This repository contains the data and code for our paper:
Bartholdy, B.P., Hasselstrøm, J.B., Sørensen, L.K., Casna, M., Hoogland, M., Historisch Genootschap Beemster, & Henry, A.G. (2023). Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population. Zenodo, Accessed 26 Sep 2023. Online at https://doi.org/10.5281/zenodo.7649151
Use the above paper to cite this compendium.
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.
If you are running Linux, you will need to install gfortran,
e.g. sudo apt install gfortran for Ubuntu.
This research compendium has been developed using the statistical programming language R. To work with the compendium, you will need installed on your computer the R software itself, optionally (but recommended) RStudio Desktop, and Quarto.
You can download the compendium as a zip from from this URL:
or clone the repository:
git clone git@github.com:bbartholdy/mb11CalculusPilot.git
Then:
- open the
.Rprojfile in RStudio - run
devtools::install()to ensure you have the packages this analysis depends on (also listed in the DESCRIPTION file). - finally, open
analysis/paper/paper.qmdand render to produce the PDF manuscript (_output/), or runquarto::quarto_render("analysis/paper/paper.qmd")in the R console.
Text and figures : CC-BY-4.0
Code : See the DESCRIPTION file
Data : CC-0 attribution requested in reuse
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.