HDSI-RUG-gtsummary

# Creating publication-ready summary tables with {gtsummary}

### Emily C. Zabor

#### RUG at HDSI

#### December 15, 2022

---
# About me

<img src="Images/Taussig.jpg" width=75%>
]

* 9 years as a Research Biostatistician at **Memorial Sloan Kettering Cancer Center**

<br>

* DrPH in Biostatistics from **Columbia University**

<br>

* Faculty Biostatistician at **Cleveland Clinic**
]
]

---

---
# The reproducibility crisis

- **Low quality code** in medical research part of the problem

- Low quality code is more likely to **contain errors**

- Reproducibility is often **cumbersome** and **time-consuming**
]
]

.pull-right[
<p align="center"><img src="Images/reproducibility-graphic-online1.jpeg" width=90%></p>
]

.footnote[Image source: https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970; Slide source: http://www.danieldsjoberg.com/rmedicine-gtsummary]

---
# Need reproducible, publication-ready tables

```r
summary(df$age)
table(df$sex)
table(df$race)
table(df$ethnicity)
```
]
]

.pull-right[
.large[
To **table** in a publication:
<p align="center"><img src="Images/table1_example.png" width=90%>
]
]

.small[
Brierley CK, Zabor EC, Komrokji RS, DeZern AE, Roboz GJ, Brunner AM, Stone RM, Sekeres MA, Steensma DP. Low participation rates and disparities in participation in interventional clinical trials for myelodysplastic syndromes. *Cancer.* 2020 Aug 7. doi: 10.1002/cncr.33105. PMID: 32767690.
]

---
# {gtsummary} overview

.pull-left[
.large[
* Create **tabular summaries** with sensible defaults but highly customizable
* Types of summaries:
  - "Table 1"-types
  - Cross-tabulation
  - Regression models
  - Survival data
  - Survey data
  - Custom tables
]

]

.pull-right[
.large[
* Report statistics from {gtsummary} tables **inline** in R Markdown
* Stack and/or merge any table type
* Use **themes** to standardize across tables
* Choose from different **print engines**
]

<img src="Images/gtsummary_logo.png" width=40% align="middle">
]

---
# Example dataset

* Simulated dataset of baseline characteristics for 200 patients who receive Drug A or Drug B

* Variables were assigned labels using the `labelled` package
]
]

```r
library(gtsummary)
library(tidyverse)
head(trial) |> gt::gt()
```

<div id="kfjoxfxtak" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;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;
}

#kfjoxfxtak .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;
}

#kfjoxfxtak .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;
}

#kfjoxfxtak .gt_caption {
  padding-top: 4px;
  padding-bottom: 4px;
}

#kfjoxfxtak .gt_title {
  color: #333333;
  font-size: 125%;
  font-weight: initial;
  padding-top: 4px;
  padding-bottom: 4px;
  padding-left: 5px;
  padding-right: 5px;
  border-bottom-color: #FFFFFF;
  border-bottom-width: 0;
}

#kfjoxfxtak .gt_subtitle {
  color: #333333;
  font-size: 85%;
  font-weight: initial;
  padding-top: 0;
  padding-bottom: 6px;
  padding-left: 5px;
  padding-right: 5px;
  border-top-color: #FFFFFF;
  border-top-width: 0;
}

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

#kfjoxfxtak .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;
}

#kfjoxfxtak .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;
}

#kfjoxfxtak .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;
}

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

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

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

#kfjoxfxtak .gt_group_heading {
  padding-top: 8px;
  padding-bottom: 8px;
  padding-left: 5px;
  padding-right: 5px;
  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;
  text-align: left;
}

#kfjoxfxtak .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;
}

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

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

#kfjoxfxtak .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;
}

#kfjoxfxtak .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: 5px;
  padding-right: 5px;
}

#kfjoxfxtak .gt_stub_row_group {
  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: 5px;
  padding-right: 5px;
  vertical-align: top;
}

