Outputs & Tables

class: title-slide, center, middle

# Outputs & Tables

## R Markdown for Pharma

### Alison Hill &#183; RStudio

#### [rmd4pharma.netlify.app/](https://rmd4pharma.netlify.app/)

---
class: middle, center

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

# Go here and log in (free):

<https://rstd.io/rmd4pharma-cloud>

---
layout: true

<div class="my-footer"><span>https://rmd4pharma.netlify.app/</span></div>

---

.left-column[
<span class="fa-stack fa-4x">
  <i class="fa fa-circle fa-stack-2x" style="color: #2f5275;"></i>
  <strong class="fa-stack-1x" style="color: #fff;">?</strong>
</span> 
]

.right-column[

# 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

.left-column[
<span class="fa-stack fa-4x">
  <i class="fa fa-circle fa-stack-2x" style="color: #2f5275;"></i>
  <strong class="fa-stack-1x" style="color: #fff;">?</strong>
</span>

]

.right-column[

# 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/)

---
class: center, middle

# Foreshadowing

???

but first a pop quiz...

---
class: pop-quiz

# Pop quiz

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

1. Metadata

1. Text

1. CSS

1. Code

1. Output

---
class: your-turn

# Your turn

## Mad libs style &mdash; with a neighbor

```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
```

_psst: answers on next slide..._

---
class: your-turn

# Your turn

## Answers

```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) 
```

---
class: your-turn

# Your turn

Find a partner and look at `02-progress.Rmd` together. 
Look at the source, then 🧶 **Knit**.

Answer the following questions:

1. What is the output **format**?

1. Are there any output **options**?

1. Are any `knitr` **global** chunk options set?

1. Anything in the code look foreign to you?

1. Anything in the output (or not in the output) surprise you?

---
class: middle, center, inverse

# Output formats

---
class: middle, center

???

Built in formats (in the `rmarkdown` package)

versus

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

---
class: middle, center

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

---
class: your-turn

# Your turn

## Use a different built-in format

.pull-left[

Use the drop-down menu for the 🧶 **Knit** button and try:

1. Knit to Word

1. Knit to PDF

]

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

]

---

# Temp check 🌡

Does your current YAML look like this?

```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: your-turn

# Your turn

## Add output options with your YAML

.pull-left[

You just used the drop-down 🧶 **Knit** button to knit to Word and PDF.

1. Change your YAML to the right...

1. Be __very careful__ about indentation and `:` here!!

1. 🧶 **Knit** to Word again- is there a TOC?

]

.pull-right[

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

]

---

# What is hard about YAML?

.pull-left[
![](https://media.giphy.com/media/Nt2cPxzpKhbCE/giphy.gif)
]

.pull-right[
+ Indentations matter

+ Rarely informative error messages

+ Knowing which output options are relevant for different formats (i.e., Word, PDF, HTML, etc.)

+ Easy to forget the right `key`

+ Easy to forget the possible `values` for a given `key`
]
---
class: your-turn

# Your turn

## Use an extension package

1. Edit your YAML again! Change the `output:` key to only `distill::distill_article`

1. Save the document; click on the dropdown 🧶 **Knit** button- what do you notice?

1. 🧶 **Knit** to distill_article.

**If this was easy**, add a table of contents too.

_psst...answers on the next slide..._

.footnote[(note: this requires you to install the [`distill` package](https://rstudio.github.io/distill/) on your own computer)]

???

At this point, I'm going to stick with the distill_article output format for the rest of this session.

---
class: your-turn

# Your turn

## Answer

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

.pull-right[
```yaml
---
author: Your name here
title: Your title here
output:
  distill::distill_article:
    toc: true
---
```
]

---
class: middle

# Pop quiz

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

```yaml
---
output: html_document: default
---
output: html_document
---
```

]

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

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

]

---
class: middle

# Pop quiz

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

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

]

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

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

]

---
class: middle, center, inverse

# Tables

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

---
class: middle, center, inverse

# Custom typed 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: your-turn

# Your turn

## Type up a Markdown table

Find this section:

