Introduction to R forApplied Epidemiology

class: center, middle, inverse, title-slide

# Introduction to R for Applied Epidemiology

### Welcome and introduction

contact@appliedepi.org

---
# Thank you for joining us

**Thank you for your service to your community in these busy times.**  
We are glad that you are learning R with us.

???
Do a brief round of introductions

---
## About Applied Epi

.pull-left[

**“By epis, for epis”**

A global **grassroots movement**, elevating frontline epidemiology.

A **nonprofit** charity organization.

We believe that public health's transition to R should be led by ground-level users.

]

.pull-right[

<img src="../../images/welcome/team_locations.png" width="100%" />
**100** epidemiologists with **R expertise** and **ground-level** public health experience.

]

.footnote[Meet [our team](https://appliedepi.org/about/people.html)]

---
# R training courses

**Synchronous** courses with **1-on-1 tutoring** and **follow-up support**.

**Over 2200 epis at 400 agencies** have taken our intro course, including at US CDC, WHO, Doctors without Borders (MSF), national & local agencies, and FETPs.

**Advanced courses** - See our advanced R courses on GIS, advanced automation, statistics, Git/Github, time series/outbreak detection, dashboards, and more!

---

# The Epidemiologist R Handbook

- Freely available at **[www.epiRhandbook.com](www.epirhandbook.com)**  
- 50 chapters of **best-practice code examples** available online and offline
- Used **4,000 times daily** by **1 million users**  
- Translated into Spanish, French, Portuguese, Vietnamese, Turkish, and more...

> *"The epidemiologist greatest companion"* - Epidemiologist, Nigeria CDC

> *"[It] weaves together so much, so succinctly, and so incredibly clearly"* - Epidemiologist, US CDC

---
# 24/7 multilingual R Support Desk

.pull-left[

**Book timely 1-on-1 calls with epidemiologist R technicians**

> "Help that was fast and high quality - **a life saver**!” -*Epi AdvisorDoctors without Borders*

Used by hundreds of agencies including the Uganda Ministry of Health for Ebola response.

]

.pull-right[

]

---
class: inverse, center, middle

# Why learn R?

---
# Learning R...

## ...is really useful

???
Mention marketable skill as well as technically for epidemic response

---
# Learning R...

## ...is freeing

---
# Learning R...

## ...can be hard work

---
# Learning R...

## ...gives moments of pure joy

---
# Learning R...

## ...is easier than ever

.pull-left[

- Friendly user interface (RStudio)
- More simple syntax ("tidyverse")  
- Books & blogs  
- Applied Epi's free resources:  
    - **Epidemiologist R Handbook**  
    - **Online tutorials**  
    - **Case studies**  
    - **Community forum**  
]

.pull-right[

]

???
- There is a bit of a learning curve - as with any software.  
- But we are here to get you over that initial hump so you can keep developing.

---
# Learning R...

## ...is more flexible

???
- R can read and write to loads of different software/databases.
- Can hold multiple datasets at once
- Can also produce many different outputs  
- Automated and reproducible workflows (saves you time and headache)

---
# Learning R...

## ...automates routine tasks

.pull-left[

* Data cleaning pipelines

* Reports (Word, PDF, HTML...)

* Slide presentations and dashboards

* Maps (GIS)

> "I actually have the time to *be an epidemiologist* now!" - Course graduate, Haiti

]

.pull-right[

]

.footnote[*317 COVID-19 reports produced daily by Public Health England in 2020 (Image: Paula Blomquist)*]

???
- Producing reports at scale, an example from our EpiRHandbook colleague Paula
- Not a fancy report, flat word document but caters to specific needs! 
- **Key example of local intelligence and no way could do without the power of R**

---
# Learning R...

## ...makes brilliant data visualizations

???
- Data viz essential to understand disease surveillance trends and outbreaks  
- **One of R's strongest features**  
- Network diagrams, maps, heat maps, integrated figures, the list goes on...

---
# Learning R...

## ...calls upon your creative side

???
Many people think about coding as creating artwork... for example creating pottery, writing poems, painting, etc.

---
# Learning R...