#kfjoxfxtak .gt_row_group_first td {
  border-top-width: 2px;
}

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

#kfjoxfxtak .gt_first_summary_row {
  border-top-style: solid;
  border-top-color: #D3D3D3;
}

#kfjoxfxtak .gt_first_summary_row.thick {
  border-top-width: 2px;
}

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

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

#kfjoxfxtak .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;
}

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

#kfjoxfxtak .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;
}

#kfjoxfxtak .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;
}

#kfjoxfxtak .gt_footnote {
  margin: 0px;
  font-size: 90%;
  padding-left: 4px;
  padding-right: 4px;
  padding-left: 5px;
  padding-right: 5px;
}

#kfjoxfxtak .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;
}

#kfjoxfxtak .gt_sourcenote {
  font-size: 90%;
  padding-top: 4px;
  padding-bottom: 4px;
  padding-left: 5px;
  padding-right: 5px;
}

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

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

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

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

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

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

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

#kfjoxfxtak .gt_footnote_marks {
  font-style: italic;
  font-weight: normal;
  font-size: 75%;
  vertical-align: 0.4em;
}

#kfjoxfxtak .gt_asterisk {
  font-size: 100%;
  vertical-align: 0;
}

#kfjoxfxtak .gt_indent_1 {
  text-indent: 5px;
}

#kfjoxfxtak .gt_indent_2 {
  text-indent: 10px;
}

#kfjoxfxtak .gt_indent_3 {
  text-indent: 15px;
}

#kfjoxfxtak .gt_indent_4 {
  text-indent: 20px;
}

#kfjoxfxtak .gt_indent_5 {
  text-indent: 25px;
}
</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" scope="col" id="trt">trt</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="age">age</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="marker">marker</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="stage">stage</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="grade">grade</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="response">response</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="death">death</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_right" rowspan="1" colspan="1" scope="col" id="ttdeath">ttdeath</th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr><td headers="trt" class="gt_row gt_left">Drug A</td>
<td headers="age" class="gt_row gt_right">23</td>
<td headers="marker" class="gt_row gt_right">0.160</td>
<td headers="stage" class="gt_row gt_center">T1</td>
<td headers="grade" class="gt_row gt_center">II</td>
<td headers="response" class="gt_row gt_right">0</td>
<td headers="death" class="gt_row gt_right">0</td>
<td headers="ttdeath" class="gt_row gt_right">24.00</td></tr>
    <tr><td headers="trt" class="gt_row gt_left">Drug B</td>
<td headers="age" class="gt_row gt_right">9</td>
<td headers="marker" class="gt_row gt_right">1.107</td>
<td headers="stage" class="gt_row gt_center">T2</td>
<td headers="grade" class="gt_row gt_center">I</td>
<td headers="response" class="gt_row gt_right">1</td>
<td headers="death" class="gt_row gt_right">0</td>
<td headers="ttdeath" class="gt_row gt_right">24.00</td></tr>
    <tr><td headers="trt" class="gt_row gt_left">Drug A</td>
<td headers="age" class="gt_row gt_right">31</td>
<td headers="marker" class="gt_row gt_right">0.277</td>
<td headers="stage" class="gt_row gt_center">T1</td>
<td headers="grade" class="gt_row gt_center">II</td>
<td headers="response" class="gt_row gt_right">0</td>
<td headers="death" class="gt_row gt_right">0</td>
<td headers="ttdeath" class="gt_row gt_right">24.00</td></tr>
    <tr><td headers="trt" class="gt_row gt_left">Drug A</td>
<td headers="age" class="gt_row gt_right">NA</td>
<td headers="marker" class="gt_row gt_right">2.067</td>
<td headers="stage" class="gt_row gt_center">T3</td>
<td headers="grade" class="gt_row gt_center">III</td>
<td headers="response" class="gt_row gt_right">1</td>
<td headers="death" class="gt_row gt_right">1</td>
<td headers="ttdeath" class="gt_row gt_right">17.64</td></tr>
    <tr><td headers="trt" class="gt_row gt_left">Drug A</td>
<td headers="age" class="gt_row gt_right">51</td>
<td headers="marker" class="gt_row gt_right">2.767</td>
<td headers="stage" class="gt_row gt_center">T4</td>
<td headers="grade" class="gt_row gt_center">III</td>
<td headers="response" class="gt_row gt_right">1</td>
<td headers="death" class="gt_row gt_right">1</td>
<td headers="ttdeath" class="gt_row gt_right">16.43</td></tr>
    <tr><td headers="trt" class="gt_row gt_left">Drug B</td>
<td headers="age" class="gt_row gt_right">39</td>
<td headers="marker" class="gt_row gt_right">0.613</td>
<td headers="stage" class="gt_row gt_center">T4</td>
<td headers="grade" class="gt_row gt_center">I</td>
<td headers="response" class="gt_row gt_right">0</td>
<td headers="death" class="gt_row gt_right">1</td>
<td headers="ttdeath" class="gt_row gt_right">15.64</td></tr>
  </tbody>
  
