class: center, middle, inverse, title-slide <style type="text/css"> .remark-slide table{ border: none } .remark-slide-table { } tr:first-child { border-top: none; } tr:last-child { border-bottom: none; } </style> # Introduction to R for</br> 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. <img src="../../images/team.png" alt="" width="100%" /> ??? 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" alt="" 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! <img src="../../images/moz-banner.png" alt="" width="75%" height="75%" /> --- # The Epidemiologist R Handbook <img src="../../images/welcome/Epi R Handbook Banner Beige 1500x500.png" alt="" width="75%" /> - 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"* <br> - Epidemiologist, Nigeria CDC > *"[It] weaves together so much, so succinctly, and so incredibly clearly"* <br> - 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**!” <br> -*Epi Advisor</br>Doctors without Borders* Used by hundreds of agencies including the Uganda Ministry of Health for Ebola response. ] .pull-right[ <img src="../../images/welcome/headphones.jpg" alt="" width="100%" height="75%" /> ] --- class: inverse, center, middle # Why learn R? --- # Learning R... ## ...is really useful <img src="../../images/welcome/stop_epidemic_dominoes2.png" alt="" width="75%" /> ??? Mention marketable skill as well as technically for epidemic response --- # Learning R... ## ...is freeing <img src="../../images/welcome/freedom_bird.png" alt="" width="50%" /> --- # Learning R... ## ...can be hard work <img src="../../images/welcome/missing_puzzle.png" alt="" width="50%" /> --- # Learning R... ## ...gives moments of pure joy <img src="../../images/welcome/joy.png" alt="" width="75%" /> --- # 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[ <img src="../../images/welcome/tidyverse-icons.png" alt="" width="80%" /> ] ??? - 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 <img src="../../images/welcome/interoperability.png" alt="" width="80%" /> ??? - 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!" </br> - Course graduate, Haiti ] .pull-right[ <img src="../../images/welcome/automated_reports.png" alt="" width="344" height="80%" /> ] .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 <img src="../../images/welcome/visualization.png" alt="" width="90%" /> ??? - 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 <img src="../../images/welcome/artistic.png" alt="" width="100%" /> ??? Many people think about coding as creating artwork... for example creating pottery, writing poems, painting, etc. --- # Learning R... ## ...with a community of millions <img src="../../images/welcome/communities.png" alt="" width="100%" /> ??? - 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-a3c08398{table-layout:auto;}.cl-a3bce7a6{font-family:'Helvetica';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a3bce7ba{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a3be49fc{margin:0;text-align:left;border-bottom: 0 solid rgba(0, 0, 0, 1.00);border-top: 0 solid rgba(0, 0, 0, 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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-a3be5960{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-a3be5961{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-a3be596a{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-a3be596b{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-a3be596c{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-a3c08398'><thead><tr style="overflow-wrap:break-word;"><th class="cl-a3be5866"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">Module</span></p></th><th class="cl-a3be5870"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">Topic</span></p></th><th class="cl-a3be5871"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">1-on-1 Support</span><br><span class="cl-a3bce7a6">(24/7 availability)</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-a3be587a"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">Pre-course</span></p></td><td class="cl-a3be5884"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Installation troubleshooting</span></p></td><td class="cl-a3be5885"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Preparation calls</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be5886"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">1</span></p></td><td class="cl-a3be588e"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">RStudio, basic R syntax</span></p></td><td rowspan="10"class="cl-a3be58ac"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Unlimited tutoring</span><br><span class="cl-a3bce7ba">on course material</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be58b6"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">2</span></p></td><td class="cl-a3be58c0"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Data cleaning</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be58d4"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">3</span></p></td><td class="cl-a3be58de"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">More complex data cleaning</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be58e8"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">4</span></p></td><td class="cl-a3be58f2"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Grouping and summarising data</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be58d4"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">5</span></p></td><td