class: class: title-slide # Review & Practice ### Day 1, Session 1 <div class="title-footer"> <img src="images/academy-logo.png"> <div> September 17, 2023</div> </div> ??? We're going to start off with some review of what we've learned for the past several weeks. --- class: inverse # Go to **Conf Session 1 - Review** .center[ <img src="images/session01/campsite_screenshot.png" width="60%" style="display: block; margin: auto;" /> [conf.posit.academy](https://conf.posit.academy/) ] ??? for this session, we'll be doing our work in the Academy website (conf.posit.academy) Go ahead and open up the milestone for this Session 1. --- ## 🚀 Rapid fire review <img src="images/session01/your-turn-example.png" width="60%" /> ??? What we'll do: I'm going to give you a prompt with a short tidyverse task, and you'll work to recreate it. You'll do your work in the Quarto document you have open so you have a record of your code. You can create as many new code chunks as you like in here. --- <!-- TODO: update --> # Review challenge * __Working together__ with your groupmates is encouraged. -- * After 1-2 minutes, we'll go over the answer together. And then move on to the next question. -- * Everyone gets a small prize at the end! 🎉 ??? Working together is okay (and encouraged) We'll go over the answer once I see that most people have finished. There are 20 prompts -- we may get through all of them (or not). But there will be a prize for everyone at the end. I should also note that there's a bit of a mish mash of difficulty. But The main idea is that you exercise some tidyverse recall and get warmed up. --- class: inverse, center, middle .pull-left[ ## Done <!-- --> ] .pull-right[ ## Help <!-- --> ] ??? You'll use the sticky system to signal that you're done or your need help --- class: center, middle, inverse background-image: url(https://images.unsplash.com/photo-1579780864813-863e246d3bc5?ixlib=rb-1.2.1&ixid=MnwxMjA3fDB8MHxwaG90by1wYWdlfHx8fGVufDB8fHx8&auto=format&fit=crop&w=1160&q=80) background-position: center background-size: cover # .big-text[`outbreaks`] ??? We'll be working with data about foodborne and waterborne disease outbreaks spread by contact with environmental sources or infected people or animals. I'll refer to this data set as `outbreaks`. It comes from the CDC's National Outbreak Reporting System (NORS). First things first, let's take a look a what's in this data set. So *here* is your first prompt: --- class: your-turn # Your Turn 1 Read in the data and explore it. Can you recreate output that looks like this? .space-saver[ ``` ## Rows: 57,649 ## Columns: 21 ## $ year <dbl> 2009, 2009, 2009, 2009, 2009, 2009, 2009,… ## $ month <dbl> 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2,… ## $ state <chr> "Minnesota", "Minnesota", "Minnesota", "M… ## $ primary_mode <chr> "Person-to-person", "Food", "Person-to-pe… ## $ etiology <chr> "Norovirus Genogroup II", "Norovirus", "N… ## $ serotype_or_genotype <chr> "unknown", NA, NA, NA, NA, NA, NA, NA, NA… ## $ etiology_status <chr> "Confirmed", "Suspected", "Suspected", "C… ## $ setting <chr> "Hotel/motel", "Restaurant - Sit-down din… ## $ illnesses <dbl> 21, 2, 50, 24, 16, 5, 3, 21, 7, 5, 22, 16… ## $ hospitalizations <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 0,… ## $ info_on_hospitalizations <dbl> 19, 2, 0, 24, 8, 5, 3, 21, 7, 5, 1, 16, 1… ## $ deaths <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,… ## $ info_on_deaths <dbl> 19, 2, 50, 24, 16, 5, 3, 21, 7, 5, 22, 16… ## $ food_vehicle <chr> NA, NA, NA, NA, NA, NA, NA, "cookies", "s… ## $ food_contaminated_ingredient <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ ifsac_category <chr> NA, NA, NA, NA, NA, NA, NA, "Multiple", "… ## $ water_exposure <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ water_type <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ animal_type <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ animal_type_specify <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ water_status <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ``` ] ??? 