  
</table>
</div>
]

---
# Example dataset

```r
sm_trial <-
  trial |> 
  select(trt, age, grade, response)
```

<div id="pivqjpwqjg" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;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;
}

#pivqjpwqjg .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;
}

#pivqjpwqjg .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;
}

#pivqjpwqjg .gt_caption {
  padding-top: 4px;
  padding-bottom: 4px;
}

#pivqjpwqjg .gt_title {
  color: #333333;
  font-size: 125%;
  font-weight: initial;
  padding-top: 4px;
  padding-bottom: 4px;
  padding-left: 5px;
  padding-right: 5px;
  border-bottom-color: #FFFFFF;
  border-bottom-width: 0;
}

#pivqjpwqjg .gt_subtitle {
  color: #333333;
  font-size: 85%;
  font-weight: initial;
  padding-top: 0;
  padding-bottom: 6px;
  padding-left: 5px;
  padding-right: 5px;
  border-top-color: #FFFFFF;
  border-top-width: 0;
}

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

#pivqjpwqjg .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;
}

#pivqjpwqjg .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;
}

#pivqjpwqjg .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;
}

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

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

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

#pivqjpwqjg .gt_group_heading {
  padding-top: 8px;
  padding-bottom: 8px;
  padding-left: 5px;
  padding-right: 5px;
  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;
  text-align: left;
}

#pivqjpwqjg .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;
}

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

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

#pivqjpwqjg .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;
}

#pivqjpwqjg .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: 5px;
  padding-right: 5px;
}

#pivqjpwqjg .gt_stub_row_group {
  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: 5px;
  padding-right: 5px;
  vertical-align: top;
}

#pivqjpwqjg .gt_row_group_first td {
  border-top-width: 2px;
}

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

#pivqjpwqjg .gt_first_summary_row {
  border-top-style: solid;
  border-top-color: #D3D3D3;
}

#pivqjpwqjg .gt_first_summary_row.thick {
  border-top-width: 2px;
}

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

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

#pivqjpwqjg .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;
}

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

#pivqjpwqjg .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;
}

#pivqjpwqjg .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;
}

#pivqjpwqjg .gt_footnote {
  margin: 0px;
  font-size: 90%;
  padding-left: 4px;
  padding-right: 4px;
  padding-left: 5px;
  padding-right: 5px;
}

#pivqjpwqjg .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;
}

#pivqjpwqjg .gt_sourcenote {
  font-size: 90%;
  padding-top: 4px;
  padding-bottom: 4px;
  padding-left: 5px;
  padding-right: 5px;
}

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

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

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

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

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

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

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

#pivqjpwqjg .gt_footnote_marks {
  font-style: italic;
  font-weight: normal;
  font-size: 75%;
  vertical-align: 0.4em;
}