class="cl-a3be58de"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Data visualization with ggplot2</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be58d4"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">6</span></p></td><td class="cl-a3be58de"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Troubleshooting and getting help</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be58f4"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">7</span></p></td><td class="cl-a3be58fc"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Automated reports with R Markdown</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be5906"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">8</span></p></td><td class="cl-a3be5907"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Transforming data with joins and pivots</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be591a"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">9</span></p></td><td class="cl-a3be5924"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">Public health plots: Heat plots, epi curves,</span><br><span class="cl-a3bce7ba">age/sex pyramids, &amp; GIS demo</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be5942"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">10</span></p></td><td class="cl-a3be5943"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">COVID-19 case study</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3be5956"><p class="cl-a3be49fc"><span class="cl-a3bce7a6">Post-course</span></p></td><td class="cl-a3be5960"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">We help you apply R to your work.</span><br><span class="cl-a3bce7ba">1 hour coupon valid 6 months.*</span></p></td><td class="cl-a3be5961"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">R Code Review</span></p></td></tr></tbody><tfoot><tr style="overflow-wrap:break-word;"><td colspan="3"class="cl-a3be596a"><p class="cl-a3be49fc"><span class="cl-a3bce7ba">*Booking code duration may vary by cohort. Additional time can be purchased.</span></p></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 --- # 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 </br> <div class="tabwid"><style>.cl-a3d7c238{}.cl-a3d35478{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a3d53716{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-a3d54922{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-a3d54940{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-a3d5494a{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-a3d54954{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-a3d54968{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-a3d5497c{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-a3d54990{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-a3d549ae{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-a3d549cc{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-a3d549e0{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-a3d549f4{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-a3d549fe{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-a3d7c238'><thead><tr style="overflow-wrap:break-word;"><th class="cl-a3d54922"><p class="cl-a3d53716"><span class="cl-a3d35478">Time</span></p></th><th class="cl-a3d54940"><p class="cl-a3d53716"><span class="cl-a3d35478">Topic</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-a3d5494a"><p class="cl-a3d53716"><span class="cl-a3d35478">45 minutes</span></p></td><td class="cl-a3d54954"><p class="cl-a3d53716"><span class="cl-a3d35478">Welcome &amp; course logistics</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3d54968"><p class="cl-a3d53716"><span class="cl-a3d35478">30 minutes</span></p></td><td class="cl-a3d5497c"><p class="cl-a3d53716"><span class="cl-a3d35478">RStudio tour and basic R syntax</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3d54990"><p class="cl-a3d53716"><span class="cl-a3d35478">2 hours</span></p></td><td class="cl-a3d549ae"><p class="cl-a3d53716"><span class="cl-a3d35478">Exercise</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3d549cc"><p class="cl-a3d53716"><span class="cl-a3d35478">15 minutes</span></p></td><td class="cl-a3d549e0"><p class="cl-a3d53716"><span class="cl-a3d35478">Debrief</span></p></td></tr></tbody><tfoot><tr style="overflow-wrap:break-word;"><td colspan="2"class="cl-a3d549f4"><p class="cl-a3d53716"><span class="cl-a3d35478">Take breaks as you wish during the exercise</span></p></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. <img src="../../images/functions_packages/project_briefcase.png" alt="" width="85%" /> ] -- .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 <img src="../../images/functions_packages/piano_man.jpg" alt="" width="50%" /> --- class: inverse, center, middle .pull-left[ ## Functions: ## Tools to accomplish a specific task ] .pull-right[ <img src="../../images/functions_packages/function_tools_pliers.png" alt="" width="75%" /> ] --- # 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? <img src="../../images/functions_packages/excel_functions.png" alt="" width="50%" /> 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[These are examples of functions in "*base R*" - functions that come installed with R.] ??? 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 ``` <br> ``` r max(2, 10, 15, 200, 9) ``` ``` ## [1] 200 ``` ] .footnote[These are examples of functions in "*base R*" - functions that come installed with R.] ??? 