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# BYOC Starch [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5604670.svg)](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.
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