```markdown
<--TODO: add markdown table of treatment arms here-->
```

.pull-left[

Using pipes `|`, make this table:

| Arm | Drug   |
|:----|:-------|
| A   | IFL    |
| F   | FOLFOX |
| G   | IROX   |

]

.pull-right[

![](https://qph.fs.quoracdn.net/main-qimg-637b91293b153c5cd40419c0872c2186)

]

_psst...answers on the next slide..._

---
class: your-turn

# Your turn

## Answers

.pull-left[
```markdown
| Arm | Drug   |
|:----|:-------|
| A   | IFL    |
| F   | FOLFOX |
| G   | IROX   |
```
]

.pull-right[
```markdown
|Arm|Drug|
|:---|:---|
|A|IFL|
|F|FOLFOX|
|G|IROX|
```
]

Spacing actually doesn't matter - it mainly helps your eyeballs.

---
class: center, middle

# Two table types

.pull-left[

### for your eyes mainly

![](images/tables-you.jpg)

]

.pull-right[

### for other people's eyes too

![](images/tables-them.jpg)
]

---

.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)]

---
class: middle, center, inverse

# EDA Tables

---

# Let's try using data now

```r
mockdata <- read_csv(here::here("static/mockpaper/data/mockdata.csv")) %>%
  mutate(fu_fct = fct_recode(as.factor(fu_stat), 
                             "Lived" = "1", 
                             "Died" = "2")) %>% 
  mutate(across(starts_with("ae_"), as.factor))
#> 
#> ── 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()
#> )
#> ℹ Use `spec()` for the full column specifications.
```

---
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

---
class: middle

.pull-left[

```r
mockdata %>%
  count(arm) %>% 
  gt()
```

<div id="hoawbmbumo" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>html {
  font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Helvetica Neue', 'Fira Sans', 'Droid Sans', Arial, sans-serif;
}

#hoawbmbumo .gt_table {
  display: table;
  border-collapse: collapse;
  margin-left: auto;
  margin-right: auto;
  color: #333333;
  font-size: 16px;
  font-weight: normal;
  font-style: normal;
  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;
}

#hoawbmbumo .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;
}

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

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

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

#hoawbmbumo .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;
}

#hoawbmbumo .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;
}

#hoawbmbumo .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;
}

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

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

#hoawbmbumo .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%;
}

#hoawbmbumo .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;
}

#hoawbmbumo .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;
}

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

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

#hoawbmbumo .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;
}

#hoawbmbumo .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;
}

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

#hoawbmbumo .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;
}

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

#hoawbmbumo .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;
}

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

#hoawbmbumo .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;
}

#hoawbmbumo .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;
}

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

#hoawbmbumo .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;
}

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

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

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

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

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

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

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

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

#hoawbmbumo .gt_footnote_marks {
  font-style: italic;
  font-weight: normal;
  font-size: 65%;
}
</style>
<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">n</th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr><td class="gt_row gt_left">A: IFL</td>
<td class="gt_row gt_right">428</td></tr>
    <tr><td class="gt_row gt_left">F: FOLFOX</td>
<td class="gt_row gt_right">691</td></tr>
    <tr><td class="gt_row gt_left">G: IROX</td>
<td class="gt_row gt_right">380</td></tr>
  </tbody>
  
  
</table>
</div>
]

.pull-right[

```r
mockdata %>%
  count(arm, sex) %>% 
  pivot_wider(names_from = sex, 
              values_from = n) %>% 
  gt()
```

<div id="bgdrhbigzu" style="overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>html {
  font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, Oxygen, Ubuntu, Cantarell, 'Helvetica Neue', 'Fira Sans', 'Droid Sans', Arial, sans-serif;
}

#bgdrhbigzu .gt_table {
  display: table;
  border-collapse: collapse;
  margin-left: auto;
  margin-right: auto;
  color: #333333;
  font-size: 16px;
  font-weight: normal;
  font-style: normal;
  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;
}

#bgdrhbigzu .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;
}

#bgdrhbigzu .gt_title {
  color: #333333;
  font-size: 125%;
  font-weight: initial;
  padding-top: 4px;
  padding-bottom: 4px;
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<table class="gt_table">
  
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      <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">Female</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1">Male</th>
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<td class="gt_row gt_right">277</td></tr>
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<td class="gt_row gt_right">152</td>
<td class="gt_row gt_right">228</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

# Simple frequency table

