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" 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" width="100%" /> **170** epidemiologists with **R expertise** and **ground-level** public health experience. ] .footnote[Meet [our team](www.appliedepi.org/people2)] --- # R training courses **Synchronous** courses with **1-on-1 tutoring** and **follow-up support**. **Over 1200 epis at 350 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" width="75%" height="75%" /> --- # The Epidemiologist R Handbook <img src="../../images/welcome/Epi R Handbook Banner Beige 1500x500.png" 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 **650,000 global 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" width="100%" height="75%" /> ] --- class: inverse, center, middle # Why learn R? --- # Learning R... ## ...is really useful <img src="../../images/welcome/stop_epidemic_dominoes2.png" width="75%" /> ??? Mention marketable skill as well as technically for epidemic response --- # Learning R... ## ...is freeing <img src="../../images/welcome/freedom_bird.png" width="50%" /> --- # Learning R... ## ...can be hard work <img src="../../images/welcome/missing_puzzle.png" width="50%" /> --- # Learning R... ## ...gives moments of pure joy <img src="../../images/welcome/joy.png" 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" 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" 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" 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" 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" 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" 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-ec63dbac{table-layout:auto;}.cl-ec5ed88c{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-ec5ed8aa{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-ec60d916{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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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-ec60e9ba{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-ec60e9bb{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-ec63dbac'><thead><tr style="overflow-wrap:break-word;"><th class="cl-ec60e91a"><p class="cl-ec60d916"><span class="cl-ec5ed88c">Module</span></p></th><th class="cl-ec60e91b"><p class="cl-ec60d916"><span class="cl-ec5ed88c">Topic</span></p></th><th class="cl-ec60e924"><p class="cl-ec60d916"><span class="cl-ec5ed88c">1-on-1 Support</span><br><span class="cl-ec5ed88c">(24/7 availability)</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-ec60e925"><p class="cl-ec60d916"><span class="cl-ec5ed88c">Pre-course</span></p></td><td class="cl-ec60e92e"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Installation troubleshooting</span></p></td><td class="cl-ec60e92f"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Preparation calls</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e938"><p class="cl-ec60d916"><span class="cl-ec5ed88c">1</span></p></td><td class="cl-ec60e942"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">RStudio, basic R syntax</span></p></td><td rowspan="10"class="cl-ec60e943"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Unlimited tutoring</span><br><span class="cl-ec5ed8aa">on course material</span><br><br><br><span class="cl-ec5ed8aa">After-hours booking</span><br><span class="cl-ec5ed8aa">link provided by email</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e944"><p class="cl-ec60d916"><span class="cl-ec5ed88c">2</span></p></td><td class="cl-ec60e94c"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Data cleaning</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e957"><p class="cl-ec60d916"><span class="cl-ec5ed88c">3</span></p></td><td class="cl-ec60e958"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">More complex data cleaning</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e96a"><p class="cl-ec60d916"><span class="cl-ec5ed88c">4</span></p></td><td class="cl-ec60e96b"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Grouping and summarising data</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e957"><p class="cl-ec60d916"><span class="cl-ec5ed88c">5</span></p></td><td class="cl-ec60e958"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Data visualization with ggplot2</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e957"><p class="cl-ec60d916"><span class="cl-ec5ed88c">6</span></p></td><td class="cl-ec60e958"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Troubleshooting and getting help</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e974"><p class="cl-ec60d916"><span class="cl-ec5ed88c">7</span></p></td><td class="cl-ec60e975"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Automated reports with R Markdown</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e97f"><p class="cl-ec60d916"><span class="cl-ec5ed88c">8</span></p></td><td class="cl-ec60e988"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Transforming data with joins and pivots</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e992"><p class="cl-ec60d916"><span class="cl-ec5ed88c">9</span></p></td><td class="cl-ec60e993"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">Public health plots: Heat plots, epi curves,</span><br><span class="cl-ec5ed8aa">age/sex pyramids, &amp; GIS demo</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e99d"><p class="cl-ec60d916"><span class="cl-ec5ed88c">10</span></p></td><td class="cl-ec60e99e"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">COVID-19 case study</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec60e9a7"><p class="cl-ec60d916"><span class="cl-ec5ed88c">Post-course</span></p></td><td class="cl-ec60e9a8"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">We help you apply R to your work.</span><br><span class="cl-ec5ed8aa">1 hour coupon valid 12 months.