An Introduction to R Markdown

class: title-slide, right, top

# An Introduction to R Markdown

## Dr. Alison Hill &#183; RStudio

#### <https://rstd.io/rmd4cdc>

---
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# <i class="fas fa-cloud"></i>

# Go here and log in (free):

https://rstd.io/rmd4medicine-cloud

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layout: true

<div class="my-footer"><span>https://rstd.io/rmd4cdc</span></div>

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# What is R Markdown?

---

# What is R Markdown?

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.

---

# What is R Markdown?

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. (🧙‍♂️)

---
background-image: url(images/rmarkdown_wizards.png)
background-size: contain

.footnote[Art by [Allison Horst](https://twitter.com/allison_horst?lang=en)]

---
class: inverse, middle, center

# Why R Markdown?

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class: center
background-image: url(https://media.giphy.com/media/11fDMHAzihB8D6/source.gif)

# Reproducibility crisis?

???

We are not here today to solve science or medicine's reproducibility crisis.

What I do think R Markdown can help you with today when you leave here is to tackle two other crises: one I think of as the confidence crisis...

---
class: center
background-image: url(https://media.giphy.com/media/OPZZ6KWJOZ3AA/source.gif)

# Confidence crisis

---
class: center
background-image: url(https://dickbrouwer.com/img/meeting_cheese.png)
background-size: contain

# 🧀 Cheese crisis 🧀

.footnote[https://dickbrouwer.com/blog/a-guide-to-better-meetings/]

---
class: center
background-image: url(images/remote-crisis.jpg)
background-size: cover

# 🚨 Current crisis 🚨

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# Change your mental model

.pull-left[

### Source &harr; output

]

.pull-right[

### Source &rarr; output

]

---
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# Change your mental model

.pull-left[

### Source &harr; output

]

.pull-right[

### Source &rarr; output

]

---
background-image: url(images/welliewishers/Slide1.png)
background-size: cover
class: top, center

.footnote[https://www.americangirl.com/shop/c/welliewishers]

---
background-image: url(images/welliewishers/Slide2.png)
background-size: cover
class: top, center

.footnote[https://www.americangirl.com/shop/c/welliewishers]

---
class: middle, inverse, center

# Same ~~doll~~ source

# Different ~~outfits~~ outputs

---
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# `html_document`

---
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# What is inside?

![](images/doc-make.jpg)

---
name: card0
background-image: url(images/card0.png)
background-size: contain

.footnote[https://www.dear-data.com/]

---
name: card1
background-image: url(images/card1.png)
background-size: contain

.footnote[https://www.dear-data.com/]

---

# metadata: YAML

.pull-left[

_"YAML Ain't Markup Language"_

```yaml
---
key: value
---
```

]

.pull-right[

]

---
class: middle, center

# Output options

---

# Save output options in your YAML

.pull-left[

```yaml
---
author: Your name here
title: Your title here
output: html_document
---
```

```yaml
---
author: Your name here
title: Your title here
output:
  html_document:
    toc: true
    toc_float: true
    theme: flatly
---
```

]

.pull-right[

]

---
background-image: url(images/Single-rmd.png)
background-size: contain

---
background-image: url(images/Single-rmd1.png)
background-size: contain

---
background-image: url(images/Single-rmd2.png)
background-size: contain

---
background-image: url(images/Single-rmd3.png)
background-size: contain

---
class: top center

---
class: middle center
background-image: url(images/Single-knit1.png)
background-size: contain

???

Here is what we knit.

???

Using the `THEME:` key in our YAML, we changed our font and colors.

???

And we have this nice table of contents floating off to the side...

---
class: middle

# Check-in

.pull-left[
How do you use only the **default** output options?

(a)
```yaml
---
output: html_document()
---
```
(b)
```yaml
---
output: html_document
---
```

]

.pull-right[
How do you add an output **option** to a format in your YAML?

(a)
```yaml
---
output: 
  html_document: 
    toc: true
---
```

(b)
```yaml
---
output: 
  html_document(toc=true)
---
```

]

---
class: middle, center

# Output formats

---
class: middle, center

https://rmarkdown.rstudio.com/docs/reference/index.html#section-output-formats

---

# 🧶 Knit

.pull-left[
<img src="images/knit-dropdown.png" width="60%" style="display: block; margin: auto;" />

]

.pull-right[

```yaml
---
author: Your name here
title: Your title here
output:
  html_document:
    toc: true
    toc_float: true
    theme: flatly
  word_document: default
  pdf_document: default
---
```
]

???

This is a great way to "control" your knit button!

Notice that when you knit, it respects those output options in your YAML.

This way you "save" your output options

---
class: middle

# Check-in

.pull-left[
How do you add another output **format** to your YAML?

(a)
```yaml
---
output: 
  html_document: default
  word_document: default
---
```
(b)
```
---
output: 
  html_document()
  word_document()
---
```

]

.pull-right[
How do you now add output **options** to your YAML?

(a)
```yaml
---
output: 
  html_document: 
    toc: true
  word_document: default
---
```
(b)
```
---
output: 
  html_document(toc=true)
  word_document(default)
---
```

]

---
class: middle, center
# Built-in output formats

---
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???

Built in formats (in the `rmarkdown` package)

versus

extensions (different packages that extend output formats available to you)

---
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# Extension output formats

---
class: middle, left

---
class: middle

.center[
# Use an extension package
]

.pull-left[
```yaml
---
author: Your name here
title: Your title here
output:
  distill::distill_article: default
  bookdown::html_document2: default
---
```
]

.pull-right[
```yaml
---
author: Your name here
title: Your title here
output:
  distill::distill_article:
    toc: true
  bookdown::html_document2:
    toc: true
    theme: flatly
    toc_float: true
---
```
]

---
template: card0

---
template: card1

---
name: card2
background-image: url(images/card2.png)
background-size: contain

.footnote[https://www.dear-data.com/]

---
class: center, middle

# Do this! 👇

# https://commonmark.org/help/tutorial/

---

# <center>Headers</center>

.pull-left[
```markdown
# HEADER 1

## HEADER 2

### HEADER 3

#### HEADER 4

##### HEADER 5

###### HEADER 6
```
]

.pull-right[
# HEADER 1

## HEADER 2

### HEADER 3

#### HEADER 4

##### HEADER 5

###### HEADER 6
]

---

![](images/rmd-nav.png)

---

# <center>Text</center>

.pull-left[
```markdown
Childhood **vaccines**  
are one of the  
_great triumphs_  
of modern medicine. 
```
]

.pull-right[

Childhood **vaccines**  
are one of the  
_great triumphs_  
of modern medicine.