## ...with a community of millions

???
- What is the largest community of R users in the world? R Ladies  
- Help communities exist in many places - we have our community forum

???
Community of people who support free software, open-access tools, and democratizing and equalizing data science

---
class: inverse, center, middle

# This course

---
# Course objectives

- Achieve basic competency in use of R for common public health tasks such as data management, data visualization, summary tables, and automated reports

- Have experience applying R to a variety of datasets

- Understand how R evolves and be equipped for sustained self-learning

---
# Course schedule

<div class="tabwid"><style>.cl-df15662c{table-layout:auto;}.cl-df031a6c{font-family:'Arial';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-df031a80{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-df0a6e5c{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-df0a9c06{background-color:rgba(0, 205, 0, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c1a{background-color:rgba(0, 205, 0, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c24{background-color:rgba(0, 205, 0, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c25{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c2e{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c2f{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c38{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c39{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c42{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c43{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c4c{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c56{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c57{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c60{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c61{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c6a{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c6b{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c74{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c7e{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c7f{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c88{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c89{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c92{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c93{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c94{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c9c{background-color:rgba(255, 255, 255, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9c9d{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9ca6{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9cb0{background-color:rgba(204, 220, 231, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9cb1{background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(255, 255, 255, 0.00);border-top: 0 solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(255, 255, 255, 0.00);border-right: 0 solid rgba(255, 255, 255, 0.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9cb2{background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(255, 255, 255, 0.00);border-top: 0 solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(255, 255, 255, 0.00);border-right: 0 solid rgba(255, 255, 255, 0.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df0a9cba{background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(255, 255, 255, 0.00);border-top: 0 solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(255, 255, 255, 0.00);border-right: 0 solid rgba(255, 255, 255, 0.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-df15662c'><thead><tr style="overflow-wrap:break-word;"><th class="cl-df0a9c06">Module</th><th class="cl-df0a9c1a">Topic</th><th class="cl-df0a9c24">1-on-1 Support (24/7 availability)</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c25">Pre-course</td><td class="cl-df0a9c2e">Installation troubleshooting</td><td class="cl-df0a9c2f">Preparation calls</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c38">1</td><td class="cl-df0a9c39">RStudio, basic R syntax</td><td rowspan="10"class="cl-df0a9c42">Unlimited tutoring on course material After-hours booking link provided by email</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c43">2</td><td class="cl-df0a9c4c">Data cleaning</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c43">3</td><td class="cl-df0a9c4c">More complex data cleaning</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c57">4</td><td class="cl-df0a9c60">Grouping and summarising data</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c6a">5</td><td class="cl-df0a9c6b">Data visualization with ggplot2</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c43">6</td><td class="cl-df0a9c4c">Troubleshooting and getting help</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c7e">7</td><td class="cl-df0a9c7f">Automated reports with R Markdown</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c57">8</td><td class="cl-df0a9c60">Transforming data with joins and pivots</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c89">9</td><td class="cl-df0a9c92">Public health plots: Heat plots, epi curves, age/sex pyramids, &amp; GIS demo</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9c94">10</td><td class="cl-df0a9c9c">COVID-19 case study</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df0a9ca6">Post-course</td><td class="cl-df0a9cb0">We help you apply R to your work. 1 hour coupon valid 12 months.*</td><td class="cl-df0a9c93">R Support Desk</td></tr></tbody><tfoot><tr style="overflow-wrap:break-word;"><td colspan="3"class="cl-df0a9cb1">*Coupon time and duration may vary by cohort. Additional time can be purchased.</td></tr></tfoot></table></div>

---
# Data used in this course

* **Module 1: Monitoring COVID-19 testing supplies**

* **Modules 2 - 9: Ebola outbreak case study**
     * Surveillance case linelist (primary dataset)  
     * Hospital records from 5 hospitals  
     * Case investigation dataset  
     * Lab results dataset  
     
* **Module 10: COVID-19 outbreak and population datasets**

.footnote[All course data are either anonymized/jittered or simulated.]

---
# Each module

- **Slides**: A brief explanation of new concepts & code

- **Demo**: Live coding demonstration of the new material

- **Exercises**: Online exercises guide you to write R code on your computer  
  * *Quiz questions* check your understanding  
  * *1-on-1 meetings* with instructors (request at any time)  
  * *Share your screen*, so we catch errors early and invite you to side room  
  * *It is OK to not finish*. Solutions are available in the course folder.  
  * *Take breaks* as you need  
  
- **Debrief**: A live coding review and tips from the instructors

- **Post-module**: Resources are available to you  
  * *Recordings* are on the course website  
  * *1-on-1 tutoring* on course material (booking link provided by email)

---
# Certificate

To receive a certificate of completion, you must:

1) **Attend 80% of the sessions** (or make them up with course tutoring)

2) **Complete the anonymous feedback survey**

3) **Submit an email to training@appliedepi.org** with:  
  * The link to your practice post in our community forum (Module 6)  
  * Your R script from the COVID-19 case study (Module 10)

