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index.qmd
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---
from: markdown+emoji
format:
revealjs:
logo: img/cesab-logo.png
footer: "{{< fa brands github >}} <https://github.com/frbcesab/good-practices>"
smaller: true
auto-stretch: false
toc-depth: 1
theme: [default, "css/custom.scss"]
engine: knitr
---
```{r}
#| child: "slides/title-slide.qmd"
```
```{r}
#| child: "slides/introduction.qmd"
```
```{r}
#| child: "slides/data-management.qmd"
```
```{r}
#| child: "slides/project-organization.qmd"
```
```{r}
#| child: "slides/code-and-software.qmd"
```
```{r}
#| child: "slides/tracking-changes.qmd"
```
```{r}
#| child: "slides/collaboration.qmd"
```
```{r}
#| child: "slides/manuscript.qmd"
```
## Table of contents
:::: { .columns }
::: { .column width="33%"}
**Data management**
**Project organization**
- RStudio project
- Build robust paths
- Naming things
- Research compendium
- (Flexible) structure
- The `DESCRIPTION` file
- The folder `R/`
- The `README`(s)
**Tracking changes**
- Version control system
**Collaboration**
- Code hosting platform
:::
::: { .column width="33%"}
**Optimization**
- Literate programming
- Functional programming
- Pipeline toolkit
- `targets`
- `makefile`
- R package
- Documentation
- Licensing
**Advanced tools**
- Managing dependencies (`renv`)
- CI/CD
- GitHub actions
- GitLab CI
- Docker
:::
::::
## Notes
<https://annakrystalli.me/talks/r-in-repro-research.html#1>
<https://library.seg.org/doi/abs/10.1190/1.1822162>
<https://inundata.org/talks/rstd19/#/>
<https://ropensci-archive.github.io/reproducibility-guide/sections/introduction/>
<https://insileco.io/workshop_reproducibility/#1>
<https://arxiv.org/pdf/1609.00037.pdf>
<https://ram.berkeley.edu/>
<https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001745#s5>
<https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005097>
<https://eliocamp.github.io/reproducibility-with-r/materials/day1/01-introduction/>
<https://www.youtube.com/watch?v=KHMW8fV2NXo>
<https://the-turing-way.netlify.app/reproducible-research/reproducible-research.html>
<https://annakrystalli.me/rrresearchACCE20/filenaming-view.html>
<https://allisonhorst.com/other-r-fun>
<https://www.tidyverse.org/blog/2017/12/workflow-vs-script/>