R Markdown Setting up

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# R Markdown Setting up

## Adapted from slides by Alison Hill (RStudio)

### Zoë Turner

#### [https://philosopher-analyst.netlify.app/rmd-workshop/](https://philosopher-analyst.netlify.app/rmd-workshop/)

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# Agenda
RMarkdown

Getting set up ; What's inside?

--------- 10 minutes Break ---------

Text ; Images ; Code chunks

--------- 1 hour Lunch -----------

Inline code ; Tabs

--------- Break ---------

Output Formats ; Parameters; Command Line

--------- 10 minutes Break ---------

Loop reports ; Extras

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<div class="my-footer">https://philosopher-analyst.netlify.app/rmd-workshop/</div>

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# What is R Markdown - what do you think?

1. An authoring framework for data science.

1. A document format (`.Rmd`).

1. An R package named `rmarkdown`.

1. A file format for making dynamic documents with R.

1. A tool for integrating prose, code, and results.

1. A computational document.

1. Wizardry.

]

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# What is R Markdown - answers?

1. ["An authoring framework for data science."](https://rmarkdown.rstudio.com/lesson-1.html) (✔️)

1. [A document format (`.Rmd`).](https://bookdown.org/yihui/rmarkdown/) (✔️)

1. [An R package named `rmarkdown`.](https://rmarkdown.rstudio.com/docs/) (✔️)

1. ["A file format for making dynamic documents with R."](https://rmarkdown.rstudio.com/articles_intro.html) (✔️)

1. ["A tool for integrating text, code, and results."](https://r4ds.had.co.nz/communicate-intro.html) (✔️)

1. ["A computational document."](http://radar.oreilly.com/2011/07/wolframs-computational-documen.html) (✔️)

1. Wizardry. (well some might say it is! 🧙‍♂️)

]

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# <center>Let's get started</center>

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# <center>Checking first...</center>

That everyone is/has:

* set up on RStudio Cloud (own laptops are fine to use instead)
* installed packages
* downloaded the files and can see them in [Cloud Project or a local Project](https://nhs-r-community.github.io/intro_r/02-workshop_projects.html#1)

## Also note...

Code doesn't copy to MS Teams with the correct indentations but code can be copied from the [slides](https://philosopher-analyst.netlify.app/rmd-workshop),

When scripts are opened in the latest version of RStudio and packages are not loaded they will be prompted at the top of the editor to install

???

Code chunks on the slide have a button in the top right to Copy Code without having to highlight and copy.

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Together we'll open an RMarkdown template:

* Go to `File/New File/RMarkdown...`
* A wizard will prompt a Title, Author and Date (in new versions of RStudio)
* **Knit** this document and save the file when the wizard appears

???

It runs extremely quickly but the file must be saved to knit as it creates the .md file and then leaves the output (after clearing away the .md file).

This template is useful for debugging as it works quickly and doesn't rely upon any packages.

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# Your turn

Time to look at `01-bakeoff-report.Rmd`. 
Look at the source, then 🧶 **Knit** to HTML.

Try to identify these parts in the source and the output:

1. The **metadata**

1. The **text**

1. The **code**

1. The **output**

**If this was easy**, try to find all code that produces a *plot*.

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# Basic anatomy I

We look at the *source* anatomy for `01-bakeoff-report.Rmd` together:

1. The **metadata**

1. The **text**

1. The **code**

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# Basic anatomy II

1. The **output**

???
Point out the parts in the Rmd script. For further documentation on metadata
https://rmarkdown.rstudio.com/docs/reference/rmd_metadata.html
    
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background-image: url(images/rmarkdown_wizards.png)
background-size: contain

???
Allison Horst was a [resident artist at RStudio](https://www.rstudio.com/blog/artist-in-residence/) in 2019 and produced and shared beautiful artwork to explain statistics and R concepts

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Original authors

### Alison Hill 
[ @apreshill](https://github.com/apreshill) 
[ @apreshill](https://twitter.com/apreshill)

### Emi Tanaka 
[ @emitanaka](https://github.com/emitanaka) 
[ @statsgen](https://twitter.com/statsgen)

.footnote[All content is CC-BY. All art (unless otherwise noted) is by [Desirée De Leon](https://desiree.rbind.io/), CC-BY-NC-ND.]