*</span></p></td><td class="cl-ec60e9b0"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">R Support Desk</span></p></td></tr></tbody><tfoot><tr style="overflow-wrap:break-word;"><td colspan="3"class="cl-ec60e9b1"><p class="cl-ec60d916"><span class="cl-ec5ed8aa">*Coupon time and 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 (booking link provided by email) --- # Certificate To receive a certificate of completion, you must: 1) **Attend 80% of the sessions** (or make them up with course tutoring) 2) **Complete the anonymous feedback survey** 3) **Submit an email to training@appliedepi.org** with: * The link to your practice post in our community forum (Module 6) * Your R script from the COVID-19 case study (Module 10) --- # Agreement with each other **Our team will:** - Create a supportive & personalized learning space - Appreciate your expertise -- **We hope that you will:** - Reach outside of your comfort zone *(you might discover a new passion!)* - Tell us if you do not understand and catch-up if you miss a session ??? We are in this course to succeed, together --- # This module **Objectives** * Within an RStudio project, write basic R code to: * Perform calculations * Create and change objects * Use functions * Install and load packages * Import and inspect a dataset </br> <div class="tabwid"><style>.cl-ec73f0be{}.cl-ec6fed2a{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-ec7194cc{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-ec71a048{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-ec71a052{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-ec71a05c{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-ec71a05d{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-ec71a05e{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-ec71a066{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-ec71a067{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-ec71a070{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-ec71a071{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-ec71a07a{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-ec71a07b{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-ec71a084{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-ec73f0be'><thead><tr style="overflow-wrap:break-word;"><th class="cl-ec71a048"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">Time</span></p></th><th class="cl-ec71a052"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">Topic</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-ec71a05c"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">45 minutes</span></p></td><td class="cl-ec71a05d"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">Welcome &amp; course logistics</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec71a05e"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">30 minutes</span></p></td><td class="cl-ec71a066"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">RStudio tour and basic R syntax</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec71a067"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">2 hours</span></p></td><td class="cl-ec71a070"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">Exercise</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec71a071"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">15 minutes</span></p></td><td class="cl-ec71a07a"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">Debrief</span></p></td></tr></tbody><tfoot><tr style="overflow-wrap:break-word;"><td colspan="2"class="cl-ec71a07b"><p class="cl-ec7194cc"><span class="cl-ec6fed2a">Take breaks as you wish during the exercise</span></p></td></tr></tfoot></table></div> ??? Note stretch breaks throughout. --- class: inverse, center, middle # Stretch break! (and time to ask questions) <img src="../../images/breakout/stretch.png" width="50%" /> <div class="countdown" id="timer_ea2b98b3" data-update-every="1" tabindex="0" style="right:0;bottom:0;"> <div class="countdown-controls"><button class="countdown-bump-down">−</button><button class="countdown-bump-up">+</button></div> <code class="countdown-time"><span class="countdown-digits minutes">05</span><span class="countdown-digits colon">:</span><span class="countdown-digits seconds">00</span></code> </div> --- # 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" 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" 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" 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" 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[Accepts numeric values and returns the maximum] ??? Demonstrate each `sqrt(49)`, `sqrt(12)`, `max(1, 15, 2, 9)` (explain commas) Explain vectors `c(1, 15, 2, 9)` and a named vector `cities <- c("Wuhan", "Milan", "New York")` Quickly note indexed vectors `cities[[2]]` and numeric: `ages <- c(15, 28, 100, 15, 65, 4, 10)` then `summary(ages)` and `summary(ages)[2]` and `summary(ages)[[2]]` --- # Simple R functions .pull-left[ - `sqrt()` * Accepts one numeric value as input, returns the square root - `max()` * Accepts numeric values and returns the maximum ] .pull-right[ ```r sqrt(49) ``` ``` ## [1] 7 ``` <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 ``` ] ??? 