#pivqjpwqjg .gt_asterisk {
  font-size: 100%;
  vertical-align: 0;
}

#pivqjpwqjg .gt_indent_1 {
  text-indent: 5px;
}

#pivqjpwqjg .gt_indent_2 {
  text-indent: 10px;
}

#pivqjpwqjg .gt_indent_3 {
  text-indent: 15px;
}

#pivqjpwqjg .gt_indent_4 {
  text-indent: 20px;
}

#pivqjpwqjg .gt_indent_5 {
  text-indent: 25px;
}
</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" scope="col" id="Variable">Variable</th>
      <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="1" colspan="1" scope="col" id="Label">Label</th>
    </tr>
  </thead>
  <tbody class="gt_table_body">
    <tr><td headers="Variable" class="gt_row gt_left">trt</td>
<td headers="Label" class="gt_row gt_left">Chemotherapy Treatment</td></tr>
    <tr><td headers="Variable" class="gt_row gt_left">age</td>
<td headers="Label" class="gt_row gt_left">Age</td></tr>
    <tr><td headers="Variable" class="gt_row gt_left">grade</td>
<td headers="Label" class="gt_row gt_left">Grade</td></tr>
    <tr><td headers="Variable" class="gt_row gt_left">response</td>
<td headers="Label" class="gt_row gt_left">Tumor Response</td></tr>
  </tbody>
  
  
</table>
</div>

---

---
# Basic tbl_summary()

```r
sm_trial |>
  select(-trt) |>
  tbl_summary()
```

- Statistics are `median (IQR)` for continuous, `n (%)` for categorical/dichotomous

- Variables coded `0/1`, `TRUE/FALSE`, `Yes/No` treated as dichotomous

- Lists `NA` values under "Unknown"

- Label attributes are printed automatically
]

]

---
# Customize tbl_summary() output

```r
sm_trial |>
  tbl_summary(
    by = trt
    )
```

- `by`: specifies a column variable for cross-tabulation
]

---
# Customize tbl_summary() output

```r
sm_trial |>
  tbl_summary(
    by = trt,
    type = age ~ "continuous2"
    )
```

- `by`: specify a column variable for cross-tabulation
- `type`: specify the summary type
]

---
# Customize tbl_summary() output

```r
sm_trial |>
  tbl_summary(
    by = trt,
    type = age ~ "continuous2",
    statistic = list(
      age ~ c("{mean} ({sd})", 
              "{min}, {max}"), 
      response ~ "{n} / {N} ({p}%)"
    )
    )
```

- `by`: specify a column variable for cross-tabulation
- `type`: specify the summary type
- `statistic`: customize the reported statistics
]

---
# Customize tbl_summary() output

```r
sm_trial |>
  tbl_summary(
    by = trt,
    type = age ~ "continuous2",
    statistic = list(
      age ~ c("{mean} ({sd})", 
              "{min}, {max}"), 
      response ~ "{n} / {N} ({p}%)"
    ),
    label = grade ~ "Pathologic grade"
    )
```

- `by`: specify a column variable for cross-tabulation
- `type`: specify the summary type
- `statistic`: customize the reported statistics
- `label`: change or customize variable labels
]

---
# Customize tbl_summary() output

- `by`: specify a column variable for cross-tabulation
- `type`: specify the summary type
- `statistic`: customize the reported statistics
- `label`: change or customize variable labels
- `digits`: specify the number of decimal places for rounding
]

---
# Customize tbl_summary() output

```r
sm_trial |>
  tbl_summary(
    statistic    =    all_continuous()        ~    "{mean} ({sd})",
    label        =    starts_with("grade")    ~    "Pathologic grade",
    digits       =    age                     ~    2
    )
```

<br>

```r
label = list(age ~ "Patient age (years)", grade = "Pathologic tumor grade")
```

---
# Add-on functions in {gtsummary}

- `add_*()` add **additional column** of statistics or information, e.g. p-values, q-values, overall statistics, N obs., and more

- `modify_*()` **modify** table headers, spanning headers, and footnotes

- `bold_*()/italicize_*()` **style** labels, variable levels, significant p-values

]