]

---
class: top

# <center>Lists</center>

.pull-left[

```markdown
Indeed, parents whose children are  
vaccinated no longer have to worry about  
their child's death or disability from:

- whooping cough, 
- polio, 
- diphtheria, 
- hepatitis, or 
- a host of other infections.

Vaccines are the most cost-effective health  
care interventions there are. We have   
three new, extremely effective vaccines to  
roll out in developing countries:

1. pneumonia
1. rotavirus
1. meningitis A
```

]

.pull-right[

Indeed, parents whose children are  
vaccinated no longer have to worry about  
their child's death or disability from:

- whooping cough, 
- polio, 
- diphtheria, 
- hepatitis, or 
- a host of other infections.

Vaccines are the most cost-effective health  
care interventions there are. We have  
three new, extremely effective vaccines to  
roll out in developing countries:

1. pneumonia
1. rotavirus
1. meningitis A

]

---

# <center>Images</center>

.pull-left[
```markdown
Receiving rubella vaccination, Brazil, 2008.
![](http://bit.ly/VaccineBySandraRugio)
```
]

.pull-right[
Receiving rubella vaccination, Brazil, 2008.
![](http://bit.ly/VaccineBySandraRugio)
]

---

# <center>Links</center>

.pull-left[
```markdown
[Photo](https://en.wikipedia.org/wiki/Vaccine)

Receiving rubella vaccination, Brazil, 2008.
![](http://bit.ly/VaccineBySandraRugio)
```
]

.pull-right[
[Photo](https://en.wikipedia.org/wiki/Vaccine)

Receiving rubella vaccination, Brazil, 2008.
![](http://bit.ly/VaccineBySandraRugio)
]

---
name: 03-formative
class: middle

# Check-in

.pull-left[

How do you add headers in Markdown?

`! Header`

`- Header`

`# Header`

`1. Header`

]

.pull-right[

What about lists? Bulleted? Numbered?

`! Item 1`

`- Item 1`

`# Item 1`

`1. Item 1`

]

---
template: card0

---
template: card1

---
template: card2

---
name: card3
background-image: url(images/card3.png)
background-size: contain

---
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# `code` -> plots
---

# Code chunks

.pull-left[

````
```{r}
mockdata %>% 
  distinct(arm)
```
````

What is the fate of this chunk?

]

.pull-right[

```r
mockdata %>% 
  distinct(arm)
#> # A tibble: 3 x 1
#>   arm      
#>   <chr>    
#> 1 A: IFL   
#> 2 F: FOLFOX
#> 3 G: IROX
```

]

---

# Code chunks

.pull-left[

````
```{r}
n_sites <- n_distinct(mockdata$site)
```
````

What fate do you predict here?

]

.pull-right[

```r
n_sites <- n_distinct(mockdata$site)
```

]

---

# Code chunks

.pull-left[

````
```{r}
n_sites <- n_distinct(mockdata$site)
n_sites
```
````

]

.pull-right[

```r
n_sites <- n_distinct(mockdata$site)
n_sites
#> [1] 1
```

]

---

# Including plots

.pull-left[

```r
# PLOT: Age distribution -------------------------------------------------------
ggplot(mockdata, aes(age)) +
  geom_histogram(color = 'white',
                 fill = scico(1, 
                              begin = .3, 
                              palette = "berlin"),
                 bins = 20) +
  labs(x = "Age", 
       y = "Count") +
  scale_y_continuous(
    breaks = scales::pretty_breaks()
  )
```

Will this print?

]

.pull-right[
<img src="index_files/figure-html/unnamed-chunk-23-1.png" width="504" />

]

---

# Including plots

.pull-left[

```r
# PLOT: Age distribution -------------------------------------------------------
age_histogram <- 
  ggplot(mockdata, aes(age)) +
  geom_histogram(color = 'white',
                 fill = scico(1, 
                              begin = .3, 
                              palette = "berlin"),
                 bins = 20) +
  labs(x = "Age", 
       y = "Count") +
  scale_y_continuous(
    breaks = scales::pretty_breaks()
  )
```

What about this?

]

.pull-right[

]

---

# Including plots

.pull-left[

]

.pull-right[
<img src="index_files/figure-html/unnamed-chunk-25-1.png" width="504" />

]

???

so, how did we get a figure into R Markdown?

Answer: it has to print!

---

# Chunk options for plots

- fig resolution
- fig size
- [fig "device"](https://r4ds.had.co.nz/graphics-for-communication.html#other-important-options)

.footnote[https://yihui.name/knitr/options/#plots]

---

# out.width

.pull-left[

````
```{r out.width="70%"}
age_histogram
```
````

<img src="index_files/figure-html/unnamed-chunk-26-1.png" width="70%" />
]

.pull-right[

````
```{r out.width="10%"}
age_histogram
```
````

See also:

+ `fig.width`
+ `fig.height` 
+ `fig.asp`

https://r4ds.had.co.nz/graphics-for-communication.html#figure-sizing

]

---

# fig.path

````
```{r fig.path="figs/", echo=FALSE}
ae_pct_plot
```
````

---

# fig.path

````
```{r ae-plot, fig.path="figs/", echo=FALSE}
ae_pct_plot
```
````

---

# Chunk labels

.pull-left[

````
```{r peek}
glimpse(mockdata)
```
````

]

.pull-right[

+ Place between curly braces<br>`{r label}`

+ Separated options with commas<br>`{r label, option1=value}`

+ Careful! No duplicate chunk labels

````
    ```{r peek}
    head(mockdata)
    ```
    ````

```
    Error in parse_block(g[-1], g[1], params.src) : 
      duplicate label 'peek'
    Calls: <Anonymous> ... process_file -> split_file -> lapply -> FUN -> parse_block
    Execution halted
    ```

]

???

how can we make it easier on ourselves to explore the code in here?

show how to add chunk labels and view in IDE interactively

---
class: top, center
background-image: url(images/plants.jpg)
background-size: 70%
background-color: #fff5ec

# Chunks as crops or houseplants?

.footnote[https://masalmon.eu/2017/08/08/chunkpets/]

---
class: middle, center

# A good chunk label

.pull-left[

### Good

`my-plot`

`myplot`

`myplot1`

`myplot-1`

`MY-PLOT`

]

.pull-right[

### Bad

`my_plot`

`my plot`

everything else!

]

---
class: middle, center

# A good chunk label

Think: kebabs, not snakes

---
background-image: url(images/pour.jpg)
background-position: left
background-size: contain
class: middle, center

.pull-right[
![](images/figs-label.png)
]

---

# fig.cap

````
```{r age-plot, echo=FALSE, fig.cap='Age distributions'}
age_histogram
```
````

.center[

**Fig. 1:** Age distributions

]

---

# Cross-reference a figure

.pull-left[

See Figure `\@ref(fig:age-plot)`.

````
```{r age-plot, echo=FALSE, fig.cap='Age distributions'}
age_histogram
```
````

]

.pull-right[

See Figure [1]().