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" width="100%" /> ] --- # This may look familiar <img src="../../images/functions_packages/excel_arguments.png" 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" 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-ec94c3f2{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-ec94c3f3{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-ec94c3f4{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-ec94c3fc{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-ec973d94'><thead><tr style="overflow-wrap:break-word;"><th class="cl-ec94c3c0"><p class="cl-ec94b718"><span class="cl-ec9208b0">case</span></p></th><th class="cl-ec94c3ca"><p class="cl-ec94b722"><span class="cl-ec9208b0">case_def</span></p></th><th class="cl-ec94c3cb"><p class="cl-ec94b722"><span class="cl-ec9208b0">sex</span></p></th><th class="cl-ec94c3cc"><p class="cl-ec94b718"><span class="cl-ec9208b0">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-ec94c3cd"><p class="cl-ec94b718"><span class="cl-ec9208ba">1</span></p></td><td class="cl-ec94c3d4"><p class="cl-ec94b722"><span class="cl-ec9208ba">Confirmed</span></p></td><td class="cl-ec94c3de"><p class="cl-ec94b722"><span class="cl-ec9208ba">female</span></p></td><td class="cl-ec94c3df"><p class="cl-ec94b718"><span class="cl-ec9208ba">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec94c3e0"><p class="cl-ec94b718"><span class="cl-ec9208ba">2</span></p></td><td class="cl-ec94c3e8"><p class="cl-ec94b722"><span class="cl-ec9208ba">Confirmed</span></p></td><td class="cl-ec94c3e9"><p class="cl-ec94b722"><span class="cl-ec9208ba">male</span></p></td><td class="cl-ec94c3ea"><p class="cl-ec94b718"><span class="cl-ec9208ba">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec94c3f2"><p class="cl-ec94b718"><span class="cl-ec9208ba">3</span></p></td><td class="cl-ec94c3f3"><p class="cl-ec94b722"><span class="cl-ec9208ba">Suspect</span></p></td><td class="cl-ec94c3f4"><p class="cl-ec94b722"><span class="cl-ec9208ba">female</span></p></td><td class="cl-ec94c3fc"><p class="cl-ec94b718"><span class="cl-ec9208ba">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec94c3f2"><p class="cl-ec94b718"><span class="cl-ec9208ba">4</span></p></td><td class="cl-ec94c3f3"><p class="cl-ec94b722"><span class="cl-ec9208ba">Suspect</span></p></td><td class="cl-ec94c3f4"><p class="cl-ec94b722"><span class="cl-ec9208ba">female</span></p></td><td class="cl-ec94c3fc"><p class="cl-ec94b718"><span class="cl-ec9208ba">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec94c3e0"><p class="cl-ec94b718"><span class="cl-ec9208ba">5</span></p></td><td class="cl-ec94c3e8"><p class="cl-ec94b722"><span class="cl-ec9208ba">Confirmed</span></p></td><td class="cl-ec94c3e9"><p class="cl-ec94b722"><span class="cl-ec9208ba">male</span></p></td><td class="cl-ec94c3ea"><p class="cl-ec94b718"><span class="cl-ec9208ba">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec94c3e0"><p class="cl-ec94b718"><span class="cl-ec9208ba">6</span></p></td><td class="cl-ec94c3e8"><p class="cl-ec94b722"><span class="cl-ec9208ba">Confirmed</span></p></td><td class="cl-ec94c3e9"><p class="cl-ec94b722"><span class="cl-ec9208ba">male</span></p></td><td class="cl-ec94c3ea"><p class="cl-ec94b718"><span class="cl-ec9208ba">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec94c3e0"><p class="cl-ec94b718"><span class="cl-ec9208ba">7</span></p></td><td class="cl-ec94c3e8"><p class="cl-ec94b722"><span class="cl-ec9208ba">Confirmed</span></p></td><td class="cl-ec94c3e9"><p class="cl-ec94b722"><span class="cl-ec9208ba">female</span></p></td><td class="cl-ec94c3ea"><p class="cl-ec94b718"><span class="cl-ec9208ba">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ec94c3e0"><p class="cl-ec94b718"><span class="cl-ec9208ba">8</span></p></td><td class="cl-ec94c3e8"><p class="cl-ec94b722"><span class="cl-ec9208ba">Confirmed</span></p></td><td class="cl-ec94c3e9"><p class="cl-ec94b722"><span class="cl-ec9208ba">female</span></p></td><td class="cl-ec94c3ea"><p class="cl-ec94b718"><span class="cl-ec9208ba">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-eca86646{}.cl-eca42fb8{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-eca42fc2{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-eca5d700{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-eca5d701{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-eca5e3a8{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-eca5e3b2{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-eca5e3b3{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-eca5e3bc{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-eca5e3bd{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-eca5e3c6{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-eca5e3c7{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-eca5e3d0{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-eca5e3d1{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-eca5e3da{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-eca5e3db{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-eca5e3e4{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-eca5e3e5{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-eca5e3ee{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-eca5e3ef{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-eca5e3f8{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-eca86646'><thead><tr style="overflow-wrap:break-word;"><th class="cl-eca5e3a8"><p class="cl-eca5d700"><span class="cl-eca42fb8">case</span></p></th><th class="cl-eca5e3b2"><p class="cl-eca5d701"><span class="cl-eca42fb8">case_def</span></p></th><th class="cl-eca5e3b3"><p class="cl-eca5d701"><span class="cl-eca42fb8">sex</span></p></th><th class="cl-eca5e3bc"><p class="cl-eca5d700"><span class="cl-eca42fb8">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-eca5e3bd"><p class="cl-eca5d700"><span class="cl-eca42fc2">1</span></p></td><td class="cl-eca5e3c6"><p class="cl-eca5d701"><span class="cl-eca42fc2">Confirmed</span></p></td><td class="cl-eca5e3c7"><p class="cl-eca5d701"><span class="cl-eca42fc2">female</span></p></td><td class="cl-eca5e3d0"><p class="cl-eca5d700"><span class="cl-eca42fc2">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-eca5e3d1"><p class="cl-eca5d700"><span class="cl-eca42fc2">2</span></p></td><td class="cl-eca5e3da"><p class="cl-eca5d701"><span class="cl-eca42fc2">Confirmed</span></p></td><td class="cl-eca5e3db"><p class="cl-eca5d701"><span class="cl-eca42fc2">male</span></p></td><td class="cl-eca5e3e4"><p class="cl-eca5d700"><span