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 <br> - `max()` * Accepts numeric values and returns the maximum <br> - `c()` * Shorthand for "concatenate" * Combines inputs into a *vector* ] .pull-right[ ``` r sqrt(49) ``` ``` ## [1] 7 ``` <br> ``` r max(2, 10, 15, 200, 9) ``` ``` ## [1] 200 ``` ``` r c(2, 5, 9, 12, 47) ``` ``` ## [1] 2 5 9 12 47 ``` ] .footnote[These are examples of functions in "*base R*" - functions that come installed with R.] ??? 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]]` --- # Arguments .pull-left[ But most functions are not so simple. </br> They must be told *how* to work, and *on what* to work. </br> You use the function's **arguments** to specify these values. </br> Arguments are like inputs and settings, with *names* ] .pull-right[ <img src="../../images/functions_packages/arguments-buttons.png" alt="" width="100%" /> ] --- # This may look familiar <img src="../../images/functions_packages/excel_arguments.png" alt="" width="50%" /> 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? -- <img src="../../images/functions_packages/Function_Bread_Example_en.png" alt="" width="100%" /> --- # `tbl_cross()` example .pull-left[ This dataset in R has the name **`surv`**. 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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-a3f023c8{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-a3f023dc{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-a3f023e6{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-a3f023e7{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-a3f244d2'><thead><tr style="overflow-wrap:break-word;"><th class="cl-a3f02332"><p class="cl-a3f014b4"><span class="cl-a3eeb7a4">case</span></p></th><th class="cl-a3f0233c"><p class="cl-a3f014b5"><span class="cl-a3eeb7a4">case_def</span></p></th><th class="cl-a3f02350"><p class="cl-a3f014b5"><span class="cl-a3eeb7a4">sex</span></p></th><th class="cl-a3f0235a"><p class="cl-a3f014b4"><span class="cl-a3eeb7a4">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-a3f02364"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">1</span></p></td><td class="cl-a3f02378"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">Confirmed</span></p></td><td class="cl-a3f02379"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">female</span></p></td><td class="cl-a3f0238c"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3f023a0"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">2</span></p></td><td class="cl-a3f023a1"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">Confirmed</span></p></td><td class="cl-a3f023aa"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">male</span></p></td><td class="cl-a3f023ab"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3f023c8"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">3</span></p></td><td class="cl-a3f023dc"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">Suspect</span></p></td><td class="cl-a3f023e6"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">female</span></p></td><td class="cl-a3f023e7"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3f023c8"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">4</span></p></td><td class="cl-a3f023dc"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">Suspect</span></p></td><td class="cl-a3f023e6"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">female</span></p></td><td class="cl-a3f023e7"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3f023a0"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">5</span></p></td><td class="cl-a3f023a1"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">Confirmed</span></p></td><td class="cl-a3f023aa"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">male</span></p></td><td class="cl-a3f023ab"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3f023a0"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">6</span></p></td><td class="cl-a3f023a1"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">Confirmed</span></p></td><td class="cl-a3f023aa"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">male</span></p></td><td class="cl-a3f023ab"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3f023a0"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">7</span></p></td><td class="cl-a3f023a1"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">Confirmed</span></p></td><td class="cl-a3f023aa"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">female</span></p></td><td class="cl-a3f023ab"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3f023a0"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">8</span></p></td><td class="cl-a3f023a1"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">Confirmed</span></p></td><td class="cl-a3f023aa"><p class="cl-a3f014b5"><span class="cl-a3eeb7d6">female</span></p></td><td class="cl-a3f023ab"><p class="cl-a3f014b4"><span