---
# Agreement with each other

**Our team will:**

- Create a supportive & personalized learning space

- Appreciate your expertise

**We hope that you will:**

- Reach outside of your comfort zone *(you might discover a new passion!)*

- Tell us if you do not understand and catch-up if you miss a session

???
We are in this course to succeed, together

---
# This module

**Objectives**

Within an RStudio project, write basic R code to: 
 * Perform calculations 
 * Create and change objects 
 * Use functions 
 * Install and load packages 
 * Import and inspect a dataset

<div class="tabwid"><style>.cl-df546ce6{}.cl-df4306e0{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-df49c7fa{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-df49f324{width:1.033in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df49f32e{width:2.468in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 1.5pt solid rgba(102, 102, 102, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df49f32f{width:1.033in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df49f338{width:2.468in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df49f339{width:1.033in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df49f33a{width:2.468in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df49f342{width:1.033in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df49f34c{width:2.468in;background-color:transparent;vertical-align: middle;border-bottom: 1.5pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df49f34d{width:1.033in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(255, 255, 255, 0.00);border-top: 0 solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(255, 255, 255, 0.00);border-right: 0 solid rgba(255, 255, 255, 0.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-df49f34e{width:2.468in;background-color:transparent;vertical-align: middle;border-bottom: 0 solid rgba(255, 255, 255, 0.00);border-top: 0 solid rgba(255, 255, 255, 0.00);border-left: 0 solid rgba(255, 255, 255, 0.00);border-right: 0 solid rgba(255, 255, 255, 0.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-df546ce6'><thead><tr style="overflow-wrap:break-word;"><th class="cl-df49f324">Time</th><th class="cl-df49f32e">Topic</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-df49f32f">45 minutes</td><td class="cl-df49f338">Welcome &amp; course logistics</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df49f32f">30 minutes</td><td class="cl-df49f338">RStudio tour and basic R syntax</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df49f339">2 hours</td><td class="cl-df49f33a">Exercise</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-df49f342">15 minutes</td><td class="cl-df49f34c">Debrief</td></tr></tbody><tfoot><tr style="overflow-wrap:break-word;"><td colspan="2"class="cl-df49f34d">Take breaks as you wish during the exercise</td></tr></tfoot></table></div>

???
Note stretch breaks throughout.

---
# RStudio projects

.pull-left[

Your work occurs in **RStudio projects**.

A project is a **self-contained and portable R working environment**

They make your life immensely easier.

]

.pull-right[

This course is organized in 3 projects.

**Each project is a folder for a distinct outbreak or analysis**, containing data, scripts, outputs, and ".Rproj" file.

📂 intro_course
* 📁 **module1**  
  * module1.Rproj  
  * 📝 data.csv  
  * 📝 analysis.R  
* 📂 **ebola**  
  * ebola.Rproj  
* 📂 **covid**  
  * covid.Rproj

]

???
We will help 
You can zip the folder and share it with a colleague, it can be hosted on a shared drive, and can be synced with a Github repository.

---
class: inverse, center, middle

# Live demonstration

## RStudio and basic syntax

---
class: inverse, center, middle

.pull-left[
## Functions: 
## Tools to accomplish a specific task 
]

.pull-right[

]

---
# Functions   
### Inputs and outputs

- A function is like a machine that:  
     - Receives inputs
     - Does some action with the inputs  
     - Returns an output

- Functions have a name (*hopefully intuitive!*), and have parentheses ( )  
     * `print()` helps you print an R object
     * `mean()`  averages some values
     * `filter()` removes certain rows in a dataset using logical criteria

.footnote[functions also appear in Excel as *equations*]

---
# Does this look familiar?

R **functions** are similar to Excel **equations**

* They accept inputs within **parentheses** 
  * The inputs are separated by **commas**

---
# Simple R functions

.pull-left[

- `sqrt()`

* Accepts one numeric value as input, returns the square root

]

.pull-right[

```r
sqrt(49)
```

```
## [1] 7
```

]

.footnote[Accepts numeric values and returns the maximum]

???
Demonstrate each `sqrt(49)`, `sqrt(12)`, `max(1, 15, 2, 9)` (explain commas)
Explain vectors `c(1, 15, 2, 9)` and a named vector `cities <- c("Wuhan", "Milan", "New York")`
Quickly note indexed vectors `cities[[2]]`
and numeric: `ages <- c(15, 28, 100, 15, 65, 4, 10)` then `summary(ages)` and `summary(ages)[2]` and `summary(ages)[[2]]`

---
# Simple R functions

.pull-left[

- `sqrt()`  
  * Accepts one numeric value as input, returns the square root

- `max()`  
  * Accepts numeric values and returns the maximum

]

.pull-right[

```r
sqrt(49)
```

```
## [1] 7
```

```r
max(2, 10, 15, 200, 9)
```

```
## [1] 200
```

]

.footnote[These are examples of functions in "*base R*" - functions that come installed with R.]

