[R] Printing/Generating/Outputting a Table (Not Latex)
Henrik Bengtsson
hb at biostat.ucsf.edu
Wed Dec 10 00:11:41 CET 2014
I'm surprised no one mentioned alternatives to LaTeX, which is not
necessarily installed on all systems and it's also quite a
heavy-weight setup (100's-1000's MBs). An alternative is to output a
table in Markdown or HTML and convert that to PDF. The poor man's
HTML-to-PDF is to manually open the HTML document in a modern web
browser and simply "save as/print to" PDF. For automatic conversion,
one can use Pandoc [http://johnmacfarlane.net/pandoc/], which is quick
to install.
There are several options to output a table in Markdown or HTML from a
data.frame, e.g. xtable, knitr, rmarkdown. Here's how you can do it
using R.rsp + knitr::kable:
Create the following RSP-embedded Markdown file 'table.md.rsp' (- - -
lines excluded):
- - - BEGIN - - -
<%
R.utils::use("knitr")
options(knitr.table.format="markdown")
%>
# A Table
<%
data <- head(datasets::iris)
%>
<%= kable(data) %>
_Table: The first <%=nrow(data)%> entries of the iris dataset._
- - - END - - -
Then just run:
> library("R.rsp")
> html <- rfile("table.md.rsp")
> !html
and print/save as PDF in the browser. (*)
If you've got Pandoc installed you can generate a PDF by making sure
to use options(knitr.table.format="pandoc") and then:
> library("R.rsp")
> md <- rfile('table-pandoc.md.rsp', postprocess=FALSE)
> pdf <- gsub("md$", "pdf", md)
> system2("pandoc", args=c(normalizePath(md), "-o", pdf))
> !pdf
See also this Gist: https://gist.github.com/HenrikBengtsson/f4e8f6fe2af5d6ccbed6
/Henrik
(*) For the lazy, to test the above HTML example "on the fly" run:
source("http://callr.org/rfile#https://gist.githubusercontent.com/HenrikBengtsson/f4e8f6fe2af5d6ccbed6/raw/table.md.rsp")
On Tue, Dec 9, 2014 at 1:02 PM, Prof Brian Ripley <ripley at stats.ox.ac.uk> wrote:
> On 09/12/2014 20:47, Richard M. Heiberger wrote:
>>
>> the last one is wrong. That is the one for which I don't know the
>> right answer on linux.
>>
>> 'xdvi' displays dvi files. you need to display a pdf file.
>> whatever is the right program on linux to display pdf files is what
>> belongs there.
>>
>> On Macintosh we can avoid knowing by using 'open', which means use the
>> system standard.
>> I don't know what the linux equivalent is, either the exact program or
>> the instruction to use the standard.
>
>
> xdg-open (but like OS X it depends on having the right associations set).
>
>
>>
>> On Tue, Dec 9, 2014 at 3:36 PM, Kate Ignatius <kate.ignatius at gmail.com>
>> wrote:
>>>
>>> I set these options:
>>>
>>> options(latexcmd='pdflatex')
>>> options(dviExtension='pdf')
>>> options(xdvicmd='xdvi')
>>>
>>> Maybe one too many? I'm running in Linux.
>>>
>>>
>>>
>>> On Tue, Dec 9, 2014 at 3:24 PM, Richard M. Heiberger <rmh at temple.edu>
>>> wrote:
>>>>
>>>> It looks like you skipped the step of setting the options.
>>>> the latex function doesn't do pdflatex (by default it does regular
>>>> latex) unless you set the options
>>>> as I indicated.
>>>>
>>>> On Tue, Dec 9, 2014 at 3:11 PM, Kate Ignatius <kate.ignatius at gmail.com>
>>>> wrote:
>>>>>
>>>>> Ah yes, you're right.
>>>>>
>>>>> The log has this error:
>>>>>
>>>>> ! LaTeX Error: Missing \begin{document}.
>>>>>
>>>>> Though can't really find much online on how to resolve it.
>>>>>
>>>>> On Tue, Dec 9, 2014 at 1:15 PM, Jeff Newmiller
>>>>> <jdnewmil at dcn.davis.ca.us> wrote:
>>>>>>
>>>>>> pdflatex appears to have run, because it exited. You should look at
>>>>>> the tex log file, the problem is more likely that the latex you sent out to
>>>>>> pdflatex was incomplete.
>>>>>>
>>>>>> ---------------------------------------------------------------------------
>>>>>> Jeff Newmiller The ..... ..... Go
>>>>>> Live...
>>>>>> DCN:<jdnewmil at dcn.davis.ca.us> Basics: ##.#. ##.#. Live
>>>>>> Go...
>>>>>> Live: OO#.. Dead: OO#..
>>>>>> Playing
>>>>>> Research Engineer (Solar/Batteries O.O#. #.O#. with
>>>>>> /Software/Embedded Controllers) .OO#. .OO#.
>>>>>> rocks...1k
>>>>>>
>>>>>> ---------------------------------------------------------------------------
>>>>>> Sent from my phone. Please excuse my brevity.
>>>>>>
>>>>>> On December 9, 2014 8:43:02 AM PST, Kate Ignatius
>>>>>> <kate.ignatius at gmail.com> wrote:
>>>>>>>
>>>>>>> Thanks! I do get several errors though when running on Linux.