1 minute --- ## Solution 1 .pull-left[ ```r library(tidyverse) outbreaks <- read_csv("data/outbreaks.csv") glimpse(outbreaks) ``` ] .pull-right.space-saver[ ``` ## Rows: 57,649 ## Columns: 21 ## $ year <dbl> 2009, 2009, 2009, 2009, 2009, 2009, 2009,… ## $ month <dbl> 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2,… ## $ state <chr> "Minnesota", "Minnesota", "Minnesota", "M… ## $ primary_mode <chr> "Person-to-person", "Food", "Person-to-pe… ## $ etiology <chr> "Norovirus Genogroup II", "Norovirus", "N… ## $ serotype_or_genotype <chr> "unknown", NA, NA, NA, NA, NA, NA, NA, NA… ## $ etiology_status <chr> "Confirmed", "Suspected", "Suspected", "C… ## $ setting <chr> "Hotel/motel", "Restaurant - Sit-down din… ## $ illnesses <dbl> 21, 2, 50, 24, 16, 5, 3, 21, 7, 5, 22, 16… ## $ hospitalizations <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 0,… ## $ info_on_hospitalizations <dbl> 19, 2, 0, 24, 8, 5, 3, 21, 7, 5, 1, 16, 1… ## $ deaths <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,… ## $ info_on_deaths <dbl> 19, 2, 50, 24, 16, 5, 3, 21, 7, 5, 22, 16… ## $ food_vehicle <chr> NA, NA, NA, NA, NA, NA, NA, "cookies", "s… ## $ food_contaminated_ingredient <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ ifsac_category <chr> NA, NA, NA, NA, NA, NA, NA, "Multiple", "… ## $ water_exposure <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ water_type <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ animal_type <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ animal_type_specify <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ## $ water_status <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N… ``` ] --- class: your-turn # Your Turn 2 What is the **earliest year** on record in this data set? __The latest__? 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facility"],"illnesses":[18,6,20,7,18,95,34,4,39,9,21,6,9,19,94,32,11,11,8,4,21,13,16,3,39,14,3,14,36,8,33,9,5,8,43,24,37,52,55,10,49,5,24,58,5,48,56,15,3,4,16,58,14,26,28,5,4,28,38,22,79,22,13,22,6,8,66,69,23,44,49,56,13,21,2,22,5,15,5,11,14,16,60,20,19,7,19,13,5,7,35,83,19,18,12,42,6,4,34,57],"hospitalizations":[0,0,1,0,0,1,4,"NA",0,0,0,0,0,1,1,1,"NA",0,0,0,0,0,0,0,3,0,0,2,0,2,0,"NA",1,0,"NA",0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,"NA",1,0,"NA",0,2,0,0,"NA",0,0,0,0,0,0,1,0,0,3,0,5,0,0,0,0,"NA",0,"NA",0,0,0,2,0,"NA",0,"NA",0,0,0,"NA","NA",0,0,0,0,0,1,2,0],"info_on_hospitalizations":[18,6,20,7,18,95,34,0,39,9,21,6,9,15,94,32,0,11,8,4,21,13,16,0,39,14,3,14,36,8,33,0,1,8,0,24,37,52,4,10,49,4,24,58,5,48,56,15,3,4,16,0,14,26,0,5,4,28,38,0,79,22,13,22,6,8,66,69,23,44,49,56,13,0,0,22,0,15,0,11,14,16,60,20,0,7,0,13,5,7,0,0,19,0,12,0,6,4,34,57],"deaths":[0,0,0,0,0,2,1,"NA",0,0,0,0,0,0,2,1,"NA",0,0,0,0,0,0,0,0,0,0,0,0,0,0,"NA","NA",0,"NA",0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,"NA",0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,"NA",0,"NA",0,0,0,0,0,0,0,"NA",0,0,0,"NA","NA",0,0,0,0,0,0,0,0],"info_on_deaths":[18,6,20,7,18,95,34,0,39,9,21,6,9,19,94,32,0,11,8,4,21,13,16,0,39,14,3,14,36,8,33,0,0,8,0,24,37,52,4,10,49,4,24,58,5,48,56,15,3,4,16,58,14,26,0,5,4,28,38,22,79,22,13,22,6,8,66,69,23,44,49,56,13,21,0,22,0,15,0,11,14,16,60,20,19,7,0,13,5,7,0,0,19,0,12,0,6,4,34,57],"food_vehicle":[null,null,null,"curry chicken; pelau dish; curry chick peas w/ potatoes",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"raw oysters",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"ice",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"food_contaminated_ingredient":[null,null,null,"chicken; peas; meat; chick