# BYOC Starch
[](https://doi.org/10.5281/zenodo.5604670)
Our pre-print is online here:
> Bartholdy, B. P. & Henry, A. G. (2021). _Investigating Biases Associated with Dietary Starch Incorporation and Retention in an Oral Biofilm Model_. bioRxiv. Online at <https://doi.org/10.1101/2021.10.27.466104>
### How to cite
Please cite this compendium as:
> Bartholdy, B. P. & Henry, A. G. (2021). _Compendium of R code and data for Investigating Biases Associated with Dietary Starch Incorporation and Retention in an Oral Biofilm Model_. Accessed 27 Oct 2021. <https://doi.org/10.5281/zenodo.5604670>
## Contents
The **analysis** directory contains:
- [:file\_folder: paper](/analysis/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,
`paper.docx`, suitable for reading (the code is replaced by figures
and tables in this file)
- [:file\_folder: data](/analysis/data): Data used in 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
This compendium can be accessed in a web browser using
[binder](https://mybinder.org/v2/gh/bbartholdy/byoc-starch/main?urlpath=rstudio).
To work with the compendium locally, you will need installed on your
computer the [R software](https://cloud.r-project.org/) itself and
optionally [RStudio
Desktop](https://rstudio.com/products/rstudio/download/).
You can download the compendium as a zip from from this URL:
[master.zip](/archive/master.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](/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
### 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.