.center[

<div class="figure">
<img src="index_files/figure-html/unnamed-chunk-29-1.png" alt="Age distributions" width="70%" />
<p class="caption">Age distributions</p>
</div>

]

.footnote[Cross-referencing only works in these output packages: distill, bookdown, blogdown]

---

# Key takeaway

Once you have:

✔️ A labeled chunk that produces a plot

✔️ A figure caption using `fig.cap`

Then you can have:

### Cross-references!*

.footnote[\* and you are using distill, bookdown, or blogdown output formats]

---

# message / warning

![](https://www.tidyverse.org/images/tidyverse_1.2.0/tidyverse_1-2-0_pkg_load.gif)

---

# message / warning

.pull-left[

````
```{r message=FALSE, warning=FALSE}
library(tidyverse)
```
````

]

.pull-right[

```r
library(tidyverse)
```

]

---

# Other useful chunk options

.pull-left[

````
```{r}
glimpse(mockdata)
```
````

]

.pull-right[

```r
glimpse(mockdata)
#> Rows: 1,499
#> Columns: 26
#> $ case          <dbl> 110754, 99706, 105271, 105001, 112263, 86205, 99508, 90…
#> $ age           <dbl> 67, 74, 50, 71, 69, 56, 50, 57, 51, 63, 61, 59, 61, 59,…
#> $ arm           <chr> "F: FOLFOX", "A: IFL", "A: IFL", "G: IROX", "F: FOLFOX"…
#> $ sex           <chr> "Male", "Female", "Female", "Female", "Female", "Male",…
#> $ race          <chr> "Caucasian", "Caucasian", "Caucasian", "Caucasian", "Ot…
#> $ fu_time       <dbl> 922, 270, 175, 128, 233, 120, 369, 421, 387, 363, 168, …
#> $ fu_stat       <dbl> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2…
#> $ ps            <dbl> 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0…
#> $ hgb           <dbl> 11.5, 10.7, 11.1, 12.6, 13.0, 10.2, 13.3, 12.1, 13.8, 1…
#> $ bmi           <dbl> 25.09861, 19.49786, NA, 29.42922, 26.35352, 19.03673, 2…
#> $ alk_phos      <dbl> 160, 290, 700, 771, 350, 569, 162, 152, 231, 492, 740, …
#> $ ast           <dbl> 35, 52, 100, 68, 35, 27, 16, 12, 25, 18, 45, 16, 50, 80…
#> $ mdquality_s   <dbl> NA, 1, 1, 1, NA, 1, 1, 1, 1, 1, NA, NA, 1, 0, 1, 1, 0, …
#> $ age_ord       <chr> "60-69", "70-79", "40-49", "70-79", "60-69", "50-59", "…
#> $ site          <chr> "Portland", "Portland", "Portland", "Portland", "Portla…
#> $ country       <chr> "USA", "USA", "USA", "USA", "USA", "USA", "USA", "USA",…
#> $ ethnicity     <chr> "White (not Hispanic)", "White (not Hispanic)", "White …
#> $ name          <chr> "Barrett Wafford", "Shelby Moore", "Farrah Morgan", "Br…
#> $ first_name    <chr> "Barrett", "Shelby", "Farrah", "Brianna", "Kareema", "J…
#> $ last_name     <chr> "Wafford", "Moore", "Morgan", "Rasico", "el-Saleh", "Pi…
#> $ ae_low_wbc    <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ ae_neuropathy <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ ae_diarrhea   <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ ae_vomiting   <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ ae_blood_clot <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ fu_fct        <fct> Died, Died, Died, Died, Died, Died, Died, Died, Died, D…
```

]

---

# echo

.pull-left[

````
```{r echo=FALSE}
glimpse(mockdata)
```
````

]

.pull-right[

```
#> Rows: 1,499
#> Columns: 26
#> $ case          <dbl> 110754, 99706, 105271, 105001, 112263, 86205, 99508, 90…
#> $ age           <dbl> 67, 74, 50, 71, 69, 56, 50, 57, 51, 63, 61, 59, 61, 59,…
#> $ arm           <chr> "F: FOLFOX", "A: IFL", "A: IFL", "G: IROX", "F: FOLFOX"…
#> $ sex           <chr> "Male", "Female", "Female", "Female", "Female", "Male",…
#> $ race          <chr> "Caucasian", "Caucasian", "Caucasian", "Caucasian", "Ot…
#> $ fu_time       <dbl> 922, 270, 175, 128, 233, 120, 369, 421, 387, 363, 168, …
#> $ fu_stat       <dbl> 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2…
#> $ ps            <dbl> 0, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0…
#> $ hgb           <dbl> 11.5, 10.7, 11.1, 12.6, 13.0, 10.2, 13.3, 12.1, 13.8, 1…
#> $ bmi           <dbl> 25.09861, 19.49786, NA, 29.42922, 26.35352, 19.03673, 2…
#> $ alk_phos      <dbl> 160, 290, 700, 771, 350, 569, 162, 152, 231, 492, 740, …
#> $ ast           <dbl> 35, 52, 100, 68, 35, 27, 16, 12, 25, 18, 45, 16, 50, 80…
#> $ mdquality_s   <dbl> NA, 1, 1, 1, NA, 1, 1, 1, 1, 1, NA, NA, 1, 0, 1, 1, 0, …
#> $ age_ord       <chr> "60-69", "70-79", "40-49", "70-79", "60-69", "50-59", "…
#> $ site          <chr> "Portland", "Portland", "Portland", "Portland", "Portla…
#> $ country       <chr> "USA", "USA", "USA", "USA", "USA", "USA", "USA", "USA",…
#> $ ethnicity     <chr> "White (not Hispanic)", "White (not Hispanic)", "White …
#> $ name          <chr> "Barrett Wafford", "Shelby Moore", "Farrah Morgan", "Br…
#> $ first_name    <chr> "Barrett", "Shelby", "Farrah", "Brianna", "Kareema", "J…
#> $ last_name     <chr> "Wafford", "Moore", "Morgan", "Rasico", "el-Saleh", "Pi…
#> $ ae_low_wbc    <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ ae_neuropathy <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ ae_diarrhea   <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ ae_vomiting   <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ ae_blood_clot <fct> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
#> $ fu_fct        <fct> Died, Died, Died, Died, Died, Died, Died, Died, Died, D…
```

]

---

# eval

.pull-left[

````
```{r eval=FALSE}
glimpse(mockdata)
```
````

]