class="cl-a3eeb7d6">31</span></p></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-a3ffe060{}.cl-a3fc6ade{font-family:'Helvetica';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a3fc6afc{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a3fdbe66{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-a3fdbe98{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-a3fdcc94{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-a3fdcc95{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-a3fdccb2{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-a3fdccc6{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-a3fdccc7{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-a3fdccd0{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-a3fdccd1{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-a3fdcce4{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-a3fdcce5{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-a3fdccee{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-a3fdccf8{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-a3fdcd02{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-a3fdcd0c{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-a3fdcd16{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-a3fdcd20{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-a3fdcd2a{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-a3ffe060'><thead><tr style="overflow-wrap:break-word;"><th class="cl-a3fdcc94"><p class="cl-a3fdbe66"><span class="cl-a3fc6ade">case</span></p></th><th class="cl-a3fdcc95"><p class="cl-a3fdbe98"><span class="cl-a3fc6ade">case_def</span></p></th><th class="cl-a3fdccb2"><p class="cl-a3fdbe98"><span class="cl-a3fc6ade">sex</span></p></th><th class="cl-a3fdccc6"><p class="cl-a3fdbe66"><span class="cl-a3fc6ade">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-a3fdccc7"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">1</span></p></td><td class="cl-a3fdccd0"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">Confirmed</span></p></td><td class="cl-a3fdccd1"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">female</span></p></td><td class="cl-a3fdcce4"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3fdcce5"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">2</span></p></td><td class="cl-a3fdccee"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">Confirmed</span></p></td><td class="cl-a3fdccf8"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">male</span></p></td><td class="cl-a3fdcd02"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3fdcd0c"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">3</span></p></td><td class="cl-a3fdcd16"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">Suspect</span></p></td><td class="cl-a3fdcd20"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">female</span></p></td><td class="cl-a3fdcd2a"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3fdcd0c"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">4</span></p></td><td class="cl-a3fdcd16"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">Suspect</span></p></td><td class="cl-a3fdcd20"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">female</span></p></td><td class="cl-a3fdcd2a"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3fdcce5"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">5</span></p></td><td class="cl-a3fdccee"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">Confirmed</span></p></td><td class="cl-a3fdccf8"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">male</span></p></td><td class="cl-a3fdcd02"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3fdcce5"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">6</span></p></td><td class="cl-a3fdccee"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">Confirmed</span></p></td><td class="cl-a3fdccf8"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">male</span></p></td><td class="cl-a3fdcd02"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3fdcce5"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">7</span></p></td><td class="cl-a3fdccee"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">Confirmed</span></p></td><td class="cl-a3fdccf8"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">female</span></p></td><td class="cl-a3fdcd02"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a3fdcce5"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">8</span></p></td><td class="cl-a3fdccee"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">Confirmed</span></p></td><td class="cl-a3fdccf8"><p class="cl-a3fdbe98"><span class="cl-a3fc6afc">female</span></p></td><td class="cl-a3fdcd02"><p class="cl-a3fdbe66"><span class="cl-a3fc6afc">31</span></p></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-a40dc748{}.cl-a40a29c6{font-family:'Helvetica';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a40a29f8{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a40b8b4a{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-a40b8b68{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-a40b9982{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-a40b9996{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-a40b99a0{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-a40b99a1{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-a40b99aa{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-a40b99b4{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-a40b99d2{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-a40b99e6{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-a40b99fa{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-a40b99fb{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-a40b99fc{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-a40b9a04{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-a40b9a05{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-a40b9a18{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-a40b9a2c{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-a40b9a36{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-a40dc748'><thead><tr