Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation

Compendium URL

https://dx.doi.org/10.6084/m9.figshare.1563661

Author

Ben Marwick (benmarwick@gmail.com)

Contents

This repository contains the research compendium for my paper in the Journal of Archaeological Method and Theory:

Marwick, B. (2016). Computational reproducibility in archaeological research: Basic principles and a case study of their implementation. Journal of Archaeological Method and Theory, 1-27. doi: 10.1007/s10816-015-9272-9

The paper is available as a free PDF, an Open Access author-accepted manuscript, or on the subscription-only site for the Journal of Archaeological Method and Theory

Here's a bibtex-style citation for easy copy-pasting:

@article{
year={2016},
issn={1072-5369},
journal={Journal of Archaeological Method and Theory},
doi={10.1007/s10816-015-9272-9},
title={Computational Reproducibility in Archaeological Research: Basic Principles and a Case Study of Their Implementation},
url={http://dx.doi.org/10.1007/s10816-015-9272-9},
publisher={Springer US},
keywords={Reproducible research; Computer programming; Software engineering; Australian archaeology; Open science},
author={Marwick, Ben},
pages={1-27},
language={English}
}

How to use

See the text directory on GitHub for the source code that generated the manuscript. The Rmd file is the original source document, and the docx file was required by the publisher for submission.

See the published PDF (view in browser or download) here in this repository.

Dependencies

I used RStudio v0.99.825 with Pandoc 1.13.2. To generate a docx from the Rmd, see the R Session Information below for the R version and packages that I used. To generate a PDF, I used LaTeX (MiKTeX 2.9).

Licenses:

Text: CC-BY-4.0 http://creativecommons.org/licenses/by/4.0/

Code: MIT http://opensource.org/licenses/MIT year: 2015, copyright holder: Ben Marwick

Data: CC0 http://creativecommons.org/publicdomain/zero/1.0/

Notes and resources

• The issues tracker is the place to report problems or ask questions

• See the repository history for a fine-grained view of progress and changes.

• The organisation of this compendium is based on the work of Carl Boettiger

R Session Information

sessionInfo()
#> R version 3.2.3 (2015-12-10)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 7 x64 (build 7601) Service Pack 1
#> 
#> locale:
#> [1] LC_COLLATE=English_United States.1252 
#> [2] LC_CTYPE=English_United States.1252   
#> [3] LC_MONETARY=English_United States.1252
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.1252    
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] magrittr_1.5    formatR_1.2.1   tools_3.2.3     htmltools_0.3  
#>  [5] yaml_2.1.13     stringi_1.0-1   rmarkdown_0.9.3 knitr_1.12     
#>  [9] stringr_1.0.0   digest_0.6.9    evaluate_0.8