peas; potatoes",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"oysters, raw",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"ifsac_category":[null,null,null,"Multiple",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Mollusks",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Other",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_exposure":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_type":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"animal_type":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"animal_type_specify":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_status":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"year","name":"year","type":"numeric","maxWidth":400,"align":"left"},{"id":"month","name":"month","type":"numeric","maxWidth":400,"align":"left"},{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"primary_mode","name":"primary_mode","type":"character","maxWidth":400,"align":"left"},{"id":"etiology","name":"etiology","type":"character","maxWidth":400,"align":"left"},{"id":"serotype_or_genotype","name":"serotype_or_genotype","type":"character","maxWidth":400,"align":"left"},{"id":"etiology_status","name":"etiology_status","type":"character","maxWidth":400,"align":"left"},{"id":"setting","name":"setting","type":"character","maxWidth":400,"align":"left"},{"id":"illnesses","name":"illnesses","type":"numeric","maxWidth":400,"align":"left"},{"id":"hospitalizations","name":"hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_hospitalizations","name":"info_on_hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"deaths","name":"deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_deaths","name":"info_on_deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"food_vehicle","name":"food_vehicle","type":"character","maxWidth":400,"align":"left"},{"id":"food_contaminated_ingredient","name":"food_contaminated_ingredient","type":"character","maxWidth":400,"align":"left"},{"id":"ifsac_category","name":"ifsac_category","type":"character","maxWidth":400,"align":"left"},{"id":"water_exposure","name":"water_exposure","type":"character","maxWidth":400,"align":"left"},{"id":"water_type","name":"water_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type","name":"animal_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type_specify","name":"animal_type_specify","type":"character","maxWidth":400,"align":"left"},{"id":"water_status","name":"water_status","type":"character","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows (Total: 57,649)"},"dataKey":"4bcb6f09e86f2f0e2436880dc5abf8d8"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> ] ] --- class: your-turn # Your Turn 3 The `state` variable appears to include US locations -- is the data limited to the 50 states? Produce a table that displays all the unique values of this variable. --- ## Solution 3 ```r outbreaks %>% distinct(state) ``` <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-3a983fc31cb7e15ae46c" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-3a983fc31cb7e15ae46c">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"state":["Minnesota","Pennsylvania","Alaska","Alabama","Illinois","Iowa","Montana","Louisiana","Tennessee","New York","Massachusetts","Ohio","Maine","Arkansas","Michigan","Florida","Wyoming","Hawaii","Wisconsin","New Hampshire","Missouri","Idaho","Connecticut","California","Oklahoma","Virginia","South Carolina","Oregon","New Jersey","Mississippi","Arizona","Maryland","Kansas","Colorado","Washington","Georgia","New Mexico","Utah","North Carolina","Indiana","Nevada","North Dakota","South Dakota","West Virginia","Vermont","Texas","Rhode Island","Puerto Rico","Kentucky","Washington DC","Multistate","Delaware","Nebraska","Republic of Palau","Guam","Commonwealth of the Northern Mariana Islands","US Virgin Islands","Republic of the Marshall Islands"]},"columns":[{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows"},"dataKey":"a9c4724661d45e3db424d6e42ca4ce1a"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- class: your-turn # Your Turn 4 What are the different etiologies that have been recorded in this data set, and how often do