Research compendium for Bartholdy et al. 2024

This repository contains the data and code for our paper:

Bartholdy, Bjørn Peare; Hasselstrøm, Jørgen B.; Sørensen, Lambert K.; Casna, Maia; Hoogland, Menno; Historisch Genootschap Beemster; Henry, Amanda G. Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population. Peer Community Journal, Volume 4 (2024), article no. e46. doi : 10.24072/pcjournal.414. https://peercommunityjournal.org/articles/10.24072/pcjournal.414/

Contents

The root directory contains:

• 📁 data-raw: R script to download and process the raw data from Zenodo (https://zenodo.org/record/8061483).
• 📁 data: Data output from data-raw/*.R, used in the analysis (.rda).
• 📁 R: R functions required in the analysis.

The analysis directory contains:

• 📁 paper: Quarto source document for manuscript. Includes code to reproduce the figures and tables generated by the analysis.
• 📁 figures: Plots and other illustrations
• 📁 supplementary-materials: Supplementary materials including notes and other documents prepared and collected during the analysis.

How to reproduce the paper

Software requirements:

• R
• Quarto
• TeX
• Git (optional)

Linux dependencies:

libx11-dev libicu-dev make zlib1g-dev libcurl4-openssl-dev libssl-dev libfontconfig1-dev libfreetype6-dev libfribidi-dev libharfbuzz-dev libjpeg-dev libpng-dev libtiff-dev pandoc libxml2-dev libgit2-dev gfortran

You can download the compendium as a zip from from this URL:

main.zip.

or clone the repository:

git clone https://github.com/bbartholdy/mb11CalculusPilot.git

Then:

1. open the folder in your preferred IDE
2. run renv::restore() to install the required R packages
3. run quarto::quarto_render("analysis/paper/paper.qmd", output_format = "html") in the R console (requires installing quarto R package) or quarto render analysis/paper/paper.qmd --to html to produce an HTML
4. open the output ./analysis/paper/_output/version-of-record.html in a browser

Licenses

Text and figures : CC-BY-4.0

Code : See the DESCRIPTION file

Data : CC-0 attribution requested in reuse

Contributions

We welcome contributions from everyone. Before you get started, please see our contributor guidelines. Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.