README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

Title <- "Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population"
```

# Research compendium for Bartholdy et al. 2023

[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/bbartholdy/mb11CalculusPilot/main?urlpath=rstudio) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7649825.svg)](https://zenodo.org/badge/DOI/10.5281/zenodo.7649825)

This repository contains the data and code for our paper:

<!--
> Authors, (YYYY). _`r Title`_. Name of journal/book <https://doi.org/xxx/xxx>

Our pre-print is online here:
-->

> Bartholdy, B.P., Hasselstrøm, J.B., Sørensen, L.K., Casna, M., Hoogland, M., Historisch Genootschap Beemster, & Henry, A.G. (2023). _`r Title`_. Zenodo, Accessed `r format(Sys.Date(), "%d %b %Y")`. Online at <https://doi.org/10.5281/zenodo.7649151>


### How to cite

Use the above paper to cite this compendium.

<!--
Please cite this compendium as:

> Bartholdy, B.P., Hasselstrøm, J.B., Sørensen, L.K., Casna, M., Hoogland, M., Historisch Genootschap Beemster, & Henry, A.G., (`r format(Sys.Date(), "%Y")`). _Compendium of R code and data for `r Title`_. Accessed `r format(Sys.Date(), "%d %b %Y")`. Online at <https://doi.org/10.5281/zenodo.7649825>
-->

## Contents

The **root** directory contains:

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

The **analysis** directory contains:

  - [:file\_folder: paper](/analysis/paper): Quarto source document
    for manuscript. Includes code to reproduce the figures and tables
    generated by the analysis.
  - [:file\_folder: figures](/analysis/figures): Plots and other
    illustrations
  - [:file\_folder:
    supplementary-materials](/analysis/supplementary-materials):
    Supplementary materials including notes and other documents
    prepared and collected during the analysis.

## How to run in your browser or download and run locally

**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](https://cloud.r-project.org/)
itself, optionally (but recommended) [RStudio Desktop](https://rstudio.com/products/rstudio/download/), and [Quarto](https://quarto.org/docs/get-started/). 

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

[main.zip](/archive/refs/heads/main.zip).

or clone the repository:

`git clone git@github.com:bbartholdy/mb11CalculusPilot.git`

Then:

- open the `.Rproj` file in RStudio
- run `devtools::install()` to ensure you have the packages this analysis depends on (also listed in the
[DESCRIPTION](/DESCRIPTION) file).
- finally, open `analysis/paper/paper.qmd` and **render** to produce the PDF manuscript (`_output/`),
  or run `quarto::quarto_render("analysis/paper/paper.qmd")` in the R console.

### Licenses

**Text and figures :**  [CC-BY-4.0](http://creativecommons.org/licenses/by/4.0/)

**Code :** See the [DESCRIPTION](DESCRIPTION) file

**Data :** [CC-0](http://creativecommons.org/publicdomain/zero/1.0/) attribution requested in reuse

### Contributions

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