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Reproducible research paper in the journal Archaeology in Oceania

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README
# -*- mode: org -*-

This directory holds the colonization.org file, which is a plain text
Org-mode document that contains the research project that resulted in
the paper "A Model-based Age Estimate for Polynesian Colonization of
Hawai`i" published in the journal Archaeology in Oceania.

Also included are data files: the *.csv files were generated by BCal,
on online Bayesian radiocarbon dating tool,
http://bcal.shef.ac.uk/top.html; the colonization.bib file contains
the bibliographic references cited in the paper.

The following instructions can be used to generate a viewable pdf
version of this document.  The generation process involves evaluating
the source code blocks embedded in colonization.org, performing the
relevant calculations, and generating the referenced figures.

1. Install the latest version of emacs "Emacs 24" from
   http://savannah.gnu.org/projects/emacs

2. Ensure that a working installation of LaTeX, http://www.ctan.org/,
   is available on your system and that it includes the file biblatex.sty
   http://www.tex.ac.uk/tex-archive/help/Catalogue/entries/biblatex.html.

3. Ensure that the following executable is installed on your system
   and in your $PATH
   - R http://www.r-project.org/

4. Your R installation must include the ggplot2 package,
   http://had.co.nz/ggplot2/

5. The ability to jump to bibliographic entries from citations in the
   Org-mode file depends on ebib, http://ebib.sourceforge.net/

6. Emacs Speaks Statistics (ESS) provides support for communication
   between Emacs and a persistent R process. To install ESS download
   the source code from http://ess.r-project.org/ -- this paper was
   tested with version 5.13.  Unpack the download into a directory on
   your machine, and update the `ess-path' variable on the second line
   of init.el in this directory to point to your local ess/lisp/
   directory.

7. Alternatively, follow steps 8 through 11 or call make from within
   the directory that holds colonization.org.  The make program will
   create the file colonization.pdf.

8. From the command line, cd into the directory that holds colonization.org
   and then launch Emacs using the following command
   
   : emacs -Q -l init.el colonization.org

9. The resulting Emacs window will be visiting the Org-mode file,
   colonization.org.  From here it is possible to navigate and edit the
   document, and to inspect and evaluate source code blocks.

10. Export the document to LaTeX with the M-x org-export-as-latex
   command---just press RET in reply to queries from R.

11. The resulting colonization.tex file can be built from the command line
   with pdflatex and bibtex.
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