Reproducible research paper in the journal Archaeology in Oceania
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Makefile
README
alpha-activity-and-beta-pre.csv
alpha-o18-and-alpha-post.csv
alpha-post-no-rat.csv
alpha-post-with-rat.csv
colonization.bib
colonization.org
init.el
theta-1-no-model.csv
theta-1-no-rat.csv
theta-4-no-model.csv
theta-4-no-rat.csv

README

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
  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.