class="cl-eca42fc2">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-eca5e3e5"><p class="cl-eca5d700"><span class="cl-eca42fc2">3</span></p></td><td class="cl-eca5e3ee"><p class="cl-eca5d701"><span class="cl-eca42fc2">Suspect</span></p></td><td class="cl-eca5e3ef"><p class="cl-eca5d701"><span class="cl-eca42fc2">female</span></p></td><td class="cl-eca5e3f8"><p class="cl-eca5d700"><span class="cl-eca42fc2">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-eca5e3e5"><p class="cl-eca5d700"><span class="cl-eca42fc2">4</span></p></td><td class="cl-eca5e3ee"><p class="cl-eca5d701"><span class="cl-eca42fc2">Suspect</span></p></td><td class="cl-eca5e3ef"><p class="cl-eca5d701"><span class="cl-eca42fc2">female</span></p></td><td class="cl-eca5e3f8"><p class="cl-eca5d700"><span class="cl-eca42fc2">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-eca5e3d1"><p class="cl-eca5d700"><span class="cl-eca42fc2">5</span></p></td><td class="cl-eca5e3da"><p class="cl-eca5d701"><span class="cl-eca42fc2">Confirmed</span></p></td><td class="cl-eca5e3db"><p class="cl-eca5d701"><span class="cl-eca42fc2">male</span></p></td><td class="cl-eca5e3e4"><p class="cl-eca5d700"><span class="cl-eca42fc2">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-eca5e3d1"><p class="cl-eca5d700"><span class="cl-eca42fc2">6</span></p></td><td class="cl-eca5e3da"><p class="cl-eca5d701"><span class="cl-eca42fc2">Confirmed</span></p></td><td class="cl-eca5e3db"><p class="cl-eca5d701"><span class="cl-eca42fc2">male</span></p></td><td class="cl-eca5e3e4"><p class="cl-eca5d700"><span class="cl-eca42fc2">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-eca5e3d1"><p class="cl-eca5d700"><span class="cl-eca42fc2">7</span></p></td><td class="cl-eca5e3da"><p class="cl-eca5d701"><span class="cl-eca42fc2">Confirmed</span></p></td><td class="cl-eca5e3db"><p class="cl-eca5d701"><span class="cl-eca42fc2">female</span></p></td><td class="cl-eca5e3e4"><p class="cl-eca5d700"><span class="cl-eca42fc2">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-eca5e3d1"><p class="cl-eca5d700"><span class="cl-eca42fc2">8</span></p></td><td class="cl-eca5e3da"><p class="cl-eca5d701"><span class="cl-eca42fc2">Confirmed</span></p></td><td class="cl-eca5e3db"><p class="cl-eca5d701"><span class="cl-eca42fc2">female</span></p></td><td class="cl-eca5e3e4"><p class="cl-eca5d700"><span class="cl-eca42fc2">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-ecbab40e{}.cl-ecb679e8{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-ecb679fc{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-ecb82202{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-ecb8220c{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-ecb82e3c{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-ecb82e46{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-ecb82e47{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-ecb82e50{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-ecb82e51{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-ecb82e5a{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-ecb82e5b{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-ecb82e64{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-ecb82e65{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-ecb82e6e{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-ecb82e6f{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-ecb82e70{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-ecb82e78{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-ecb82e79{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-ecb82e82{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-ecb82e83{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-ecbab40e'><thead><tr style="overflow-wrap:break-word;"><th class="cl-ecb82e3c"><p class="cl-ecb82202"><span class="cl-ecb679e8">case</span></p></th><th class="cl-ecb82e46"><p class="cl-ecb8220c"><span class="cl-ecb679e8">case_def</span></p></th><th class="cl-ecb82e47"><p class="cl-ecb8220c"><span class="cl-ecb679e8">sex</span></p></th><th class="cl-ecb82e50"><p class="cl-ecb82202"><span class="cl-ecb679e8">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-ecb82e51"><p class="cl-ecb82202"><span class="cl-ecb679fc">1</span></p></td><td class="cl-ecb82e5a"><p class="cl-ecb8220c"><span class="cl-ecb679fc">Confirmed</span></p></td><td class="cl-ecb82e5b"><p class="cl-ecb8220c"><span class="cl-ecb679fc">female</span></p></td><td class="cl-ecb82e64"><p class="cl-ecb82202"><span class="cl-ecb679fc">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecb82e65"><p class="cl-ecb82202"><span class="cl-ecb679fc">2</span></p></td><td class="cl-ecb82e6e"><p class="cl-ecb8220c"><span class="cl-ecb679fc">Confirmed</span></p></td><td class="cl-ecb82e6f"><p class="cl-ecb8220c"><span class="cl-ecb679fc">male</span></p></td><td class="cl-ecb82e70"><p class="cl-ecb82202"><span class="cl-ecb679fc">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecb82e78"><p class="cl-ecb82202"><span class="cl-ecb679fc">3</span></p></td><td class="cl-ecb82e79"><p class="cl-ecb8220c"><span class="cl-ecb679fc">Suspect</span></p></td><td class="cl-ecb82e82"><p class="cl-ecb8220c"><span class="cl-ecb679fc">female</span></p></td><td class="cl-ecb82e83"><p class="cl-ecb82202"><span class="cl-ecb679fc">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecb82e78"><p class="cl-ecb82202"><span class="cl-ecb679fc">4</span></p></td><td class="cl-ecb82e79"><p class="cl-ecb8220c"><span class="cl-ecb679fc">Suspect</span></p></td><td class="cl-ecb82e82"><p class="cl-ecb8220c"><span class="cl-ecb679fc">female</span></p></td><td class="cl-ecb82e83"><p class="cl-ecb82202"><span class="cl-ecb679fc">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecb82e65"><p class="cl-ecb82202"><span class="cl-ecb679fc">5</span></p></td><td class="cl-ecb82e6e"><p class="cl-ecb8220c"><span class="cl-ecb679fc">Confirmed</span></p></td><td