.pull-right[

```r
glimpse(mockdata)
```

]

---

# include

.pull-left[

````
```{r include=FALSE}
glimpse(mockdata)
```
````

]

.pull-right[

]

---

# Using chunk options

.pull-left[

````
```{r echo=TRUE, results='hide'}
glimpse(mockdata)
```
````

]

.pull-right[

```r
glimpse(mockdata)
```

]

+ Place between curly braces<br>`{r option=value}`

+ Multiple options separated by commas<br>`{r option1=value, option2=value}`

+ Careful! The `r` part is the **code engine** (other engines possible)

---

# A global `setup` chunk 🌍

One chunk to rule them all

.pull-left[

````
```{r setup, include = FALSE}
knitr::opts_chunk$set(
  warning = FALSE,
  message = FALSE,
  echo = FALSE,
  fig.path = "alison-figs/"
)
```
````

]

.pull-right[

+ A special chunk label: `setup`

+ Typically the first chunk

+ All following chunks will use these options (i.e., sets global chunk options)

+ **Tip**: set `include=FALSE`

+ You can (and should) use individual chunk options too

]

---

.left-column[
# Default options
]

.right-column[

```r
str(knitr::opts_chunk$get())
#> List of 53
#>  $ eval         : logi TRUE
#>  $ echo         : logi TRUE
#>  $ results      : chr "markup"
#>  $ tidy         : logi FALSE
#>  $ tidy.opts    : NULL
#>  $ collapse     : logi TRUE
#>  $ prompt       : logi FALSE
#>  $ comment      : chr "#>"
#>  $ highlight    : logi TRUE
#>  $ strip.white  : logi TRUE
#>  $ size         : chr "normalsize"
#>  $ background   : chr "#F7F7F7"
#>  $ cache        : logi FALSE
#>  $ cache.path   : chr "index_cache/html/"
#>  $ cache.vars   : NULL
#>  $ cache.lazy   : logi TRUE
#>  $ dependson    : NULL
#>  $ autodep      : logi FALSE
#>  $ cache.rebuild: logi FALSE
#>  $ fig.keep     : chr "high"
#>  $ fig.show     : chr "asis"
#>  $ fig.align    : chr "default"
#>  $ fig.path     : chr "index_files/figure-html/"
#>  $ dev          : chr "png"
#>  $ dev.args     : NULL
#>  $ dpi          : num 72
#>  $ fig.ext      : NULL
#>  $ fig.width    : num 7
#>  $ fig.height   : num 7
#>  $ fig.env      : chr "figure"
#>  $ fig.cap      : NULL
#>  $ fig.scap     : NULL
#>  $ fig.lp       : chr "fig:"
#>  $ fig.subcap   : NULL
#>  $ fig.pos      : chr ""
#>  $ out.width    : NULL
#>  $ out.height   : NULL
#>  $ out.extra    : NULL
#>  $ fig.retina   : num 1
#>  $ external     : logi TRUE
#>  $ sanitize     : logi FALSE
#>  $ interval     : num 1
#>  $ aniopts      : chr "controls,loop"
#>  $ warning      : logi TRUE
#>  $ error        : logi FALSE
#>  $ message      : logi TRUE
#>  $ render       : NULL
#>  $ ref.label    : NULL
#>  $ child        : NULL
#>  $ engine       : chr "R"
#>  $ split        : logi FALSE
#>  $ include      : logi TRUE
#>  $ purl         : logi TRUE
```

]

---
template: card0

---
template: card1

---
template: card2

---
template: card3

---
background-image: url(images/card4.png)
background-size: contain

---
class: center
background-image: url(images/typewriter.jpg)
background-size: contain
background-color: #f6f6f6

# Markdown tables

---
class: center

# Markdown tables

.pull-left[

```markdown
| Time          | Session | Topic    |
|:--------------|:-------:|---------:|
| _left_        | _center_| _right_  |
| 01:00 - 01:50 | 1       | Anatomy  |
| 01:50 - 02:00 |         | *Break*  |
| 02:00 - 02:45 | 2       | Tables   |
| 02:45 - 03:00 |         | *Break*  |

```
]

.pull-right[

| Time          | Session | Topic    |
|:--------------|:-------:|---------:|
| _left_        | _center_| _right_  |
| 01:00 - 01:50 | 1       | Anatomy  |
| 01:50 - 02:00 |         | *Break*  |
| 02:00 - 02:45 | 2       | Tables   |
| 02:45 - 03:00 |         | *Break*  |

]

---
class: middle, center, inverse

# Tables

![](https://media.giphy.com/media/i9c6lFmOSXKZW/giphy.gif)

---
class: center, middle

# Two table types

.pull-left[

### for you

]

.pull-right[

### for everyone else

<img src="images/tables-them.jpg" width="3691" />
]

---

.pull-left[

![](images/imani-_TuIdedBPwQ-unsplash.jpg)
]

.pull-right[
![](images/gear_shift.jpg)
]

.footnote[Images from [Unsplash](https://unsplash.com/photos/_TuIdedBPwQ) and [Wikipedia](https://commons.wikimedia.org/wiki/File:FIAT_500L_gear_shift.jpg)]

---

# Let's try using data now

```r
mockdata <- read_csv(here::here("mockpaper/data/mockdata.csv")) %>%
  mutate(fu_fct = fct_recode(as.factor(fu_stat), 
                             "Lived" = "1", 
                             "Died" = "2")) %>% 
  mutate_at(vars(starts_with("ae_")), ~as.factor(.))
#> Parsed with column specification:
#> cols(
#>   .default = col_double(),
#>   arm = col_character(),
#>   sex = col_character(),
#>   race = col_character(),
#>   age_ord = col_character(),
#>   site = col_character(),
#>   country = col_character(),
#>   ethnicity = col_character(),
#>   name = col_character(),
#>   first_name = col_character(),
#>   last_name = col_character()
#> )
#> See spec(...) for full column specifications.
```

---
class: middle

.left-column[

![](https://raw.githubusercontent.com/sfirke/janitor/master/man/figures/logo_small.png)
]

.right-column[
# the janitor package

<http://sfirke.github.io/janitor/>
]

---

# 1-way frequency `tabyl()`

.pull-left[

```r
mockdata %>% 
  tabyl(arm)
#>        arm   n   percent
#>     A: IFL 428 0.2855237
#>  F: FOLFOX 691 0.4609740
#>    G: IROX 380 0.2535023
```

]

.pull-right[

```r
mockdata %>% 
  tabyl(arm) %>% 
  adorn_totals("row") %>%
  adorn_pct_formatting()
#>        arm    n percent
#>     A: IFL  428   28.6%
#>  F: FOLFOX  691   46.1%
#>    G: IROX  380   25.4%
#>      Total 1499  100.0%
```

