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README.Rmd
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---
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-"
)
# Please put your title here to include it in the file below.
Title <- "Investigating Biases Associated with Dietary Starch Incorporation and Retention in an Oral Biofilm Model"
```
# byocstarch
[](https://mybinder.org/v2/gh/bbartholdy/byoc-starch/main?urlpath=rstudio)
[](https://doi.org/10.5281/zenodo.5604670)
<!-- DOI badge: [](repo link) -->
<!-- Document structure provided by rrtools package -->
This repository contains the data and code for our paper:
> _`r Title`_.
Bjørn Peare Bartholdy, Amanda G. Henry,
bioRxiv 2021.10.27.466104; doi: <https://doi.org/10.1101/2021.10.27.466104>
<!--
Our pre-print is online here:
> Authors, (YYYY). _`r Title`_. Name of journal/book, Accessed `r format(Sys.Date(), "%d %b %Y")`. Online at <https://doi.org/xxx/xxx>
### How to cite
Please cite this compendium as:
> Authors, (`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/xxx/xxx> -->
## 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](https://github.com/bbartholdy/byoc-starch/blob/main/analysis/paper/index.pdf)
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:
[main.zip](/archive/refs/heads/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](/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.