This repository contains the data and code for our paper:
Investigating Biases Associated with Dietary Starch Incorporation and Retention in an Oral Biofilm Model. Bjørn Peare Bartholdy, Amanda G. Henry, bioRxiv 2021.10.27.466104; doi: https://doi.org/10.1101/2021.10.27.466104
The analysis directory contains:
- 📁 paper: R Markdown source document for manuscript. Includes code to reproduce the figures and tables generated by the analysis. It also has a rendered version suitable for reading (the code is replaced by figures and tables in this file)
- 📁 data: Data used in the analysis.
- 📁 figures: Plots and other illustrations
- 📁 supplementary-materials: Supplementary materials including notes and other documents prepared and collected during the analysis.
This compendium can be accessed in a web browser using binder.
To work with the compendium locally, you will need installed on your computer the R software itself and optionally RStudio Desktop.
You can download the compendium as a zip from from this URL:
main.zip. After unzipping: - open the
.Rproj file 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.Rmd and knit to produce the paper.pdf, or run
rmarkdown::render("analysis/paper/paper.Rmd") 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.