]

---

# 2-way frequency `tabyl()`

.pull-left[

```r
mockdata %>% 
  tabyl(arm, fu_fct)
#>        arm Lived Died
#>     A: IFL    18  410
#>  F: FOLFOX    99  592
#>    G: IROX    26  354
```

]

.pull-right[

```r
mockdata %>% 
  tabyl(arm, fu_fct) %>% 
  adorn_totals("row") %>% 
  adorn_percentages() %>%
  adorn_pct_formatting() %>%
  adorn_ns()
#>        arm       Lived         Died
#>     A: IFL  4.2%  (18) 95.8%  (410)
#>  F: FOLFOX 14.3%  (99) 85.7%  (592)
#>    G: IROX  6.8%  (26) 93.2%  (354)
#>      Total  9.5% (143) 90.5% (1356)
```

]

---
class: middle

.left-column[

]

.right-column[
# the gt package

<https://gt.rstudio.com/>
]

---
background-image: url(https://gt.rstudio.com/reference/figures/gt_parts_of_a_table.svg)
background-size: contain

---
background-image: url(https://gt.rstudio.com/reference/figures/gt_workflow_diagram.svg)
background-size: contain

---

.pull-left[

```r
mockdata %>% 
  tabyl(arm, fu_fct) %>% 
  gt::gt()
```

#wthvrqazra .gt_table {
  display: table;
  border-collapse: collapse;
  margin-left: auto;
  margin-right: auto;
  color: #333333;
  font-size: 16px;
  background-color: #FFFFFF;
  width: auto;
  border-top-style: solid;
  border-top-width: 2px;
  border-top-color: #A8A8A8;
  border-right-style: none;
  border-right-width: 2px;
  border-right-color: #D3D3D3;
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #A8A8A8;
  border-left-style: none;
  border-left-width: 2px;
  border-left-color: #D3D3D3;
}

#wthvrqazra .gt_heading {
  background-color: #FFFFFF;
  text-align: center;
  border-bottom-color: #FFFFFF;
  border-left-style: none;
  border-left-width: 1px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
}

#wthvrqazra .gt_title {
  color: #333333;
  font-size: 125%;
  font-weight: initial;
  padding-top: 4px;
  padding-bottom: 4px;
  border-bottom-color: #FFFFFF;
  border-bottom-width: 0;
}

#wthvrqazra .gt_subtitle {
  color: #333333;
  font-size: 85%;
  font-weight: initial;
  padding-top: 0;
  padding-bottom: 4px;
  border-top-color: #FFFFFF;
  border-top-width: 0;
}

#wthvrqazra .gt_bottom_border {
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
}

#wthvrqazra .gt_col_headings {
  border-top-style: solid;
  border-top-width: 2px;
  border-top-color: #D3D3D3;
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
  border-left-style: none;
  border-left-width: 1px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
}

#wthvrqazra .gt_col_heading {
  color: #333333;
  background-color: #FFFFFF;
  font-size: 100%;
  font-weight: normal;
  text-transform: inherit;
  border-left-style: none;
  border-left-width: 1px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
  vertical-align: bottom;
  padding-top: 5px;
  padding-bottom: 6px;
  padding-left: 5px;
  padding-right: 5px;
  overflow-x: hidden;
}

#wthvrqazra .gt_column_spanner_outer {
  color: #333333;
  background-color: #FFFFFF;
  font-size: 100%;
  font-weight: normal;
  text-transform: inherit;
  padding-top: 0;
  padding-bottom: 0;
  padding-left: 4px;
  padding-right: 4px;
}

#wthvrqazra .gt_column_spanner_outer:first-child {
  padding-left: 0;
}

#wthvrqazra .gt_column_spanner_outer:last-child {
  padding-right: 0;
}

#wthvrqazra .gt_column_spanner {
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
  vertical-align: bottom;
  padding-top: 5px;
  padding-bottom: 6px;
  overflow-x: hidden;
  display: inline-block;
  width: 100%;
}

#wthvrqazra .gt_group_heading {
  padding: 8px;
  color: #333333;
  background-color: #FFFFFF;
  font-size: 100%;
  font-weight: initial;
  text-transform: inherit;
  border-top-style: solid;
  border-top-width: 2px;
  border-top-color: #D3D3D3;
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
  border-left-style: none;
  border-left-width: 1px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
  vertical-align: middle;
}

#wthvrqazra .gt_empty_group_heading {
  padding: 0.5px;
  color: #333333;
  background-color: #FFFFFF;
  font-size: 100%;
  font-weight: initial;
  border-top-style: solid;
  border-top-width: 2px;
  border-top-color: #D3D3D3;
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
  vertical-align: middle;
}

#wthvrqazra .gt_striped {
  background-color: rgba(128, 128, 128, 0.05);
}

#wthvrqazra .gt_from_md > :first-child {
  margin-top: 0;
}

#wthvrqazra .gt_from_md > :last-child {
  margin-bottom: 0;
}

#wthvrqazra .gt_row {
  padding-top: 8px;
  padding-bottom: 8px;
  padding-left: 5px;
  padding-right: 5px;
  margin: 10px;
  border-top-style: solid;
  border-top-width: 1px;
  border-top-color: #D3D3D3;
  border-left-style: none;
  border-left-width: 1px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
  vertical-align: middle;
  overflow-x: hidden;
}

#wthvrqazra .gt_stub {
  color: #333333;
  background-color: #FFFFFF;
  font-size: 100%;
  font-weight: initial;
  text-transform: inherit;
  border-right-style: solid;
  border-right-width: 2px;
  border-right-color: #D3D3D3;
  padding-left: 12px;
}

#wthvrqazra .gt_summary_row {
  color: #333333;
  background-color: #FFFFFF;
  text-transform: inherit;
  padding-top: 8px;
  padding-bottom: 8px;
  padding-left: 5px;
  padding-right: 5px;
}

#wthvrqazra .gt_first_summary_row {
  padding-top: 8px;
  padding-bottom: 8px;
  padding-left: 5px;
  padding-right: 5px;
  border-top-style: solid;
  border-top-width: 2px;
  border-top-color: #D3D3D3;
}

#wthvrqazra .gt_grand_summary_row {
  color: #333333;
  background-color: #FFFFFF;
  text-transform: inherit;
  padding-top: 8px;
  padding-bottom: 8px;
  padding-left: 5px;
  padding-right: 5px;
}

#wthvrqazra .gt_first_grand_summary_row {
  padding-top: 8px;
  padding-bottom: 8px;
  padding-left: 5px;
  padding-right: 5px;
  border-top-style: double;
  border-top-width: 6px;
  border-top-color: #D3D3D3;
}