class="cl-ecb82e6f"><p class="cl-ecb8220c"><span class="cl-ecb679fc">male</span></p></td><td class="cl-ecb82e70"><p class="cl-ecb82202"><span class="cl-ecb679fc">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecb82e65"><p class="cl-ecb82202"><span class="cl-ecb679fc">6</span></p></td><td class="cl-ecb82e6e"><p class="cl-ecb8220c"><span class="cl-ecb679fc">Confirmed</span></p></td><td class="cl-ecb82e6f"><p class="cl-ecb8220c"><span class="cl-ecb679fc">male</span></p></td><td class="cl-ecb82e70"><p class="cl-ecb82202"><span class="cl-ecb679fc">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecb82e65"><p class="cl-ecb82202"><span class="cl-ecb679fc">7</span></p></td><td class="cl-ecb82e6e"><p class="cl-ecb8220c"><span class="cl-ecb679fc">Confirmed</span></p></td><td class="cl-ecb82e6f"><p class="cl-ecb8220c"><span class="cl-ecb679fc">female</span></p></td><td class="cl-ecb82e70"><p class="cl-ecb82202"><span class="cl-ecb679fc">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecb82e65"><p class="cl-ecb82202"><span class="cl-ecb679fc">8</span></p></td><td class="cl-ecb82e6e"><p class="cl-ecb8220c"><span class="cl-ecb679fc">Confirmed</span></p></td><td class="cl-ecb82e6f"><p class="cl-ecb8220c"><span class="cl-ecb679fc">female</span></p></td><td class="cl-ecb82e70"><p class="cl-ecb82202"><span class="cl-ecb679fc">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-eccd5532{}.cl-ecc7e44e{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-ecc7e458{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-ecc99758{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-ecc99762{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-ecc9a3f6{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-ecc9a400{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-ecc9a40a{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-ecc9a40b{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-ecc9a414{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-ecc9a41e{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-ecc9a41f{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-ecc9a420{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-ecc9a428{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-ecc9a429{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-ecc9a432{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-ecc9a433{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-ecc9a43c{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-ecc9a43d{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-ecc9a446{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-ecc9a447{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-eccd5532'><thead><tr style="overflow-wrap:break-word;"><th class="cl-ecc9a3f6"><p class="cl-ecc99758"><span class="cl-ecc7e44e">case</span></p></th><th class="cl-ecc9a400"><p class="cl-ecc99762"><span class="cl-ecc7e44e">case_def</span></p></th><th class="cl-ecc9a40a"><p class="cl-ecc99762"><span class="cl-ecc7e44e">sex</span></p></th><th class="cl-ecc9a40b"><p class="cl-ecc99758"><span class="cl-ecc7e44e">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-ecc9a414"><p class="cl-ecc99758"><span class="cl-ecc7e458">1</span></p></td><td class="cl-ecc9a41e"><p class="cl-ecc99762"><span class="cl-ecc7e458">Confirmed</span></p></td><td class="cl-ecc9a41f"><p class="cl-ecc99762"><span class="cl-ecc7e458">female</span></p></td><td class="cl-ecc9a420"><p class="cl-ecc99758"><span class="cl-ecc7e458">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecc9a428"><p class="cl-ecc99758"><span class="cl-ecc7e458">2</span></p></td><td class="cl-ecc9a429"><p class="cl-ecc99762"><span class="cl-ecc7e458">Confirmed</span></p></td><td class="cl-ecc9a432"><p class="cl-ecc99762"><span class="cl-ecc7e458">male</span></p></td><td class="cl-ecc9a433"><p class="cl-ecc99758"><span class="cl-ecc7e458">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecc9a43c"><p class="cl-ecc99758"><span class="cl-ecc7e458">3</span></p></td><td class="cl-ecc9a43d"><p class="cl-ecc99762"><span class="cl-ecc7e458">Suspect</span></p></td><td class="cl-ecc9a446"><p class="cl-ecc99762"><span class="cl-ecc7e458">female</span></p></td><td class="cl-ecc9a447"><p class="cl-ecc99758"><span class="cl-ecc7e458">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecc9a43c"><p class="cl-ecc99758"><span class="cl-ecc7e458">4</span></p></td><td class="cl-ecc9a43d"><p class="cl-ecc99762"><span class="cl-ecc7e458">Suspect</span></p></td><td class="cl-ecc9a446"><p class="cl-ecc99762"><span class="cl-ecc7e458">female</span></p></td><td class="cl-ecc9a447"><p class="cl-ecc99758"><span class="cl-ecc7e458">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecc9a428"><p class="cl-ecc99758"><span class="cl-ecc7e458">5</span></p></td><td class="cl-ecc9a429"><p class="cl-ecc99762"><span class="cl-ecc7e458">Confirmed</span></p></td><td class="cl-ecc9a432"><p class="cl-ecc99762"><span class="cl-ecc7e458">male</span></p></td><td class="cl-ecc9a433"><p class="cl-ecc99758"><span class="cl-ecc7e458">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecc9a428"><p class="cl-ecc99758"><span class="cl-ecc7e458">6</span></p></td><td class="cl-ecc9a429"><p class="cl-ecc99762"><span class="cl-ecc7e458">Confirmed</span></p></td><td class="cl-ecc9a432"><p class="cl-ecc99762"><span class="cl-ecc7e458">male</span></p></td><td class="cl-ecc9a433"><p class="cl-ecc99758"><span class="cl-ecc7e458">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecc9a428"><p class="cl-ecc99758"><span class="cl-ecc7e458">7</span></p></td><td class="cl-ecc9a429"><p class="cl-ecc99762"><span class="cl-ecc7e458">Confirmed</span></p></td><td class="cl-ecc9a432"><p class="cl-ecc99762"><span class="cl-ecc7e458">female</span></p></td><td class="cl-ecc9a433"><p class="cl-ecc99758"><span class="cl-ecc7e458">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecc9a428"><p class="cl-ecc99758"><span