---
# Simple R functions

.pull-left[

- `sqrt()` 
 * Accepts one numeric value as input, returns the square root

- `max()` 
 * Accepts numeric values and returns the maximum

- `c()`  
  * Shorthand for "concatenate"  
  * Combines inputs into a *vector*  
]

.pull-right[

```r
sqrt(49)
```

```
## [1] 7
```

```r
max(2, 10, 15, 200, 9)
```

```
## [1] 200
```

```r
c(2, 5, 9, 12, 47)
```

```
## [1]  2  5  9 12 47
```
]

---
# Arguments

.pull-left[

But most functions are not so simple.

They must be told *how* to work, and *on what* to work.

You use the function's **arguments** to specify these values.

Arguments are like inputs and settings, with *names*

]

.pull-right[

]

---

# This may look familiar

Once again, Excel is not so different from R: 
  * Arguments have names and are separated by commas  
  * Values can be numeric (12), character ("Apple"), or other objects (A1:A5)  
  * Some arguments are optional or have defaults

???
What is returned by this Excel equation?

---
# Baking example

Let us pretend that **`oven_bake()`** is a function used to bake bread.

What *arguments* might this function take?

Hint: Which *settings* must be adjusted? What *object* must be put in the oven?

---
# `tbl_cross()` example

.pull-left[

This dataset in R has the name **`surv`**.

We want a cross-tabulation of columns `case_def` and `sex`.

<div class="tabwid"><style>.cl-e0411dca{}.cl-e0346d3c{font-family:'Arial';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e0346d50{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e0399d7a{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e0399d8e{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e039ba8a{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039ba94{width:0.99in;background-color:rgba(255, 255, 0, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039ba95{width:0.744in;background-color:rgba(255, 255, 0, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039ba9e{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039ba9f{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039baa8{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039bab2{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039bab3{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039babc{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039bac6{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039bac7{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039bad0{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039bad1{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e039bad2{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-e0411dca'><thead><tr style="overflow-wrap:break-word;"><th class="cl-e039ba8a">case</th><th class="cl-e039ba94">case_def</th><th class="cl-e039ba95">sex</th><th class="cl-e039ba9e">age</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-e039ba9f">1</td><td class="cl-e039baa8">Confirmed</td><td class="cl-e039bab2">female</td><td class="cl-e039bab3">1</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e039babc">2</td><td class="cl-e039bac6">Confirmed</td><td class="cl-e039bac7">male</td><td class="cl-e039bad0">16</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e039ba8a">3</td><td class="cl-e039bad1">Suspect</td><td class="cl-e039bad2">female</td><td class="cl-e039ba9e">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e039ba8a">4</td><td class="cl-e039bad1">Suspect</td><td class="cl-e039bad2">female</td><td class="cl-e039ba9e">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e039babc">5</td><td class="cl-e039bac6">Confirmed</td><td class="cl-e039bac7">male</td><td class="cl-e039bad0">64</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e039babc">6</td><td class="cl-e039bac6">Confirmed</td><td class="cl-e039bac7">male</td><td class="cl-e039bad0">8</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e039babc">7</td><td class="cl-e039bac6">Confirmed</td><td class="cl-e039bac7">female</td><td class="cl-e039bad0">22</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e039babc">8</td><td class="cl-e039bac6">Confirmed</td><td class="cl-e039bac7">female</td><td class="cl-e039bad0">31</td></tr></tbody></table></div>

]

.pull-right[

The function `tbl_cross()` has three arguments:

```r
tbl_cross(data =, row =, col = )
```
]

---
# `tbl_cross()` example

.pull-left[

This dataset in R has the name **`surv`**.

We want a cross-tabulation of columns `case_def` and `sex`.