style="overflow-wrap:break-word;"><th class="cl-a40b9982"><p class="cl-a40b8b4a"><span class="cl-a40a29c6">case</span></p></th><th class="cl-a40b9996"><p class="cl-a40b8b68"><span class="cl-a40a29c6">case_def</span></p></th><th class="cl-a40b99a0"><p class="cl-a40b8b68"><span class="cl-a40a29c6">sex</span></p></th><th class="cl-a40b99a1"><p class="cl-a40b8b4a"><span class="cl-a40a29c6">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-a40b99aa"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">1</span></p></td><td class="cl-a40b99b4"><p class="cl-a40b8b68"><span class="cl-a40a29f8">Confirmed</span></p></td><td class="cl-a40b99d2"><p class="cl-a40b8b68"><span class="cl-a40a29f8">female</span></p></td><td class="cl-a40b99e6"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a40b99fa"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">2</span></p></td><td class="cl-a40b99fb"><p class="cl-a40b8b68"><span class="cl-a40a29f8">Confirmed</span></p></td><td class="cl-a40b99fc"><p class="cl-a40b8b68"><span class="cl-a40a29f8">male</span></p></td><td class="cl-a40b9a04"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a40b9a05"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">3</span></p></td><td class="cl-a40b9a18"><p class="cl-a40b8b68"><span class="cl-a40a29f8">Suspect</span></p></td><td class="cl-a40b9a2c"><p class="cl-a40b8b68"><span class="cl-a40a29f8">female</span></p></td><td class="cl-a40b9a36"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a40b9a05"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">4</span></p></td><td class="cl-a40b9a18"><p class="cl-a40b8b68"><span class="cl-a40a29f8">Suspect</span></p></td><td class="cl-a40b9a2c"><p class="cl-a40b8b68"><span class="cl-a40a29f8">female</span></p></td><td class="cl-a40b9a36"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a40b99fa"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">5</span></p></td><td class="cl-a40b99fb"><p class="cl-a40b8b68"><span class="cl-a40a29f8">Confirmed</span></p></td><td class="cl-a40b99fc"><p class="cl-a40b8b68"><span class="cl-a40a29f8">male</span></p></td><td class="cl-a40b9a04"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a40b99fa"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">6</span></p></td><td class="cl-a40b99fb"><p class="cl-a40b8b68"><span class="cl-a40a29f8">Confirmed</span></p></td><td class="cl-a40b99fc"><p class="cl-a40b8b68"><span class="cl-a40a29f8">male</span></p></td><td class="cl-a40b9a04"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a40b99fa"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">7</span></p></td><td class="cl-a40b99fb"><p class="cl-a40b8b68"><span class="cl-a40a29f8">Confirmed</span></p></td><td class="cl-a40b99fc"><p class="cl-a40b8b68"><span class="cl-a40a29f8">female</span></p></td><td class="cl-a40b9a04"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a40b99fa"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">8</span></p></td><td class="cl-a40b99fb"><p class="cl-a40b8b68"><span class="cl-a40a29f8">Confirmed</span></p></td><td class="cl-a40b99fc"><p class="cl-a40b8b68"><span class="cl-a40a29f8">female</span></p></td><td class="cl-a40b9a04"><p class="cl-a40b8b4a"><span class="cl-a40a29f8">31</span></p></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-a41bc2a8{}.cl-a4183142{font-family:'Helvetica';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a418314c{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a41995fa{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-a4199618{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-a419a48c{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-a419a4a0{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-a419a4b4{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-a419a4d2{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-a419a4d3{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-a419a4f0{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-a419a4f1{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-a419a4fa{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-a419a4fb{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-a419a50e{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-a419a50f{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-a419a522{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-a419a536{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-a419a540{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-a419a54a{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-a419a54b{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-a41bc2a8'><thead><tr style="overflow-wrap:break-word;"><th class="cl-a419a48c"><p class="cl-a41995fa"><span class="cl-a4183142">case</span></p></th><th class="cl-a419a4a0"><p class="cl-a4199618"><span class="cl-a4183142">case_def</span></p></th><th class="cl-a419a4b4"><p class="cl-a4199618"><span class="cl-a4183142">sex</span></p></th><th class="cl-a419a4d2"><p class="cl-a41995fa"><span class="cl-a4183142">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-a419a4d3"><p class="cl-a41995fa"><span class="cl-a418314c">1</span></p></td><td class="cl-a419a4f0"><p class="cl-a4199618"><span class="cl-a418314c">Confirmed</span></p></td><td class="cl-a419a4f1"><p class="cl-a4199618"><span