#wthvrqazra .gt_table_body {
  border-top-style: solid;
  border-top-width: 2px;
  border-top-color: #D3D3D3;
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
}

#wthvrqazra .gt_footnotes {
  color: #333333;
  background-color: #FFFFFF;
  border-bottom-style: none;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
  border-left-style: none;
  border-left-width: 2px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 2px;
  border-right-color: #D3D3D3;
}

#wthvrqazra .gt_footnote {
  margin: 0px;
  font-size: 90%;
  padding: 4px;
}

#wthvrqazra .gt_sourcenotes {
  color: #333333;
  background-color: #FFFFFF;
  border-bottom-style: none;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
  border-left-style: none;
  border-left-width: 2px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 2px;
  border-right-color: #D3D3D3;
}

#wthvrqazra .gt_sourcenote {
  font-size: 90%;
  padding: 4px;
}

#wthvrqazra .gt_left {
  text-align: left;
}

#wthvrqazra .gt_center {
  text-align: center;
}

#wthvrqazra .gt_right {
  text-align: right;
  font-variant-numeric: tabular-nums;
}

#wthvrqazra .gt_font_normal {
  font-weight: normal;
}

#wthvrqazra .gt_font_bold {
  font-weight: bold;
}

#wthvrqazra .gt_font_italic {
  font-style: italic;
}

#wthvrqazra .gt_super {
  font-size: 65%;
}

#wthvrqazra .gt_footnote_marks {
  font-style: italic;
  font-size: 65%;
}
</style>
<div id="wthvrqazra" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;"><table class="gt_table">
  
  <thead class="gt_col_headings">
    <tr>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">arm</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Lived</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Died</th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr>
      <td class="gt_row gt_left">A: IFL</td>
      <td class="gt_row gt_right">18</td>
      <td class="gt_row gt_right">410</td>
    </tr>
    <tr>
      <td class="gt_row gt_left">F: FOLFOX</td>
      <td class="gt_row gt_right">99</td>
      <td class="gt_row gt_right">592</td>
    </tr>
    <tr>
      <td class="gt_row gt_left">G: IROX</td>
      <td class="gt_row gt_right">26</td>
      <td class="gt_row gt_right">354</td>
    </tr>
  </tbody>
  
  
</table></div>

]

.pull-right[

```r
mockdata %>% 
  tabyl(arm, fu_fct) %>% 
  adorn_totals("row") %>% 
  adorn_percentages() %>%
  adorn_pct_formatting() %>%
  adorn_ns() %>%
  gt::gt()
```

#rakfcsfwkl .gt_table {
  display: table;
  border-collapse: collapse;
  margin-left: auto;
  margin-right: auto;
  color: #333333;
  font-size: 16px;
  background-color: #FFFFFF;
  width: auto;
  border-top-style: solid;
  border-top-width: 2px;
  border-top-color: #A8A8A8;
  border-right-style: none;
  border-right-width: 2px;
  border-right-color: #D3D3D3;
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #A8A8A8;
  border-left-style: none;
  border-left-width: 2px;
  border-left-color: #D3D3D3;
}

#rakfcsfwkl .gt_heading {
  background-color: #FFFFFF;
  text-align: center;
  border-bottom-color: #FFFFFF;
  border-left-style: none;
  border-left-width: 1px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
}

#rakfcsfwkl .gt_title {
  color: #333333;
  font-size: 125%;
  font-weight: initial;
  padding-top: 4px;
  padding-bottom: 4px;
  border-bottom-color: #FFFFFF;
  border-bottom-width: 0;
}

#rakfcsfwkl .gt_subtitle {
  color: #333333;
  font-size: 85%;
  font-weight: initial;
  padding-top: 0;
  padding-bottom: 4px;
  border-top-color: #FFFFFF;
  border-top-width: 0;
}

#rakfcsfwkl .gt_bottom_border {
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
}

#rakfcsfwkl .gt_col_headings {
  border-top-style: solid;
  border-top-width: 2px;
  border-top-color: #D3D3D3;
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
  border-left-style: none;
  border-left-width: 1px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
}

#rakfcsfwkl .gt_col_heading {
  color: #333333;
  background-color: #FFFFFF;
  font-size: 100%;
  font-weight: normal;
  text-transform: inherit;
  border-left-style: none;
  border-left-width: 1px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
  vertical-align: bottom;
  padding-top: 5px;
  padding-bottom: 6px;
  padding-left: 5px;
  padding-right: 5px;
  overflow-x: hidden;
}

#rakfcsfwkl .gt_column_spanner_outer {
  color: #333333;
  background-color: #FFFFFF;
  font-size: 100%;
  font-weight: normal;
  text-transform: inherit;
  padding-top: 0;
  padding-bottom: 0;
  padding-left: 4px;
  padding-right: 4px;
}

#rakfcsfwkl .gt_column_spanner_outer:first-child {
  padding-left: 0;
}

#rakfcsfwkl .gt_column_spanner_outer:last-child {
  padding-right: 0;
}

#rakfcsfwkl .gt_column_spanner {
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
  vertical-align: bottom;
  padding-top: 5px;
  padding-bottom: 6px;
  overflow-x: hidden;
  display: inline-block;
  width: 100%;
}

#rakfcsfwkl .gt_group_heading {
  padding: 8px;
  color: #333333;
  background-color: #FFFFFF;
  font-size: 100%;
  font-weight: initial;
  text-transform: inherit;
  border-top-style: solid;
  border-top-width: 2px;
  border-top-color: #D3D3D3;
  border-bottom-style: solid;
  border-bottom-width: 2px;
  border-bottom-color: #D3D3D3;
  border-left-style: none;
  border-left-width: 1px;
  border-left-color: #D3D3D3;
  border-right-style: none;
  border-right-width: 1px;
  border-right-color: #D3D3D3;
  vertical-align: middle;
}

#rakfcsfwkl .gt_empty_group_heading {
  padding: 0.5px;
  color: #333333;
  background-color: #FFFFFF;
  font-size: 100%;
  font-weight: initial;
  border-top-style: solid;
  border-top-width: 2px;
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<div id="rakfcsfwkl" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;"><table class="gt_table">
  
  <thead class="gt_col_headings">
    <tr>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">arm</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Lived</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1">Died</th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr>
      <td class="gt_row gt_left">A: IFL</td>
      <td class="gt_row gt_left">4.2%  (18)</td>
      <td class="gt_row gt_left">95.8%  (410)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left">F: FOLFOX</td>
      <td class="gt_row gt_left">14.3%  (99)</td>
      <td class="gt_row gt_left">85.7%  (592)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left">G: IROX</td>
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      <td class="gt_row gt_left">93.2%  (354)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left">Total</td>
      <td class="gt_row gt_left">9.5% (143)</td>
      <td class="gt_row gt_left">90.5% (1356)</td>
    </tr>
  </tbody>
  