<div class="tabwid"><style>.cl-e0810692{}.cl-e0758c40{font-family:'Arial';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e0758c4a{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e079eb6e{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e079eb82{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e07a082e{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0838{width:0.99in;background-color:rgba(255, 255, 0, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0839{width:0.744in;background-color:rgba(255, 255, 0, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0842{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0843{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a084c{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0856{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0857{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0860{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0861{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a086a{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a086b{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0874{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e07a0875{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-e0810692'><thead><tr style="overflow-wrap:break-word;"><th class="cl-e07a082e">case</th><th class="cl-e07a0838">case_def</th><th class="cl-e07a0839">sex</th><th class="cl-e07a0842">age</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-e07a0843">1</td><td class="cl-e07a084c">Confirmed</td><td class="cl-e07a0856">female</td><td class="cl-e07a0857">1</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e07a0860">2</td><td class="cl-e07a0861">Confirmed</td><td class="cl-e07a086a">male</td><td class="cl-e07a086b">16</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e07a082e">3</td><td class="cl-e07a0874">Suspect</td><td class="cl-e07a0875">female</td><td class="cl-e07a0842">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e07a082e">4</td><td class="cl-e07a0874">Suspect</td><td class="cl-e07a0875">female</td><td class="cl-e07a0842">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e07a0860">5</td><td class="cl-e07a0861">Confirmed</td><td class="cl-e07a086a">male</td><td class="cl-e07a086b">64</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e07a0860">6</td><td class="cl-e07a0861">Confirmed</td><td class="cl-e07a086a">male</td><td class="cl-e07a086b">8</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e07a0860">7</td><td class="cl-e07a0861">Confirmed</td><td class="cl-e07a086a">female</td><td class="cl-e07a086b">22</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e07a0860">8</td><td class="cl-e07a0861">Confirmed</td><td class="cl-e07a086a">female</td><td class="cl-e07a086b">31</td></tr></tbody></table></div>

]

.pull-right[

The command can also be written more vertically, like this:

```r
tbl_cross(
  data = 
  row  =  
  col  =       )
```

]

---
# `tbl_cross()` example

.pull-left[

This dataset in R has the name **`surv`**.

We want a cross-tabulation of columns `case_def` and `sex`.

<div class="tabwid"><style>.cl-e0c2aac0{}.cl-e0b545a6{font-family:'Arial';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e0b545ba{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e0baddb8{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e0baddcc{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e0bb0572{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb0586{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb0587{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb0590{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb059a{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb059b{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb05a4{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb05a5{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb05a6{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb05ae{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb05af{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e0bb05b8{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-e0c2aac0'><thead><tr style="overflow-wrap:break-word;"><th class="cl-e0bb0572">case</th><th class="cl-e0bb0586">case_def</th><th class="cl-e0bb0587">sex</th><th class="cl-e0bb0590">age</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-e0bb059a">1</td><td class="cl-e0bb059b">Confirmed</td><td class="cl-e0bb05a4">female</td><td class="cl-e0bb05a5">1</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e0bb05a6">2</td><td class="cl-e0bb05ae">Confirmed</td><td class="cl-e0bb05af">male</td><td class="cl-e0bb05b8">16</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e0bb0572">3</td><td class="cl-e0bb0586">Suspect</td><td class="cl-e0bb0587">female</td><td class="cl-e0bb0590">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e0bb0572">4</td><td class="cl-e0bb0586">Suspect</td><td class="cl-e0bb0587">female</td><td class="cl-e0bb0590">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e0bb05a6">5</td><td class="cl-e0bb05ae">Confirmed</td><td class="cl-e0bb05af">male</td><td class="cl-e0bb05b8">64</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e0bb05a6">6</td><td class="cl-e0bb05ae">Confirmed</td><td class="cl-e0bb05af">male</td><td class="cl-e0bb05b8">8</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e0bb05a6">7</td><td class="cl-e0bb05ae">Confirmed</td><td class="cl-e0bb05af">female</td><td class="cl-e0bb05b8">22</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e0bb05a6">8</td><td class="cl-e0bb05ae">Confirmed</td><td class="cl-e0bb05af">female</td><td class="cl-e0bb05b8">31</td></tr></tbody></table></div>

]

.pull-right[

The dataset that we want to use is named **surv**

```r
tbl_cross(
* data = surv,
  row  =  
  col  =    )
```

*In R, you must tell R which dataset to use, because you can store multiple*.

]

---
# `tbl_cross()` example

.pull-left[

This dataset in R has the name **`surv`**.

We want a cross-tabulation of columns `case_def` and `sex`.

