Reproducible reports in R Markdown

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# Reproducible reports in R Markdown
### Jacquie Tran | <span class="citation">@jacquietran</span> | 18 Aug 2020
### bit.ly/jt_rladies_2020

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# From academia to industry

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.small[
Image credit: [Andrew Petrischev](https://unsplash.com/photos/X03NgRx9f6A)
]

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Image credit: [Emil Widlund](https://unsplash.com/photos/ZtI4l8EvyUw)

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# What makes a report reproducible?

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## Four facets of reproducibility

The Carpentries, [Reproducible Research with R](https://datacarpentry.org/rr-intro/01-introduction/index.html)

1. Documentation

2. Organisation

3. Automation

4. Dissemination

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## R Markdown for
# Documentation

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## Document as you go!

![](https://raw.githubusercontent.com/jacquietran/2020_aug_rladies_akl/master/images/penguins_example_screenshot_01.PNG)

[**Live demo of HTML output**](https://jacquietran.github.io/2020_aug_rladies_akl/penguins_example.html)

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## Show your "working out"

```r
knitr::opts_chunk$set(echo = TRUE)
```

[**Live demo of HTML output**](https://jacquietran.github.io/2020_aug_rladies_akl/penguins_example_echoed.html)

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## R Markdown for
# Organisation

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## Source scripts into an R Markdown file

![](https://raw.githubusercontent.com/jacquietran/2020_aug_rladies_akl/master/images/penguins_example_screenshot_03.PNG)

In the R Markdown file, source the script from within a code chunk:

```r
source(here::here("plot_penguins.R"))
```

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## R Markdown for
# Automation

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## Build reports on a set schedule

[**Job scheduling R Markdown reports via R**](https://beta.rstudioconnect.com/content/3132/Job_Scheduling_R_Markdown_Reports_via_R.html)

![](https://raw.githubusercontent.com/jacquietran/2020_aug_rladies_akl/master/images/scheduling.PNG)

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## R Markdown for
# Dissemination

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## Rmd: One file format, many outputs!

Render an R Markdown report to:

- **HTML**
- **PDF**
- **Word**

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## HTML outputs are particularly powerful

Turn an R Markdown file into:

- A **slidedeck** (like this one!) using `{xaringan}`

- An **interactive dashboard** using `{flexdashboard}`

- An **e-book** using `{bookdown}`

- A **website** using packages like `{blogdown}` and `{distill}`

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## Useful links

[R Markdown articles from R Studio](https://rmarkdown.rstudio.com/articles.html)

Yihui Xie, J.J. Allaire, & Garrett Grolemund, [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/)

Emily Riederer, [R Markdown Driven Development](https://emilyriederer.netlify.app/post/rmarkdown-driven-development/)

Tom Mock:

- The Mockup Blog, [How I share knowledge around R Markdown](https://themockup.blog/posts/2020-07-25-meta-rmarkdown/)
- [Higher, further, faster with marvelous R Markdown](https://bit.ly/marvelRMD), presented at the 2020 New York R Conference

### Looking for this slidedeck + related files?

Slides: [bit.ly/jt_rladies_2020](https://bit.ly/jt_rladies_2020)

GitHub repo: [https://github.com/jacquietran/2020_aug_rladies_akl](https://github.com/jacquietran/2020_aug_rladies_akl)