  
</table></div>

]

---
class: middle

.left-column[

![](http://www.danieldsjoberg.com/gtsummary/reference/figures/logo.png)
]

.right-column[
# the gtsummary package

<http://www.danieldsjoberg.com/gtsummary/index.html>
]

---
class: middle

# A `tbl_summary()`

.left-column[

```r
library(gtsummary)
mockdata %>% 
  select(arm, sex) %>% 
  tbl_summary(by = arm) %>% 
  add_p() %>% 
  add_overall()
```
]

.right-column[
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<div id="aemfdmqwqj" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;"><table class="gt_table">
  
  <thead class="gt_col_headings">
    <tr>
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      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>Overall</strong>, N = 1499</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>A: IFL</strong>, N = 428<sup class="gt_footnote_marks">1</sup></th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>F: FOLFOX</strong>, N = 691<sup class="gt_footnote_marks">1</sup></th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>G: IROX</strong>, N = 380<sup class="gt_footnote_marks">1</sup></th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>p-value</strong><sup class="gt_footnote_marks">2</sup></th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr>
      <td class="gt_row gt_left">sex</td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center">0.2</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Female</td>
      <td class="gt_row gt_center">583 (39%)</td>
      <td class="gt_row gt_center">151 (35%)</td>
      <td class="gt_row gt_center">280 (41%)</td>
      <td class="gt_row gt_center">152 (40%)</td>
      <td class="gt_row gt_center"></td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Male</td>
      <td class="gt_row gt_center">916 (61%)</td>
      <td class="gt_row gt_center">277 (65%)</td>
      <td class="gt_row gt_center">411 (59%)</td>
      <td class="gt_row gt_center">228 (60%)</td>
      <td class="gt_row gt_center"></td>
    </tr>
  </tbody>
  
  <tfoot>
    <tr class="gt_footnotes">
      <td colspan="6">
        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>1</em>
          </sup>
           
          Statistics presented: n (%)
          <br />
        </p>
        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>2</em>
          </sup>
           
          Statistical tests performed: chi-square test of independence
          <br />
        </p>
      </td>
    </tr>
  </tfoot>
</table></div>

]

---
class: middle

# A bigger `tbl_summary()`

.left-column[

```r
library(gtsummary)
mockdata %>% 
  select(arm, 
         starts_with("ae")) %>% 
  tbl_summary(by = arm)  
```
]

.right-column[
<style>html {
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  border-top-width: 2px;
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  border-right-color: #D3D3D3;
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  border-bottom-width: 2px;
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  width: 100%;
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#rvzpafjkms .gt_group_heading {
  padding: 8px;
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  font-style: italic;
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</style>
<div id="rvzpafjkms" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;"><table class="gt_table">
  
  <thead class="gt_col_headings">
    <tr>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1"><strong>Characteristic</strong></th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>A: IFL</strong>, N = 428<sup class="gt_footnote_marks">1</sup></th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>F: FOLFOX</strong>, N = 691<sup class="gt_footnote_marks">1</sup></th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>G: IROX</strong>, N = 380<sup class="gt_footnote_marks">1</sup></th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr>
      <td class="gt_row gt_left">ae_low_wbc</td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">0</td>
      <td class="gt_row gt_center">354 (83%)</td>
      <td class="gt_row gt_center">551 (80%)</td>
      <td class="gt_row gt_center">347 (91%)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">1</td>
      <td class="gt_row gt_center">74 (17%)</td>
      <td class="gt_row gt_center">140 (20%)</td>
      <td class="gt_row gt_center">33 (8.7%)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left">ae_neuropathy</td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">0</td>
      <td class="gt_row gt_center">354 (83%)</td>
      <td class="gt_row gt_center">580 (84%)</td>
      <td class="gt_row gt_center">347 (91%)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">1</td>
      <td class="gt_row gt_center">74 (17%)</td>
      <td class="gt_row gt_center">111 (16%)</td>
      <td class="gt_row gt_center">33 (8.7%)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left">ae_diarrhea</td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">0</td>
      <td class="gt_row gt_center">339 (79%)</td>
      <td class="gt_row gt_center">546 (79%)</td>
      <td class="gt_row gt_center">333 (88%)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">1</td>
      <td class="gt_row gt_center">89 (21%)</td>
      <td class="gt_row gt_center">145 (21%)</td>
      <td class="gt_row gt_center">47 (12%)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left">ae_vomiting</td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">0</td>
      <td class="gt_row gt_center">339 (79%)</td>
      <td class="gt_row gt_center">571 (83%)</td>
      <td class="gt_row gt_center">333 (88%)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">1</td>
      <td class="gt_row gt_center">89 (21%)</td>
      <td class="gt_row gt_center">120 (17%)</td>
      <td class="gt_row gt_center">47 (12%)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left">ae_blood_clot</td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
      <td class="gt_row gt_center"></td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">0</td>
      <td class="gt_row gt_center">411 (96%)</td>
      <td class="gt_row gt_center">658 (95%)</td>
      <td class="gt_row gt_center">365 (96%)</td>
    </tr>
    <tr>
      <td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">1</td>
      <td class="gt_row gt_center">17 (4.0%)</td>
      <td class="gt_row gt_center">33 (4.8%)</td>
      <td class="gt_row gt_center">15 (3.9%)</td>
    </tr>
  </tbody>
  
  <tfoot>
    <tr class="gt_footnotes">
      <td colspan="4">
        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>1</em>
          </sup>
           
          Statistics presented: n (%)
          <br />
        </p>
      </td>
    </tr>
  </tfoot>
</table></div>

]

---
class: middle, center

# Take-aways

✔️ **Document your document:** use YAML to set up meaningful metadata

✔️ **Style your document:** use YAML to add options to your chosen output format

✔️ **Organize your text:** use markdown headers with `#`

✔️ **Organize your code:** use `knitr` chunk labels

✔️ **Style your text:** use markdown **bold**, _italics_, <i class="fas fa-list-ul"></i> bullets, and <i class="fas fa-list-ol"></i> lists

✔️ **Style your output:** use `knitr` chunk options

🧶 early, 🧶 often

---
class: top

# How does R Markdown work?

1. 🤷

1. I press knit, a document appears, and I believe that anything happening in between could be actual magic.

1. `knitr` executes the code and converts `.Rmd` to `.md`; **Pandoc** renders the `.md` file to the output format you want.