<div class="tabwid"><style>.cl-e1066d64{}.cl-e0fd0346{font-family:'Arial';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e0fd0350{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e100d926{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e100d93a{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e100f258{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f262{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f263{width:0.744in;background-color:rgba(255, 255, 0, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f26c{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f26d{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f276{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f277{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f278{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f280{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f281{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f282{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f28a{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e100f28b{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-e1066d64'><thead><tr style="overflow-wrap:break-word;"><th class="cl-e100f258">case</th><th class="cl-e100f262">case_def</th><th class="cl-e100f263">sex</th><th class="cl-e100f26c">age</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-e100f26d">1</td><td class="cl-e100f276">Confirmed</td><td class="cl-e100f277">female</td><td class="cl-e100f278">1</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e100f280">2</td><td class="cl-e100f281">Confirmed</td><td class="cl-e100f282">male</td><td class="cl-e100f28a">16</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e100f258">3</td><td class="cl-e100f262">Suspect</td><td class="cl-e100f28b">female</td><td class="cl-e100f26c">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e100f258">4</td><td class="cl-e100f262">Suspect</td><td class="cl-e100f28b">female</td><td class="cl-e100f26c">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e100f280">5</td><td class="cl-e100f281">Confirmed</td><td class="cl-e100f282">male</td><td class="cl-e100f28a">64</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e100f280">6</td><td class="cl-e100f281">Confirmed</td><td class="cl-e100f282">male</td><td class="cl-e100f28a">8</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e100f280">7</td><td class="cl-e100f281">Confirmed</td><td class="cl-e100f282">female</td><td class="cl-e100f28a">22</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e100f280">8</td><td class="cl-e100f281">Confirmed</td><td class="cl-e100f282">female</td><td class="cl-e100f28a">31</td></tr></tbody></table></div>

]

.pull-right[

The *rows* of the cross-table should come from the column **`sex`**

```r
tbl_cross(
  data = surv,
* row  = sex,  
  col  =    )
```

]

---
# `tbl_cross()` example

.pull-left[

This dataset in R has the name **`surv`**.

We want a cross-tabulation of columns `case_def` and `sex`.

<div class="tabwid"><style>.cl-e1319124{}.cl-e1289808{font-family:'Arial';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e1289812{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e12c60a0{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e12c60b4{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e12c7bda{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7be4{width:0.99in;background-color:rgba(255, 255, 0, 1.00);vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7bee{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7bef{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7bf8{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7c02{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7c03{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7c0c{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7c0d{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7c16{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7c20{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7c2a{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e12c7c34{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-e1319124'><thead><tr style="overflow-wrap:break-word;"><th class="cl-e12c7bda">case</th><th class="cl-e12c7be4">case_def</th><th class="cl-e12c7bee">sex</th><th class="cl-e12c7bef">age</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-e12c7bf8">1</td><td class="cl-e12c7c02">Confirmed</td><td class="cl-e12c7c03">female</td><td class="cl-e12c7c0c">1</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e12c7c0d">2</td><td class="cl-e12c7c16">Confirmed</td><td class="cl-e12c7c20">male</td><td class="cl-e12c7c2a">16</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e12c7bda">3</td><td class="cl-e12c7c34">Suspect</td><td class="cl-e12c7bee">female</td><td class="cl-e12c7bef">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e12c7bda">4</td><td class="cl-e12c7c34">Suspect</td><td class="cl-e12c7bee">female</td><td class="cl-e12c7bef">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e12c7c0d">5</td><td class="cl-e12c7c16">Confirmed</td><td class="cl-e12c7c20">male</td><td class="cl-e12c7c2a">64</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e12c7c0d">6</td><td class="cl-e12c7c16">Confirmed</td><td class="cl-e12c7c20">male</td><td class="cl-e12c7c2a">8</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e12c7c0d">7</td><td class="cl-e12c7c16">Confirmed</td><td class="cl-e12c7c20">female</td><td class="cl-e12c7c2a">22</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e12c7c0d">8</td><td class="cl-e12c7c16">Confirmed</td><td class="cl-e12c7c20">female</td><td class="cl-e12c7c2a">31</td></tr></tbody></table></div>

]

.pull-right[

The *columns* of the cross-table should come from the column **`case_def`**

```r
tbl_cross(
  data = surv,
  row  = sex,  
* col  = case_def)
```

]

---
# `tbl_cross()` example

.pull-left[

This dataset in R has the name **`surv`**.

We want a cross-tabulation of columns `case_def` and `sex`.