class="cl-a418314c">female</span></p></td><td class="cl-a419a4fa"><p class="cl-a41995fa"><span class="cl-a418314c">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a419a4fb"><p class="cl-a41995fa"><span class="cl-a418314c">2</span></p></td><td class="cl-a419a50e"><p class="cl-a4199618"><span class="cl-a418314c">Confirmed</span></p></td><td class="cl-a419a50f"><p class="cl-a4199618"><span class="cl-a418314c">male</span></p></td><td class="cl-a419a522"><p class="cl-a41995fa"><span class="cl-a418314c">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a419a536"><p class="cl-a41995fa"><span class="cl-a418314c">3</span></p></td><td class="cl-a419a540"><p class="cl-a4199618"><span class="cl-a418314c">Suspect</span></p></td><td class="cl-a419a54a"><p class="cl-a4199618"><span class="cl-a418314c">female</span></p></td><td class="cl-a419a54b"><p class="cl-a41995fa"><span class="cl-a418314c">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a419a536"><p class="cl-a41995fa"><span class="cl-a418314c">4</span></p></td><td class="cl-a419a540"><p class="cl-a4199618"><span class="cl-a418314c">Suspect</span></p></td><td class="cl-a419a54a"><p class="cl-a4199618"><span class="cl-a418314c">female</span></p></td><td class="cl-a419a54b"><p class="cl-a41995fa"><span class="cl-a418314c">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a419a4fb"><p class="cl-a41995fa"><span class="cl-a418314c">5</span></p></td><td class="cl-a419a50e"><p class="cl-a4199618"><span class="cl-a418314c">Confirmed</span></p></td><td class="cl-a419a50f"><p class="cl-a4199618"><span class="cl-a418314c">male</span></p></td><td class="cl-a419a522"><p class="cl-a41995fa"><span class="cl-a418314c">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a419a4fb"><p class="cl-a41995fa"><span class="cl-a418314c">6</span></p></td><td class="cl-a419a50e"><p class="cl-a4199618"><span class="cl-a418314c">Confirmed</span></p></td><td class="cl-a419a50f"><p class="cl-a4199618"><span class="cl-a418314c">male</span></p></td><td class="cl-a419a522"><p class="cl-a41995fa"><span class="cl-a418314c">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a419a4fb"><p class="cl-a41995fa"><span class="cl-a418314c">7</span></p></td><td class="cl-a419a50e"><p class="cl-a4199618"><span class="cl-a418314c">Confirmed</span></p></td><td class="cl-a419a50f"><p class="cl-a4199618"><span class="cl-a418314c">female</span></p></td><td class="cl-a419a522"><p class="cl-a41995fa"><span class="cl-a418314c">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a419a4fb"><p class="cl-a41995fa"><span class="cl-a418314c">8</span></p></td><td class="cl-a419a50e"><p class="cl-a4199618"><span class="cl-a418314c">Confirmed</span></p></td><td class="cl-a419a50f"><p class="cl-a4199618"><span class="cl-a418314c">female</span></p></td><td class="cl-a419a522"><p class="cl-a41995fa"><span class="cl-a418314c">31</span></p></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-a429d334{}.cl-a4263e90{font-family:'Helvetica';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a4263e9a{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a4279d30{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-a4279d3a{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-a427ab9a{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-a427ab9b{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-a427abae{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-a427abb8{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-a427abb9{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-a427abc2{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-a427abc3{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-a427abc4{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-a427abc5{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-a427abc6{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-a427abd6{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-a427abea{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-a427abeb{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-a427abfe{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-a427ac12{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-a427ac1c{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-a429d334'><thead><tr style="overflow-wrap:break-word;"><th class="cl-a427ab9a"><p class="cl-a4279d30"><span class="cl-a4263e90">case</span></p></th><th class="cl-a427ab9b"><p class="cl-a4279d3a"><span class="cl-a4263e90">case_def</span></p></th><th class="cl-a427abae"><p class="cl-a4279d3a"><span class="cl-a4263e90">sex</span></p></th><th class="cl-a427abb8"><p class="cl-a4279d30"><span class="cl-a4263e90">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-a427abb9"><p class="cl-a4279d30"><span class="cl-a4263e9a">1</span></p></td><td class="cl-a427abc2"><p class="cl-a4279d3a"><span class="cl-a4263e9a">Confirmed</span></p></td><td class="cl-a427abc3"><p class="cl-a4279d3a"><span class="cl-a4263e9a">female</span></p></td><td class="cl-a427abc4"><p class="cl-a4279d30"><span class="cl-a4263e9a">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a427abc5"><p class="cl-a4279d30"><span class="cl-a4263e9a">2</span></p></td><td class="cl-a427abc6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">Confirmed</span></p></td><td class="cl-a427abd6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">male</span></p></td><td class="cl-a427abea"><p class="cl-a4279d30"><span