Working with Tables and Pandoc

2012-10-10

A quick note on the latest development version of Pandoc which remains by far one of the best software I've used.

Working with Tables in MultiMarkdown or Pandoc isn't fancy at all if you are to write them by hand. Hopefully, some editors like Emacs or Vim allow to simplify things a bit. For short statistical PDF reports which I now tend to write in Markdown since 4 months or so, I'm missing the ability to have Tables written in plain text, as produced with Emacs Table mode or orgtbl,(a) and converted automagically in a basic tabular (LaTeX) or table (ConTeX). That may just be because I was really working with an old version of Pandoc.

After googling a bit, I discovered that Pandoc now offers some support for orgtbl tables with pipes. Of course that means I need to update my current version of Pandoc (1.9.3, it was in fact compiled from the latest development snapshot available at that time), i.e. reinstalling everything. Why everything? Because it appears that the development version (yes, that's so good to live on the bleeding edge :-) now requires cabal-dev which is used to maintains sandboxed build environments (much like Python virtualenv). So I started to git pull my old repository and followed instructions on Pandoc wiki. Guess what: that didn't work! When calling

$ make prep

which purports to install all dependencies, I got a weird error with zip-archive-0.1.1.8 during the building phase. As I had no idea why this happened (and Google wasn't of any help this time), I thought that maybe my GHC install was also just too old.

$ ghc --version
The Glorious Glasgow Haskell Compilation System, version 7.0.4
[772] aliquote (0) ~
$ cabal --version
cabal-install version 1.16.0
using version 1.16.0.1 of the Cabal library 

I upgraded to the latest Haskell Platform. Now I'm done with

$ ghc --version
The Glorious Glasgow Haskell Compilation System, version 7.4.1

Then, I fetched Pandoc from Github again. I got no complaints with cabal install cabal-dev && make prep, and zip-archive-0.1.1.8 compiled without problem.

$ cabal-dev/bin/pandoc --version
pandoc 1.10
Compiled with citeproc-hs 0.3.5, texmath 0.6.1.1, highlighting-kate 0.5.3.2.
Syntax highlighting is supported for the following languages:
    Actionscript, Ada, Alert, Alert_indent, Apache, Asn1, Asp, Awk, Bash,
    Bibtex, Boo, C, Changelog, Clojure, Cmake, Coffee, Coldfusion, Commonlisp,
    Cpp, Cs, Css, D, Diff, Djangotemplate, Doxygen, Doxygenlua, Dtd, Eiffel,
    Email, Erlang, Fortran, Fsharp, Gnuassembler, Go, Haskell, Haxe, Html, Ini,
    Java, Javadoc, Javascript, Json, Jsp, Latex, Lex, LiterateHaskell, Lua,
    Makefile, Mandoc, Matlab, Maxima, Metafont, Mips, Modula2, Modula3,
    Monobasic, Nasm, Noweb, Objectivec, Objectivecpp, Ocaml, Octave, Pascal,
    Perl, Php, Pike, Postscript, Prolog, Python, R, Relaxngcompact, Rhtml, Ruby,
    Scala, Scheme, Sci, Sed, Sgml, Sql, SqlMysql, SqlPostgresql, Tcl, Texinfo,
    Verilog, Vhdl, Xml, Xorg, Xslt, Xul, Yacc, Yaml
Copyright (C) 2006-2012 John MacFarlane
Web:  http://johnmacfarlane.net/pandoc
This is free software; see the source for copying conditions.  There is no
warranty, not even for merchantability or fitness for a particular purpose.

Now, using orgtbl to make my table works like a charm. I just have to understand why Pandoc doesn't like my "grid tables".

Pandoc table editing in vim has some good tips on managing ASCII Table with Pandoc. For online previewing, you can try Format Text as a Table. And, of course, it is always a good idea to visit the Extras wiki page from time to time.

Notes

It should be noted that Emacs Table mode is fully compatible with ASCII tables returned by the Hmisc R package, like this:

f <- function(x, digits=1) {
  out <- round(c(min(x), max(x), median(x), mean(x), sd(x)), digits=digits)
  names(out) <- c("Min", "Max", "Median", "Mean", "SD")
  return(out)
}
grp <- sample(gl(4, 10, 40, labels=LETTERS[1:4]))
y <- rnorm(40, 12, 2)
summary(y ~ grp, fun=f)

y    N=40

+-------+-+--+----+----+------+----+---+
|       | |N |Min |Max |Median|Mean|SD |
+-------+-+--+----+----+------+----+---+
|grp    |A|10| 9.3|13.9|11.6  |11.7|1.3|
|       |B|10| 7.4|14.9|12.2  |11.8|2.3|
|       |C|10| 8.4|14.1|13.0  |12.4|2.0|
|       |D|10|11.3|14.3|13.5  |13.3|0.9|
+-------+-+--+----+----+------+----+---+
|Overall| |40| 7.4|14.9|12.8  |12.3|1.8|
+-------+-+--+----+----+------+----+---+
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