<div class="tabwid"><style>.cl-e15fc530{}.cl-e15593d0{font-family:'Arial';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e15593da{font-family:'Arial';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-e15a0898{margin:0;text-align:right;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e15a08ac{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0 solid rgba(0, 0, 0, 1.00);border-right: 0 solid rgba(0, 0, 0, 1.00);padding-bottom:5pt;padding-top:5pt;padding-left:5pt;padding-right:5pt;line-height: 1;background-color:transparent;}.cl-e15a218e{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a2198{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a2199{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a21a2{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a21ac{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a21ad{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a21ae{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a21b6{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0 solid rgba(0, 0, 0, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a21b7{width:0.608in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a21b8{width:0.99in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a21c0{width:0.744in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}.cl-e15a21ca{width:0.54in;background-color:transparent;vertical-align: middle;border-bottom: 0.75pt solid rgba(102, 102, 102, 1.00);border-top: 0.75pt solid rgba(102, 102, 102, 1.00);border-left: 0.75pt solid rgba(102, 102, 102, 1.00);border-right: 0.75pt solid rgba(102, 102, 102, 1.00);margin-bottom:0;margin-top:0;margin-left:0;margin-right:0;}</style><table data-quarto-disable-processing='true' class='cl-e15fc530'><thead><tr style="overflow-wrap:break-word;"><th class="cl-e15a218e">case</th><th class="cl-e15a2198">case_def</th><th class="cl-e15a2199">sex</th><th class="cl-e15a21a2">age</th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-e15a21ac">1</td><td class="cl-e15a21ad">Confirmed</td><td class="cl-e15a21ae">female</td><td class="cl-e15a21b6">1</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e15a21b7">2</td><td class="cl-e15a21b8">Confirmed</td><td class="cl-e15a21c0">male</td><td class="cl-e15a21ca">16</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e15a218e">3</td><td class="cl-e15a2198">Suspect</td><td class="cl-e15a2199">female</td><td class="cl-e15a21a2">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e15a218e">4</td><td class="cl-e15a2198">Suspect</td><td class="cl-e15a2199">female</td><td class="cl-e15a21a2">10</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e15a21b7">5</td><td class="cl-e15a21b8">Confirmed</td><td class="cl-e15a21c0">male</td><td class="cl-e15a21ca">64</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e15a21b7">6</td><td class="cl-e15a21b8">Confirmed</td><td class="cl-e15a21c0">male</td><td class="cl-e15a21ca">8</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e15a21b7">7</td><td class="cl-e15a21b8">Confirmed</td><td class="cl-e15a21c0">female</td><td class="cl-e15a21ca">22</td></tr><tr style="overflow-wrap:break-word;"><td class="cl-e15a21b7">8</td><td class="cl-e15a21b8">Confirmed</td><td class="cl-e15a21c0">female</td><td class="cl-e15a21ca">31</td></tr></tbody></table></div>

]

.pull-right[

Now we run the command to create the cross-table

```r
tbl_cross(
  data = surv,
  row  = sex,  
  col  = case_def)
```

<div id="wmxvwcnhof" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;">
<style>#wmxvwcnhof table {
 font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji';
 -webkit-font-smoothing: antialiased;
 -moz-osx-font-smoothing: grayscale;
}

#wmxvwcnhof thead, #wmxvwcnhof tbody, #wmxvwcnhof tfoot, #wmxvwcnhof tr, #wmxvwcnhof td, #wmxvwcnhof th {
  border-style: none;
}

#wmxvwcnhof p {
  margin: 0;
  padding: 0;
}

#wmxvwcnhof .gt_table {
  display: table;
  border-collapse: collapse;
  line-height: normal;
  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;
}

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

#wmxvwcnhof .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;
}

#wmxvwcnhof .gt_subtitle {
  color: #333333;
  font-size: 85%;
  font-weight: initial;
  padding-top: 3px;
  padding-bottom: 5px;
  padding-left: 5px;
  padding-right: 5px;
  border-top-color: #FFFFFF;
  border-top-width: 0;
}

#wmxvwcnhof .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;
}

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

#wmxvwcnhof .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;
}

#wmxvwcnhof .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;
}

#wmxvwcnhof .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;
}

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

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

#wmxvwcnhof .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%;
}

#wmxvwcnhof .gt_spanner_row {
  border-bottom-style: hidden;
}

#wmxvwcnhof .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;
}

#wmxvwcnhof .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;
}

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

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

#wmxvwcnhof .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;
}

#wmxvwcnhof .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;
}

#wmxvwcnhof .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;
}

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

#wmxvwcnhof .gt_row_group_first th {
  border-top-width: 2px;
}

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

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

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

#wmxvwcnhof .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;
}

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

#wmxvwcnhof .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;
}

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

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

#wmxvwcnhof .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;
}

#wmxvwcnhof .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;
}

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

#wmxvwcnhof .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;
}

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

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

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

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

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

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

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

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

#wmxvwcnhof .gt_footnote_marks {
  font-size: 75%;
  vertical-align: 0.4em;
  position: initial;
}

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

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

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

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

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

#wmxvwcnhof .gt_indent_5 {
 text-indent: 25px;
}
</style>
<table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false">
 <thead>
 