```r
library(gtsummary)
mockdata %>%
  select(arm) %>% 
  tbl_summary()
```

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      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>N = 1,499</strong><sup class="gt_footnote_marks">1</sup></th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr><td class="gt_row gt_left">arm</td>
<td class="gt_row gt_center"></td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">A: IFL</td>
<td class="gt_row gt_center">428 (29%)</td></tr>
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<td class="gt_row gt_center">691 (46%)</td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">G: IROX</td>
<td class="gt_row gt_center">380 (25%)</td></tr>
  </tbody>
  
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    <tr class="gt_footnotes">
      <td colspan="2">
        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>1</em>
          </sup>
           
          n (%)
          <br />
        </p>
      </td>
    </tr>
  </tfoot>
</table>
</div>

---

## Cross-tables

.pull-left[

```r
library(gtsummary)
mockdata %>%
  select(fu_fct, arm) %>% 
  tbl_summary(by = fu_fct)
```

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  <thead class="gt_col_headings">
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      <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>Lived</strong>, N = 143<sup class="gt_footnote_marks">1</sup></th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>Died</strong>, N = 1,356<sup class="gt_footnote_marks">1</sup></th>
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  </thead>
  <tbody class="gt_table_body">
    <tr><td class="gt_row gt_left">arm</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;">A: IFL</td>
<td class="gt_row gt_center">18 (13%)</td>
<td class="gt_row gt_center">410 (30%)</td></tr>
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<td class="gt_row gt_center">99 (69%)</td>
<td class="gt_row gt_center">592 (44%)</td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">G: IROX</td>
<td class="gt_row gt_center">26 (18%)</td>
<td class="gt_row gt_center">354 (26%)</td></tr>
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        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>1</em>
          </sup>
           
          n (%)
          <br />
        </p>
      </td>
    </tr>
  </tfoot>
</table>
</div>
]

.pull-right[

```r
library(gtsummary)
mockdata %>%
  select(fu_fct, arm) %>% 
  tbl_cross(
    row = arm,
    col = fu_fct,
    percent = "cell",
    label = fu_fct ~ "Follow-up")
```

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    <tr><td class="gt_row gt_left" style="font-weight: bold;">arm</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;">A: IFL</td>
<td class="gt_row gt_center">18 (1.2%)</td>
<td class="gt_row gt_center">410 (27%)</td>
<td class="gt_row gt_center">428 (29%)</td></tr>
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<td class="gt_row gt_center">99 (6.6%)</td>
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<td class="gt_row gt_center">691 (46%)</td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">G: IROX</td>
<td class="gt_row gt_center">26 (1.7%)</td>
<td class="gt_row gt_center">354 (24%)</td>
<td class="gt_row gt_center">380 (25%)</td></tr>
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<td class="gt_row gt_center">143 (9.5%)</td>
<td class="gt_row gt_center">1,356 (90%)</td>
<td class="gt_row gt_center">1,499 (100%)</td></tr>
  </tbody>
  
  
</table>
</div>
]

---
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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<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>Overall</strong>, N = 1,499<sup class="gt_footnote_marks">1</sup></th>
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<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>
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        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>1</em>
          </sup>
           
          n (%)
          <br />
        </p>
        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>2</em>
          </sup>
           
          Pearson's Chi-squared test
          <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[
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  <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>
           
          n (%)
          <br />
        </p>
      </td>
    </tr>
  </tfoot>
</table>
</div>

]

---
class: middle, center, inverse

# Table One

---