class="cl-ecc7e458">8</span></p></td><td class="cl-ecc9a429"><p class="cl-ecc99762"><span class="cl-ecc7e458">Confirmed</span></p></td><td class="cl-ecc9a432"><p class="cl-ecc99762"><span class="cl-ecc7e458">female</span></p></td><td class="cl-ecc9a433"><p class="cl-ecc99758"><span class="cl-ecc7e458">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-ecdeb8d6{}.cl-ecda7820{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-ecda782a{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-ecdc254e{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-ecdc2558{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-ecdc3232{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-ecdc323c{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-ecdc323d{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-ecdc3246{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-ecdc3247{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-ecdc3250{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-ecdc3251{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-ecdc325a{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-ecdc325b{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-ecdc3264{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-ecdc3265{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-ecdc326e{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-ecdc326f{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-ecdc3278{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-ecdc3279{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-ecdc3282{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-ecdeb8d6'><thead><tr style="overflow-wrap:break-word;"><th class="cl-ecdc3232"><p class="cl-ecdc254e"><span class="cl-ecda7820">case</span></p></th><th class="cl-ecdc323c"><p class="cl-ecdc2558"><span class="cl-ecda7820">case_def</span></p></th><th class="cl-ecdc323d"><p class="cl-ecdc2558"><span class="cl-ecda7820">sex</span></p></th><th class="cl-ecdc3246"><p class="cl-ecdc254e"><span class="cl-ecda7820">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-ecdc3247"><p class="cl-ecdc254e"><span class="cl-ecda782a">1</span></p></td><td class="cl-ecdc3250"><p class="cl-ecdc2558"><span class="cl-ecda782a">Confirmed</span></p></td><td class="cl-ecdc3251"><p class="cl-ecdc2558"><span class="cl-ecda782a">female</span></p></td><td class="cl-ecdc325a"><p class="cl-ecdc254e"><span class="cl-ecda782a">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecdc325b"><p class="cl-ecdc254e"><span class="cl-ecda782a">2</span></p></td><td class="cl-ecdc3264"><p class="cl-ecdc2558"><span class="cl-ecda782a">Confirmed</span></p></td><td class="cl-ecdc3265"><p class="cl-ecdc2558"><span class="cl-ecda782a">male</span></p></td><td class="cl-ecdc326e"><p class="cl-ecdc254e"><span class="cl-ecda782a">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecdc326f"><p class="cl-ecdc254e"><span class="cl-ecda782a">3</span></p></td><td class="cl-ecdc3278"><p class="cl-ecdc2558"><span class="cl-ecda782a">Suspect</span></p></td><td class="cl-ecdc3279"><p class="cl-ecdc2558"><span class="cl-ecda782a">female</span></p></td><td class="cl-ecdc3282"><p class="cl-ecdc254e"><span class="cl-ecda782a">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecdc326f"><p class="cl-ecdc254e"><span class="cl-ecda782a">4</span></p></td><td class="cl-ecdc3278"><p class="cl-ecdc2558"><span class="cl-ecda782a">Suspect</span></p></td><td class="cl-ecdc3279"><p class="cl-ecdc2558"><span class="cl-ecda782a">female</span></p></td><td class="cl-ecdc3282"><p class="cl-ecdc254e"><span class="cl-ecda782a">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecdc325b"><p class="cl-ecdc254e"><span class="cl-ecda782a">5</span></p></td><td class="cl-ecdc3264"><p class="cl-ecdc2558"><span class="cl-ecda782a">Confirmed</span></p></td><td class="cl-ecdc3265"><p class="cl-ecdc2558"><span class="cl-ecda782a">male</span></p></td><td class="cl-ecdc326e"><p class="cl-ecdc254e"><span class="cl-ecda782a">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecdc325b"><p class="cl-ecdc254e"><span class="cl-ecda782a">6</span></p></td><td class="cl-ecdc3264"><p class="cl-ecdc2558"><span class="cl-ecda782a">Confirmed</span></p></td><td class="cl-ecdc3265"><p class="cl-ecdc2558"><span class="cl-ecda782a">male</span></p></td><td class="cl-ecdc326e"><p class="cl-ecdc254e"><span class="cl-ecda782a">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecdc325b"><p class="cl-ecdc254e"><span class="cl-ecda782a">7</span></p></td><td class="cl-ecdc3264"><p class="cl-ecdc2558"><span class="cl-ecda782a">Confirmed</span></p></td><td class="cl-ecdc3265"><p class="cl-ecdc2558"><span class="cl-ecda782a">female</span></p></td><td class="cl-ecdc326e"><p class="cl-ecdc254e"><span class="cl-ecda782a">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecdc325b"><p class="cl-ecdc254e"><span class="cl-ecda782a">8</span></p></td><td class="cl-ecdc3264"><p class="cl-ecdc2558"><span class="cl-ecda782a">Confirmed</span></p></td><td class="cl-ecdc3265"><p class="cl-ecdc2558"><span class="cl-ecda782a">female</span></p></td><td class="cl-ecdc326e"><p class="cl-ecdc254e"><span class="cl-ecda782a">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-ecf0f96a{}.cl-ecebcbd4{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-ecebcbe8{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-ecee74a6{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-ecee74b0{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-ecee8216{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-ecee8220{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-ecee8221{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, 