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.
- Install the latest version of emacs “Emacs 24” from http://savannah.gnu.org/projects/emacs
- 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.
- Ensure that the following executable is installed on your system and in your $PATH
- Your R installation must include the ggplot2 package, http://had.co.nz/ggplot2/
- The ability to jump to bibliographic entries from citations in the Org-mode file depends on ebib, http://ebib.sourceforge.net/
- 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.
- 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.
- 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
- 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.
- Export the document to LaTeX with the M-x org-export-as-latex command—just press RET in reply to queries from R.
- The resulting colonization.tex file can be built from the command line with pdflatex and bibtex.