class="cl-a4263e9a">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a427abeb"><p class="cl-a4279d30"><span class="cl-a4263e9a">3</span></p></td><td class="cl-a427abfe"><p class="cl-a4279d3a"><span class="cl-a4263e9a">Suspect</span></p></td><td class="cl-a427ac12"><p class="cl-a4279d3a"><span class="cl-a4263e9a">female</span></p></td><td class="cl-a427ac1c"><p class="cl-a4279d30"><span class="cl-a4263e9a">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a427abeb"><p class="cl-a4279d30"><span class="cl-a4263e9a">4</span></p></td><td class="cl-a427abfe"><p class="cl-a4279d3a"><span class="cl-a4263e9a">Suspect</span></p></td><td class="cl-a427ac12"><p class="cl-a4279d3a"><span class="cl-a4263e9a">female</span></p></td><td class="cl-a427ac1c"><p class="cl-a4279d30"><span class="cl-a4263e9a">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a427abc5"><p class="cl-a4279d30"><span class="cl-a4263e9a">5</span></p></td><td class="cl-a427abc6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">Confirmed</span></p></td><td class="cl-a427abd6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">male</span></p></td><td class="cl-a427abea"><p class="cl-a4279d30"><span class="cl-a4263e9a">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a427abc5"><p class="cl-a4279d30"><span class="cl-a4263e9a">6</span></p></td><td class="cl-a427abc6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">Confirmed</span></p></td><td class="cl-a427abd6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">male</span></p></td><td class="cl-a427abea"><p class="cl-a4279d30"><span class="cl-a4263e9a">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a427abc5"><p class="cl-a4279d30"><span class="cl-a4263e9a">7</span></p></td><td class="cl-a427abc6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">Confirmed</span></p></td><td class="cl-a427abd6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">female</span></p></td><td class="cl-a427abea"><p class="cl-a4279d30"><span class="cl-a4263e9a">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a427abc5"><p class="cl-a4279d30"><span class="cl-a4263e9a">8</span></p></td><td class="cl-a427abc6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">Confirmed</span></p></td><td class="cl-a427abd6"><p class="cl-a4279d3a"><span class="cl-a4263e9a">female</span></p></td><td class="cl-a427abea"><p class="cl-a4279d30"><span class="cl-a4263e9a">31</span></p></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-a437cbce{}.cl-a4343dec{font-family:'Helvetica';font-size:11pt;font-weight:bold;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a4343df6{font-family:'Helvetica';font-size:11pt;font-weight:normal;font-style:normal;text-decoration:none;color:rgba(0, 0, 0, 1.00);background-color:transparent;}.cl-a4359dd6{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-a4359de0{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-a435ad8a{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-a435ad94{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-a435ada8{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-a435adc6{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-a435adc7{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-a435adc8{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-a435adc9{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-a435add0{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-a435add1{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-a435add2{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-a435add3{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-a435ade4{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-a435ade5{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-a435adf8{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-a435adf9{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-a435ae0c{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-a437cbce'><thead><tr style="overflow-wrap:break-word;"><th class="cl-a435ad8a"><p class="cl-a4359dd6"><span class="cl-a4343dec">case</span></p></th><th class="cl-a435ad94"><p class="cl-a4359de0"><span class="cl-a4343dec">case_def</span></p></th><th class="cl-a435ada8"><p class="cl-a4359de0"><span class="cl-a4343dec">sex</span></p></th><th class="cl-a435adc6"><p class="cl-a4359dd6"><span class="cl-a4343dec">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-a435adc7"><p class="cl-a4359dd6"><span class="cl-a4343df6">1</span></p></td><td class="cl-a435adc8"><p class="cl-a4359de0"><span class="cl-a4343df6">Confirmed</span></p></td><td class="cl-a435adc9"><p class="cl-a4359de0"><span class="cl-a4343df6">female</span></p></td><td class="cl-a435add0"><p class="cl-a4359dd6"><span class="cl-a4343df6">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a435add1"><p class="cl-a4359dd6"><span class="cl-a4343df6">2</span></p></td><td class="cl-a435add2"><p class="cl-a4359de0"><span class="cl-a4343df6">Confirmed</span></p></td><td class="cl-a435add3"><p class="cl-a4359de0"><span class="cl-a4343df6">male</span></p></td><td class="cl-a435ade4"><p class="cl-a4359dd6"><span class="cl-a4343df6">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a435ade5"><p class="cl-a4359dd6"><span class="cl-a4343df6">3</span></p></td><td class="cl-a435adf8"><p class="cl-a4359de0"><span class="cl-a4343df6">Suspect</span></p></td><td class="cl-a435adf9"><p class="cl-a4359de0"><span class="cl-a4343df6">female</span></p></td><td class="cl-a435ae0c"><p class="cl-a4359dd6"><span class="cl-a4343df6">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a435ade5"><p class="cl-a4359dd6"><span class="cl-a4343df6">4</span></p></td><td class="cl-a435adf8"><p class="cl-a4359de0"><span class="cl-a4343df6">Suspect</span></p></td><td class="cl-a435adf9"><p class="cl-a4359de0"><span class="cl-a4343df6">female</span></p></td><td class="cl-a435ae0c"><p class="cl-a4359dd6"><span class="cl-a4343df6">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a435add1"><p class="cl-a4359dd6"><span class="cl-a4343df6">5</span></p></td><td class="cl-a435add2"><p class="cl-a4359de0"><span class="cl-a4343df6">Confirmed</span></p></td><td class="cl-a435add3"><p class="cl-a4359de0"><span class="cl-a4343df6">male</span></p></td><td class="cl-a435ade4"><p class="cl-a4359dd6"><span class="cl-a4343df6">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a435add1"><p class="cl-a4359dd6"><span class="cl-a4343df6">6</span></p></td><td class="cl-a435add2"><p class="cl-a4359de0"><span class="cl-a4343df6">Confirmed</span></p></td><td class="cl-a435add3"><p class="cl-a4359de0"><span class="cl-a4343df6">male</span></p></td><td class="cl-a435ade4"><p class="cl-a4359dd6"><span class="cl-a4343df6">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a435add1"><p class="cl-a4359dd6"><span class="cl-a4343df6">7</span></p></td><td class="cl-a435add2"><p class="cl-a4359de0"><span class="cl-a4343df6">Confirmed</span></p></td><td class="cl-a435add3"><p class="cl-a4359de0"><span class="cl-a4343df6">female</span></p></td><td class="cl-a435ade4"><p class="cl-a4359dd6"><span class="cl-a4343df6">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-a435add1"><p class="cl-a4359dd6"><span class="cl-a4343df6">8</span></p></td><td class="cl-a435add2"><p class="cl-a4359de0"><span class="cl-a4343df6">Confirmed</span></p></td><td class="cl-a435add3"><p class="cl-a4359de0"><span class="cl-a4343df6">female</span></p></td><td class="cl-a435ade4"><p class="cl-a4359dd6"><span class="cl-a4343df6">31</span></p></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="vgakvnrfjc" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> 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#D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #vgakvnrfjc .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #vgakvnrfjc .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; } #vgakvnrfjc .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #vgakvnrfjc .gt_left { text-align: left; } #vgakvnrfjc .gt_center { text-align: center; } #vgakvnrfjc .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #vgakvnrfjc .gt_font_normal { font-weight: normal; } #vgakvnrfjc .gt_font_bold { font-weight: bold; } #vgakvnrfjc .gt_font_italic { font-style: italic; } #vgakvnrfjc .gt_super { font-size: 65%; } #vgakvnrfjc .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #vgakvnrfjc .gt_asterisk { font-size: 100%; vertical-align: 0; } #vgakvnrfjc .gt_indent_1 { text-indent: 5px; } #vgakvnrfjc .gt_indent_2 { text-indent: 10px; } #vgakvnrfjc .gt_indent_3 { text-indent: 15px; } #vgakvnrfjc .gt_indent_4 { text-indent: 20px; } #vgakvnrfjc .gt_indent_5 { text-indent: 25px; } #vgakvnrfjc .katex-display { display: inline-flex !important; margin-bottom: 0.75em !important; } #vgakvnrfjc div.Reactable > div.rt-table > div.rt-thead > div.rt-tr.rt-tr-group-header > div.rt-th-group:after { height: 0px !important; } </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="label"></th> <th class="gt_center gt_columns_top_border gt_column_spanner_outer" rowspan="1" colspan="2" scope="colgroup" id="case_def"> <div class="gt_column_spanner"><span class='gt_from_md'>case_def</span></div> </th> <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="2" colspan="1" scope="col" id="stat_0"><span class='gt_from_md'>Total</span></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="stat_1"><span class='gt_from_md'>Confirmed</span></th> <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="stat_2"><span class='gt_from_md'>Suspect</span></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"><br /></td> <td headers="stat_2" class="gt_row gt_center"><br /></td> <td headers="stat_0" class="gt_row gt_center"><br /></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. <img src="../../images/functions_packages/gt_summary.png" alt="" width="50%" /> ] --- # 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 <img src="../../images/functions_packages/ggplot2.png" alt="" width="20%" /><img src="../../images/functions_packages/lubridate.png" alt="" width="20%" /><img src="../../images/functions_packages/janitor.png" alt="" width="20%" /><img src="../../images/functions_packages/rmarkdown.png" alt="" width="20%" /> --- # 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.* <img src="../../images/functions_packages/library.png" alt="" width="50%" /> ] -- .pull-right[ **Step 2 - Load** Begin **every R session** by loading the packages you want to use. *Like borrowing a book from your library*. <img src="../../images/functions_packages/bookshelf1.png" alt="" width="70%" /> ] --- # 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" alt="" width="100%" /> .footnote[Other importing scenarios are addressed in the next module] ] .pull-right[ <img src="../../images/functions_packages/rio.png" alt="" width="40%" /> `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 <img src="../../images/breakout/teamwork2.png" alt="" width="50%" />