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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-ecee8234{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-ecee8235{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-ecee823e{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-ecee823f{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-ecee8248{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-ecee8249{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-ecee8252{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-ecee8253{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-ecee825c{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-ecee825d{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-ecf0f96a'><thead><tr style="overflow-wrap:break-word;"><th class="cl-ecee8216"><p class="cl-ecee74a6"><span class="cl-ecebcbd4">case</span></p></th><th class="cl-ecee8220"><p class="cl-ecee74b0"><span class="cl-ecebcbd4">case_def</span></p></th><th class="cl-ecee8221"><p class="cl-ecee74b0"><span class="cl-ecebcbd4">sex</span></p></th><th class="cl-ecee8222"><p class="cl-ecee74a6"><span class="cl-ecebcbd4">age</span></p></th></tr></thead><tbody><tr style="overflow-wrap:break-word;"><td class="cl-ecee822a"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">1</span></p></td><td class="cl-ecee822b"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">Confirmed</span></p></td><td class="cl-ecee8234"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">female</span></p></td><td class="cl-ecee8235"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">1</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecee823e"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">2</span></p></td><td class="cl-ecee823f"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">Confirmed</span></p></td><td class="cl-ecee8248"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">male</span></p></td><td class="cl-ecee8249"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">16</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecee8252"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">3</span></p></td><td class="cl-ecee8253"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">Suspect</span></p></td><td class="cl-ecee825c"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">female</span></p></td><td class="cl-ecee825d"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecee8252"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">4</span></p></td><td class="cl-ecee8253"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">Suspect</span></p></td><td class="cl-ecee825c"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">female</span></p></td><td class="cl-ecee825d"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">10</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecee823e"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">5</span></p></td><td class="cl-ecee823f"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">Confirmed</span></p></td><td class="cl-ecee8248"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">male</span></p></td><td class="cl-ecee8249"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">64</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecee823e"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">6</span></p></td><td class="cl-ecee823f"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">Confirmed</span></p></td><td class="cl-ecee8248"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">male</span></p></td><td class="cl-ecee8249"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">8</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecee823e"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">7</span></p></td><td class="cl-ecee823f"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">Confirmed</span></p></td><td class="cl-ecee8248"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">female</span></p></td><td class="cl-ecee8249"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">22</span></p></td></tr><tr style="overflow-wrap:break-word;"><td class="cl-ecee823e"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">8</span></p></td><td class="cl-ecee823f"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">Confirmed</span></p></td><td class="cl-ecee8248"><p class="cl-ecee74b0"><span class="cl-ecebcbe8">female</span></p></td><td class="cl-ecee8249"><p class="cl-ecee74a6"><span class="cl-ecebcbe8">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="pldbzbcabh" style="padding-left:0px;padding-right:0px;padding-top:10px;padding-bottom:10px;overflow-x:auto;overflow-y:auto;width:auto;height:auto;"> <style>#pldbzbcabh table { font-family: system-ui, 'Segoe UI', Roboto, Helvetica, Arial, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', 'Segoe UI Symbol', 'Noto Color Emoji'; -webkit-font-smoothing: antialiased; -moz-osx-font-smoothing: grayscale; } #pldbzbcabh thead, #pldbzbcabh tbody, #pldbzbcabh tfoot, #pldbzbcabh tr, #pldbzbcabh td, #pldbzbcabh th { border-style: none; } #pldbzbcabh p { margin: 0; padding: 0; } #pldbzbcabh .gt_table { display: table; border-collapse: collapse; line-height: normal; margin-left: auto; margin-right: auto; color: #333333; font-size: 16px; font-weight: normal; font-style: normal; background-color: #FFFFFF; width: auto; border-top-style: solid; border-top-width: 2px; border-top-color: #A8A8A8; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #A8A8A8; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; } #pldbzbcabh 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{ color: #333333; background-color: #FFFFFF; font-size: 100%; font-weight: initial; text-transform: inherit; border-right-style: solid; border-right-width: 2px; border-right-color: #D3D3D3; padding-left: 5px; padding-right: 5px; vertical-align: top; } #pldbzbcabh .gt_row_group_first td { border-top-width: 2px; } #pldbzbcabh .gt_row_group_first th { border-top-width: 2px; } #pldbzbcabh .gt_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #pldbzbcabh .gt_first_summary_row { border-top-style: solid; border-top-color: #D3D3D3; } #pldbzbcabh .gt_first_summary_row.thick { border-top-width: 2px; } #pldbzbcabh .gt_last_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #pldbzbcabh .gt_grand_summary_row { color: #333333; background-color: #FFFFFF; text-transform: inherit; padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; } #pldbzbcabh .gt_first_grand_summary_row { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-top-style: double; border-top-width: 6px; border-top-color: #D3D3D3; } #pldbzbcabh .gt_last_grand_summary_row_top { padding-top: 8px; padding-bottom: 8px; padding-left: 5px; padding-right: 5px; border-bottom-style: double; border-bottom-width: 6px; border-bottom-color: #D3D3D3; } #pldbzbcabh .gt_striped { background-color: rgba(128, 128, 128, 0.05); } #pldbzbcabh .gt_table_body { border-top-style: solid; border-top-width: 2px; border-top-color: #D3D3D3; border-bottom-style: solid; border-bottom-width: 2px; border-bottom-color: #D3D3D3; } #pldbzbcabh .gt_footnotes { color: #333333; background-color: #FFFFFF; border-bottom-style: none; border-bottom-width: 2px; border-bottom-color: #D3D3D3; border-left-style: none; border-left-width: 2px; border-left-color: #D3D3D3; border-right-style: none; border-right-width: 2px; border-right-color: #D3D3D3; } #pldbzbcabh .gt_footnote { margin: 0px; font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #pldbzbcabh .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; } #pldbzbcabh .gt_sourcenote { font-size: 90%; padding-top: 4px; padding-bottom: 4px; padding-left: 5px; padding-right: 5px; } #pldbzbcabh .gt_left { text-align: left; } #pldbzbcabh .gt_center { text-align: center; } #pldbzbcabh .gt_right { text-align: right; font-variant-numeric: tabular-nums; } #pldbzbcabh .gt_font_normal { font-weight: normal; } #pldbzbcabh .gt_font_bold { font-weight: bold; } #pldbzbcabh .gt_font_italic { font-style: italic; } #pldbzbcabh .gt_super { font-size: 65%; } #pldbzbcabh .gt_footnote_marks { font-size: 75%; vertical-align: 0.4em; position: initial; } #pldbzbcabh .gt_asterisk { font-size: 100%; vertical-align: 0; } #pldbzbcabh .gt_indent_1 { text-indent: 5px; } #pldbzbcabh .gt_indent_2 { text-indent: 10px; } #pldbzbcabh .gt_indent_3 { text-indent: 15px; } #pldbzbcabh .gt_indent_4 { text-indent: 20px; } #pldbzbcabh .gt_indent_5 { text-indent: 25px; } </style> <table class="gt_table" data-quarto-disable-processing="false" data-quarto-bootstrap="false"> <thead> <tr class="gt_col_headings gt_spanner_row"> <th class="gt_col_heading gt_columns_bottom_border gt_left" rowspan="2" colspan="1" scope="col" id=""></th> <th class="gt_center gt_columns_top_border gt_column_spanner_outer" rowspan="1" colspan="2" scope="colgroup" id="case_def"> <span class="gt_column_spanner">case_def</span> </th> <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="2" colspan="1" scope="col" id="Total">Total</th> </tr> <tr class="gt_col_headings"> <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="Confirmed">Confirmed</th> <th class="gt_col_heading gt_columns_bottom_border gt_center" rowspan="1" colspan="1" scope="col" id="Suspect">Suspect</th> </tr> </thead> <tbody class="gt_table_body"> <tr><td headers="label" class="gt_row gt_left">sex</td> <td headers="stat_1" class="gt_row gt_center"><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" 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" width="20%" /><img src="../../images/functions_packages/lubridate.png" width="20%" /><img src="../../images/functions_packages/janitor.png" width="20%" /><img src="../../images/functions_packages/rmarkdown.png" 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" width="80%" /> ] -- .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" width="80%" /> ] --- # The {pacman} package Using R is often a choice between approaches. We are here to coach you. .pull-left[ **The traditional "base R" approach** ```r install.packages("janitor") library(janitor) # loads ``` * Re-installs every time run * Multiple commands * Difficult syntax * Rarely necessary ] .pull-right[ **The efficient "pacman" approach** ```r pacman::p_load(janitor) ``` * Installs packages *only if necessary*, **and** loads them * Good for shared scripts * {pacman} = **pac**kage **man**ager * Requires the {pacman} package ] --- # Which code is more simple? These commands install and load the same 5 packages. .pull-left[ Using {base} R functions ```r # install the packages install.packages( c("rio", "janitor", "gtsummary", "here", "tidyverse")) # load the packages for use library(rio) library(janitor) library(gtsummary) library(here) library(tidyverse) ``` ] .pull-right[ Using {pacman} ```r # install if necessary, and load pacman::p_load( rio, janitor, gtsummary, here, tidyverse) ``` ] ??? This is common R, where there are many ways do a task. Our job is boil it all down and share with you the easiest and most simple approaches. --- class: inverse, center, middle # Importing data into R --- # Smoothly importing data Recent advancements have made importing data into R much easier: * **RStudio projects** * The **`import()`** function from the **{rio}** package * The **{here}** package In this module you will use **`import()`** to import data from your **RStudio project**. In the next module we will discuss **{here}**. --- # Using `import()` The **`import()`** function uses the file extension (.csv, .xlsx) to understand the data type. This avoids past confusion e.g. `read_csv()`, `read.csv()`, `read_excel()`... .pull-left[ ```r import("testing_data.csv") ``` For a file in the project "root" folder, no other information is needed... and it works on any computer! <img src="../../images/functions_packages/import_root.png" width="100%" /> .footnote[Other importing scenarios are addressed in the next module] ] .pull-right[ <img src="../../images/functions_packages/rio.png" 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" width="50%" />