 <tr class="gt_col_headings gt_spanner_row">
 <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="2" colspan="1" scope="col" id=""></th>
 <th class="gt_center gt_columns_top_border gt_column_spanner_outer" rowspan="1" colspan="2" scope="colgroup" id="case_def">
 case_def
 </th>
 <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="2" colspan="1" scope="col" id="Total">Total</th>
 </tr>
 <tr class="gt_col_headings">
 <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="Confirmed">Confirmed</th>
 <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="Suspect">Suspect</th>
 </tr>
 </thead>
 <tbody class="gt_table_body">
 <tr><td headers="label" class="gt_row gt_left">sex</td>
<td headers="stat_1" class="gt_row gt_center"></td>
<td headers="stat_2" class="gt_row gt_center"></td>
<td headers="stat_0" class="gt_row gt_center"></td></tr>
 <tr><td headers="label" class="gt_row gt_left">    female</td>
<td headers="stat_1" class="gt_row gt_center">3</td>
<td headers="stat_2" class="gt_row gt_center">2</td>
<td headers="stat_0" class="gt_row gt_center">5</td></tr>
 <tr><td headers="label" class="gt_row gt_left">    male</td>
<td headers="stat_1" class="gt_row gt_center">3</td>
<td headers="stat_2" class="gt_row gt_center">0</td>
<td headers="stat_0" class="gt_row gt_center">3</td></tr>
 <tr><td headers="label" class="gt_row gt_left">Total</td>
<td headers="stat_1" class="gt_row gt_center">6</td>
<td headers="stat_2" class="gt_row gt_center">2</td>
<td headers="stat_0" class="gt_row gt_center">8</td></tr>
 </tbody>
 
 
</table>
</div>

]

---
# Packages

.pull-left[

The functions `sqrt()`, `sum()`, `max()`, `min()` and `c()` are ready-to-use when you install R.

These are called **{base} R** functions.

]

.pull-right[

However, most functions must be downloaded with their **R package**.

For example, `tbl_cross()` is contained in the R package named {gtsummary}.

R packages are often referred to in {brackets} and have "hex" logos.

]

---

# Packages

An R package is a **shareable bundle of related functions** to download and use.  
Packages typically have a theme, for example:

* **{ggplot2}** is the most common data visualization package  
* **{lubridate}** makes it easier to work with dates  
* **{janitor}** helps clean and summarize data  
* **{rmarkdown}** helps you make automated reports

---
# Install vs. Load

.pull-left[

**Step 1 - Install**

A package is **installed once** and stored in your R “library”.

*The package is like a "book" of functions.*

]

.pull-right[

**Step 2 - Load**

Begin **every R session** by loading the packages you want to use.

*Like borrowing a book from your library*.

]

---
# The {pacman} package

Using R is often a choice between approaches. We are here to coach you.

.pull-left[

**The traditional "base R" approach**

```r
install.packages("janitor") 
library(janitor) # loads            
```

* Re-installs every time run  
* Multiple commands  
* Difficult syntax  
* Rarely necessary

]

.pull-right[

**The efficient "pacman" approach**

```r
pacman::p_load(janitor)
```

* Installs packages *only if necessary*, **and** loads them  
* Good for shared scripts  
* {pacman} = **pac**kage **man**ager  
* Requires the {pacman} package

]

---
# Which code is more simple?

These commands install and load the same 5 packages.

.pull-left[

Using {base} R functions

```r
# install the packages
install.packages(
     c("rio",
       "janitor",
       "gtsummary",
       "here",
       "tidyverse"))

# load the packages for use
library(rio)
library(janitor)
library(gtsummary)
library(here)
library(tidyverse)
```

]

.pull-right[

Using {pacman}

```r
# install if necessary, and load
pacman::p_load(
  rio,
  janitor,
  gtsummary,
  here,
  tidyverse)
```

]

???
This is common R, where there are many ways do a task. Our job is boil it all down and share with you the easiest and most simple approaches.

---
class: inverse, center, middle
# Importing data into R

---
# Smoothly importing data

Recent advancements have made importing data into R much easier:

* **RStudio projects**  
* The **`import()`** function from the **{rio}** package  
* The **{here}** package

In this module you will use **`import()`** to import data from your **RStudio project**.

In the next module we will discuss **{here}**.

---
# Using `import()`

The **`import()`** function uses the file extension (.csv, .xlsx) to understand the data type. This avoids past confusion e.g. `read_csv()`, `read.csv()`, `read_excel()`...

.pull-left[

```r
import("testing_data.csv")
```

For a file in the project "root" folder,
no other information is needed... and it works on any computer!

<img src="../../images/functions_packages/import_root.png" width="100%" />
 
.footnote[Other importing scenarios are addressed in the next module]

]

.pull-right[

`import()` is from the {rio} package, 
shorthand for "**R** **I**nputs/**O**utputs"

]

---
class: inverse, center, middle

## Exercise!

In the course website, open the exercise for Module 1 and login  
Follow instructions to create an RStudio project and begin coding  
Notify us if you cannot login or are unsure what to do