they appear in the data? Display your results in a table like the one below. <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-75eba7953a47c660f911" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-75eba7953a47c660f911">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"etiology":["Acanthamoeba unknown","Adenovirus","Adenovirus B","Adenovirus F; Escherichia coli, Enteroaggregative","Adenovirus F; Escherichia coli, Enteropathogenic","Adenovirus F; Escherichia coli, Enteropathogenic; Clostridium difficile","Adenovirus other; Adenovirus","Adenovirus unknown","Adenovirus; Clostridium","Adenovirus; Norovirus Genogroup II","Adenovirus; Norovirus Genogroup II; Clostridium other","Alkaline Water","Amnesic shellfish poison","Anatoxin-a; Other - Chemical/Toxin","Anisakis","Arsenic","Astrovirus","Astrovirus; Norovirus","Astrovirus; Norovirus unknown","Astrovirus; Salmonella unknown","Astrovirus; Sapovirus unknown","Avian schistosomes","Bacillus","Bacillus cereus","Bacillus cereus; Bacillus other","Bacillus cereus; Bacillus subtilus; Bacillus stearothermophilus","Bacillus cereus; Clostridium perfringens","Bacillus cereus; Clostridium perfringens; Other - Bacterium","Bacillus cereus; Clostridium perfringens; Staphylococcus aureus","Bacillus cereus; Clostridium perfringens; Staphylococcus aureus; Norovirus Genogroup II","Bacillus cereus; Norovirus","Bacillus cereus; Norovirus Genogroup I","Bacillus cereus; Staphylococcus aureus","Bacillus cereus; Staphylococcus other","Bacillus other","Bacillus unknown","Bacillus; Clostridium","Bacillus; Clostridium perfringens","Bacillus; Other - Chemical/Toxin","Bacillus; Staphylococcus","Bromate; Disinfection byproducts","Bromine","Brucella","Brucella unknown","Campylobacter","Campylobacter coli","Campylobacter coli; Campylobacter jejuni","Campylobacter coli; Campylobacter jejuni; Campylobacter unknown","Campylobacter coli; Campylobacter unknown","Campylobacter coli; Escherichia coli, Enteropathogenic","Campylobacter fetus","Campylobacter jejuni","Campylobacter jejuni; Bacillus cereus","Campylobacter jejuni; Campylobacter coli","Campylobacter jejuni; Campylobacter jejuni","Campylobacter jejuni; Campylobacter lari; Cryptosporidium unknown; Helicobacter canadensis","Campylobacter jejuni; Campylobacter other","Campylobacter jejuni; Campylobacter unknown","Campylobacter jejuni; Clostridium perfringens","Campylobacter jejuni; Cryptosporidium parvum","Campylobacter jejuni; Entamoeba unknown; Giardia unknown","Campylobacter jejuni; Escherichia coli, Shiga toxin-producing","Campylobacter jejuni; Escherichia coli, Shiga toxin-producing; Escherichia coli, Shiga toxin-producing; Cryptosporidium","Campylobacter jejuni; Escherichia coli, Shiga toxin-producing; Giardia","Campylobacter jejuni; Giardia unknown","Campylobacter jejuni; Listeria monocytogenes","Campylobacter jejuni; Norovirus other; Giardia duodenalis","Campylobacter jejuni; Norovirus unknown","Campylobacter jejuni; Plesiomonas shigelloides","Campylobacter jejuni; Salmonella enterica","Campylobacter jejuni; Salmonella enterica; Salmonella enterica","Campylobacter jejuni; Shigella unknown","Campylobacter jejuni; Shigella unknown; Blastocystis hominis; Endolimax nana; Norovirus Genogroup I","Campylobacter jejuni; Staphylococcus aureus","Campylobacter jejuni; Yersinia enterocolitica","Campylobacter lari","Campylobacter lari; Campylobacter jejuni","Campylobacter other","Campylobacter other; Campylobacter coli","Campylobacter other; Campylobacter other","Campylobacter other; Norovirus Genogroup II","Campylobacter other; Vibrio other; Vibrio cholerae","Campylobacter unknown","Campylobacter unknown; Campylobacter coli; Campylobacter jejuni","Campylobacter unknown; Campylobacter jejuni","Campylobacter unknown; Campylobacter unknown","Campylobacter unknown; Escherichia coli, Shiga toxin-producing","Campylobacter unknown; Giardia duodenalis","Campylobacter unknown; Giardia unknown","Campylobacter unknown; