~ group - 1) # omitting intercept
>
>  print(ascii(anova(lm.D9)), type="org")
> #+end_src
>
>
> Cheers,
> Andreas
>
>
>

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