---
class: top

# How *does* R Markdown work?

1. 🤷 (✔️)

1. ["I press knit, a document appears, and I believe that anything happening in between could be actual magic."](https://twitter.com/allison_horst/status/1070323369600442368?s=20) (🧙‍♂️)

1. `knitr` executes the code and converts `.Rmd` to `.md`; **Pandoc** renders the `.md` file to the output format you want. (✔️)

---
class: middle, center

> "In a nutshell, R Markdown stands on the shoulders of `knitr` and **Pandoc**.

> The former executes the computer code embedded in Markdown, and converts R Markdown to Markdown.

> The latter renders Markdown to the output format you want (such as PDF, HTML, Word, and so on)."

> &mdash; [R Markdown: The Definitive Guide](https://bookdown.org/yihui/rmarkdown/)

---

# Check-in

Which of the following is **NOT** a part of R Markdown basic anatomy?

1. Metadata

1. Text

1. Data

1. Code

1. Output

---

# Mad libs check-in

```markdown
 ___________ is written at the top between `---` in ________.
    noun                                             syntax
                                                     
  ______ is written in Markdown.
   noun         
  
  ______ is written in R (or other programming language).
   noun   
   
  The ______ package evaluates the code and produces the ______.
       noun                                               noun
```

---

# Mad libs check-in

```markdown
 Metadata is written at the top between `---` in YAML.
   (noun)                                      (syntax)
                                                     
  Text is written in Markdown.
 (noun)         
  
  Code is written in R (or other programming language).
 (noun)   
   
  The knitr package evaluates the code and produces the output.
     (noun)                                             (noun) 
```

---

# Projects

---
class: center, middle

# R projects

---
class: middle, center

.pull-left[
# <i class="fas fa-mouse-pointer"></i>

_File > New Project..._
<img src="images/rstudio-new.png" width="2056" />
]
--

.pull-right[
# <i class="fas fa-mouse-pointer"></i>

Pick one
<img src="images/rstudio-newproj.png" width="1773" />
]

---
class: middle, center

.pull-left[
# <i class="fas fa-mouse-pointer"></i>

_File > New File > R Markdown..._
<img src="images/rstudio-newfile.png" width="2037" />
]
--

.pull-right[
# <i class="fas fa-mouse-pointer"></i>

Fill in, can leave as HTML
<img src="images/rstudio-newrmd.png" width="1768" />
]

---
class: middle, center

.pull-left[
# <i class="fas fa-trash-alt"></i>

![](images/rstudio-freshrmd.png)
]

.pull-right[
# <i class="fas fa-save"></i>

![](images/rstudio-blankrmd.png)
]

---
class: middle

# Working with data

.pull-left[

### <i class="far fa-thumbs-down"></i>

```r
"~/mm/nope.csv"
setwd("/haha/good/luck/")
setwd('c:\iamyournightmare\!')
setwd("C:\user\oh\no")
setwd("path/that/only/works/on/my/machine")
```

### <i class="far fa-thumbs-up"></i>

```r
mockdata <- read_csv(
  here::here("data/mockdata.csv")
  )
```

]

.pull-right[
<div class="figure" style="text-align: center">
<img src="images/horst_here.png" alt="Art by Allison Horst" width="90%" />
<p class="caption">Art by Allison Horst</p>
</div>
]

https://whattheyforgot.org/project-oriented-workflow.html#setwd

---

# Extension formats

---
class: middle, center

# Dashboards

https://jenthompson.me/examples/progressdash.html

https://jenthompson.me/2018/02/09/flexdashboards-monitoring/

---
class: middle, center

<https://bookdown.org/yihui/bookdown/>

---
class: center, middle

<https://bookdown.org/yihui/blogdown/>

---
class: middle, center, inverse

# Cheatsheets!

---
class: middle

.left-column[

# 📌

]

.right-column[

_Help > Cheatsheets > RStudio IDE_

<a href="https://www.rstudio.com/resources/cheatsheets/#ide" target="_blank"><img src="https://d33wubrfki0l68.cloudfront.net/0dc0efccfaf638de8be4ce43e2bab8a91541d3d2/c4fdc/wp-content/uploads/2018/08/rstudio-ide.png" width="50%" /></a>
]

.footnote[https://www.rstudio.com/resources/cheatsheets/#ide]

---
class: middle

.left-column[
# 📌
]

.right-column[
_Help > Cheatsheets > R Markdown Cheat Sheet_

<a href="https://www.rstudio.com/resources/cheatsheets/#rmarkdown" target="_blank"><img src="https://d33wubrfki0l68.cloudfront.net/65dffd1bdcaa0025006262164d98e8068e8b4387/c3895/wp-content/uploads/2018/08/rmarkdown-2.0.png" width="50%" /></a>
]

.footnote[https://www.rstudio.com/resources/cheatsheets/#rmarkdown]

---
class: middle

.left-column[
# 📌
]

.right-column[
_Help > Cheatsheets > R Markdown Reference Guide_

]

.footnote[https://www.rstudio.com/wp-content/uploads/2015/03/rmarkdown-reference.pdf]

---
class: middle, center, inverse

# Book!

---
class: middle

.left-column[
# 📖
]

.right-column[

<a href="https://bookdown.org/yihui/rmarkdown/" target="_blank"><img src="https://bookdown.org/yihui/rmarkdown/images/cover.png" width="40%" /></a>
]

.footnote[https://bookdown.org/yihui/rmarkdown/]

---
class: middle, center, inverse

# Websites!

---
class: middle

.left-column[
# 🔗
]

.right-column[

<a href="https://rmarkdown.rstudio.com/" target="_blank"><img src="images/rmarkdown-site.png" width="80%" /></a>
]

.footnote[https://rmarkdown.rstudio.com/]

---
class: middle

.left-column[
# 🔗
]

.right-column[

<a href="https://rmarkdown.rstudio.com/docs/" target="_blank"><img src="images/rmarkdowndocs-site.png" width="80%" /></a>
]

.footnote[https://rmarkdown.rstudio.com/docs/]

---
class: middle

.left-column[
# 🎯
]

.right-column[

<a href="https://community.rstudio.com/c/R-Markdown" target="_blank"><img src="images/rmarkdowncommunity-site.png" width="80%" /></a>
]

.footnote[https://community.rstudio.com/c/R-Markdown]

---
class: middle

.left-column[
# 🤖
]

.right-column[

<a href="https://rmarkdown.rstudio.com/lesson-6.html" target="_blank"><img src="https://raw.githubusercontent.com/rstudio/rmarkdown/gh-pages/lesson-images/params-1-hawaii.png" width="80%" /></a>
]

.footnote[https://bookdown.org/yihui/rmarkdown/parameterized-reports.html,<br>
https://rmarkdown.rstudio.com/lesson-6.html]

---
class: inverse, middle, center

# Thank you!