```r
library(gtsummary)
mockdata %>% 
  select(age, fu_fct) %>% 
  tbl_summary()
```

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  <thead class="gt_col_headings">
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      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>N = 1,499</strong><sup class="gt_footnote_marks">1</sup></th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr><td class="gt_row gt_left">age</td>
<td class="gt_row gt_center">61 (52, 68)</td></tr>
    <tr><td class="gt_row gt_left">fu_fct</td>
<td class="gt_row gt_center"></td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Lived</td>
<td class="gt_row gt_center">143 (9.5%)</td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Died</td>
<td class="gt_row gt_center">1,356 (90%)</td></tr>
  </tbody>
  
  <tfoot>
    <tr class="gt_footnotes">
      <td colspan="2">
        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>1</em>
          </sup>
           
          Median (IQR); n (%)
          <br />
        </p>
      </td>
    </tr>
  </tfoot>
</table>
</div>

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

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      <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>
      <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">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">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">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>
    <tr><td class="gt_row gt_left">age</td>
<td class="gt_row gt_center">61 (53, 68)</td>
<td class="gt_row gt_center">61 (52, 69)</td>
<td class="gt_row gt_center">61 (52, 68)</td>
<td class="gt_row gt_center">0.6</td></tr>
    <tr><td class="gt_row gt_left">bmi</td>
<td class="gt_row gt_center">26.2 (23.6, 30.6)</td>
<td class="gt_row gt_center">26.5 (23.7, 30.1)</td>
<td class="gt_row gt_center">26.0 (23.2, 29.6)</td>
<td class="gt_row gt_center">0.6</td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Unknown</td>
<td class="gt_row gt_center">9</td>
<td class="gt_row gt_center">20</td>
<td class="gt_row gt_center">4</td>
<td class="gt_row gt_center"></td></tr>
  </tbody>
  
  <tfoot>
    <tr class="gt_footnotes">
      <td colspan="5">
        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>1</em>
          </sup>
           
          n (%); Median (IQR)
          <br />
        </p>
        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>2</em>
          </sup>
           
          Pearson's Chi-squared test; Kruskal-Wallis rank sum test
          <br />
        </p>
      </td>
    </tr>
  </tfoot>
</table>
</div>

---

```r
library(gtsummary)
mockdata %>% 
  select(sex, age, bmi, arm) %>% 
  tbl_summary(by = arm, 
              type = all_continuous() ~ "continuous2") %>% 
  add_p()
```

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      <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</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>F: FOLFOX</strong>, N = 691</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1"><strong>G: IROX</strong>, N = 380</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">1</sup></th>
    </tr>
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  <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">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">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">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>
    <tr><td class="gt_row gt_left">age</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">0.6</td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Median (IQR)</td>
<td class="gt_row gt_center">61 (53, 68)</td>
<td class="gt_row gt_center">61 (52, 69)</td>
<td class="gt_row gt_center">61 (52, 68)</td>
<td class="gt_row gt_center"></td></tr>
    <tr><td class="gt_row gt_left">bmi</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">0.6</td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Median (IQR)</td>
<td class="gt_row gt_center">26.2 (23.6, 30.6)</td>
<td class="gt_row gt_center">26.5 (23.7, 30.1)</td>
<td class="gt_row gt_center">26.0 (23.2, 29.6)</td>
<td class="gt_row gt_center"></td></tr>
    <tr><td class="gt_row gt_left" style="text-align: left; text-indent: 10px;">Unknown</td>
<td class="gt_row gt_center">9</td>
<td class="gt_row gt_center">20</td>
<td class="gt_row gt_center">4</td>
<td class="gt_row gt_center"></td></tr>
  </tbody>
  
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    <tr class="gt_footnotes">
      <td colspan="5">
        <p class="gt_footnote">
          <sup class="gt_footnote_marks">
            <em>1</em>
          </sup>
           
          Pearson's Chi-squared test; Kruskal-Wallis rank sum test
          <br />
        </p>
      </td>
    </tr>
  </tfoot>
</table>
</div>

---
class: your-turn

# Your turn

## Make an adverse events table

Find this section:

```markdown

```

1. When you select variables, add all that start with "ae" (hint: `starts_with("string"))`.

1. Make the table grouped by treatment arm.

---
class: middle, center

# ⏱

# Time for a break!