>>>>>>>
>>>>>>> Running your code, I get this:
>>>>>>>
>>>>>>> Error in system(cmd, intern = TRUE, wait = TRUE) :
>>>>>>> error in running command
>>>>>>>
>>>>>>> Fiddling around with the code and running this:
>>>>>>>
>>>>>>> tmp <- matrix(1:9,3,3)
>>>>>>> tmp.tex <- latex(tmp, file='tmp.tex')
>>>>>>> print.default(tmp.tex)
>>>>>>> tmp.dvi <- dvi(tmp.tex)
>>>>>>> tmp.dvi
>>>>>>> tmp.tex
>>>>>>> dvips(tmp.dvi)
>>>>>>> dvips(tmp.tex)
>>>>>>> library(tools)
>>>>>>> texi2dvi(file='tmp.tex', pdf=TRUE, clean=TRUE)
>>>>>>>
>>>>>>> I get this:
>>>>>>>
>>>>>>> Error in texi2dvi(file="tmp.tex",, :
>>>>>>> Running 'texi2dvi' on 'tmp.tex' failed.
>>>>>>> Messages:
>>>>>>> /usr/bin/texi2dvi: pdflatex exited with bad status, quitting.
>>>>>>>
>>>>>>> I've read that it may have something to do with the path of pdflatex.
>>>>>>>
>>>>>>> Sys.which('pdflatex')
>>>>>>>
>>>>>>> pdflatex
>>>>>>>
>>>>>>> "/usr/bin/pdflatex"
>>>>>>>
>>>>>>>
>>>>>>> Sys.which('texi2dvi')
>>>>>>>
>>>>>>> texi2dvi
>>>>>>>
>>>>>>> "/usr/bin/texi2dvi"
>>>>>>>
>>>>>>>> file.exists(Sys.which('texi2dvi'))
>>>>>>>
>>>>>>>
>>>>>>> [1] TRUE
>>>>>>>
>>>>>>>> file.exists(Sys.which('pdflatex'))
>>>>>>>
>>>>>>>
>>>>>>> [1] TRUE
>>>>>>>
>>>>>>> Is there a specific path I should be giving with pdflatex and/or
>>>>>>> 'texi2dvi to make this work?
>>>>>>>
>>>>>>> Thanks!
>>>>>>>
>>>>>>> On Mon, Dec 8, 2014 at 11:13 PM, Richard M. Heiberger
>>>>>>> <rmh at temple.edu>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> yes of course, and the answer is latex() in the Hmisc package.
>>>>>>>> Why were you excluding it?
>>>>>>>> Details follow
>>>>>>>>
>>>>>>>> Rich
>>>>>>>>
>>>>>>>>
>>>>>>>> The current release of the Hmisc package has this capability on
>>>>>>>> Macintosh and Linux.
>>>>>>>> For Windows, you need the next release 3.14-7 which is available now
>>>>>>>
>>>>>>> at github.
>>>>>>>>
>>>>>>>>
>>>>>>>> ## windows needs these lines until the new Hmisc version is on CRAN
>>>>>>>> install.packages("devtools")
>>>>>>>> devtools::install_github("Hmisc", "harrelfe")
>>>>>>>>
>>>>>>>> ## All operating systems
>>>>>>>> options(latexcmd='pdflatex')
>>>>>>>> options(dviExtension='pdf')
>>>>>>>>
>>>>>>>> ## Macintosh
>>>>>>>> options(xdvicmd='open')
>>>>>>>>
>>>>>>>> ## Windows, one of the following
>>>>>>>>
>>>>>>>
>>>>>>> options(xdvicmd='c:\\progra~1\\Adobe\\Reader~1.0\\Reader\\AcroRd32.exe')
>>>>>>>>
>>>>>>>> ## 32-bit windows
>>>>>>>>
>>>>>>>
>>>>>>> options(xdvicmd='c:\\progra~2\\Adobe\\Reader~1.0\\Reader\\AcroRd32.exe')
>>>>>>>>
>>>>>>>> ## 64 bit windows
>>>>>>>>
>>>>>>>> ## Linux
>>>>>>>> ## I don't know the xdvicmd value
>>>>>>>>
>>>>>>>>
>>>>>>>> ## this works on all R systems
>>>>>>>> library(Hmisc)
>>>>>>>> tmp <- matrix(1:9,3,3)
>>>>>>>> tmp.dvi <- dvi(latex(tmp))
>>>>>>>> print.default(tmp.dvi) ## prints filepath of the pdf file
>>>>>>>> tmp.dvi ## displays the pdf file on your screen
>>>>>>>>
>>>>>>>> On Mon, Dec 8, 2014 at 9:31 PM, Kate Ignatius
>>>>>>>
>>>>>>> <kate.ignatius at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I have a simple question. I know there are plenty of packages out
>>>>>>>>> there that can provide code to generate a table in latex. But I
>>>>>>>>> was
>>>>>>>>> wondering whether there was one out there where I can generate a
>>>>>>>
>>>>>>> table
>>>>>>>>>
>>>>>>>>> from my data (which ever way I please) then allow me to save it as
>>>>>>>>> a
>>>>>>>>> pdf?
>>>>>>>>>
>>>>>>>>> Thanks
>>>>>>>>>
>>>>>>>>> K.
>>>>>>>>>
>>>>>>>>> ______________________________________________
>>>>>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>>>> PLEASE do read the posting guide
>>>>>>>
>>>>>>> http://www.R-project.org/posting-guide.html
>>>>>>>>>
>>>>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>>>
>>>>>>>
>>>>>>> ______________________________________________
>>>>>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>> PLEASE do read the posting guide
>>>>>>> http://www.R-project.org/posting-guide.html
>>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>>>
>>>>>>
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
> --
> Brian D. Ripley, ripley at stats.ox.ac.uk
> Emeritus Professor of Applied Statistics, University of Oxford
> 1 South Parks Road, Oxford OX1 3TG, UK
>
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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