Paper sekelton in Markdown - for use with pandoc. Export to Latex, PDF and Microsoft Word docx

paper_skeleton.txt

[//]: # (Claas Heuer, November 2015)
[//]: # (Run pandoc like this)
[//]: # (pandoc --filter pandoc-crossref -s -S --bibliography references.bib paper_skeleton.txt -o test.docx)
[//]: # (pandoc --filter pandoc-crossref -s -S --bibliography references.bib paper_skeleton.txt -o test.pdf)


# First Section {#sec:first_section}

This is the first section and we are writing an equation that we want to reference to later in
the document:

$$
\mathbf{y} = \mathbf{Xb} + \mathbf{Zu} + \mathbf{e}
$$ {#eq:first_equation}

This is our first citation [@Bib2014]


# Second Section

I want to reference to tables, figures and equations as said in chapter @sec:first_section 
just like equation @eq:first_equation.
Most importantly, we want to be able to reference figures, like @fig:first_figure
and tables like @tbl:first_table

This is our second citation [@Bib2013]

\newpage

# Table Section

| Tables        | Are           | Cool  |
| ------------- |:-------------:| -----:|
| col 3 is      | right-aligned | $1600 |
| col 2 is      | centered      |   $12 |
| zebra stripes | are neat      |    $1 | 

: An example table {#tbl:first_table}

\newpage

# Figure Section

![An Example Figure](http://www.molecularecologist.com/wp-content/uploads/2013/11/github-logo.jpg){#fig:first_figure}

\newpage

# Useful 

Pandoc Cross-ref: \url{https://github.com/lierdakil/pandoc-crossref}

Markdown Cheat-Sheet: \url{https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet#code}

Latex to Word: \url{https://abnormaldata.wordpress.com/2014/11/17/converting-latex-to-word/}

Citations: \url{http://pandoc.org/demo/example19/Extension-citations.html}

# References

references.bib

% This file was created with JabRef 2.10.
% Encoding: UTF8


@Article{Bib2014,
  Title                    = {Their second paper},
  Author                   = {Bib, Name and LastName, FirstName and Author, Another},
  Journal                  = {Some journal},
  Year                     = {2014},
  Month                    = {Oct},
  Note                     = {Oct 15, 2014},
  Number                   = {1},
  Pages                    = {876--89},
  Volume                   = {22},

}

@InProceedings{Bib2013,
  Title                    = {Their first paper},
  Author                   = {Bib2, Name and LastName, FirstName and Author, Another},
  Booktitle                = {Some conference proceedings},
  Year                     = {2013},
  Month                    = {June},
  Note                     = {June 20, 2013},
  Number                   = {1},
  Pages                    = {12--18},
  Volume                   = {3}
}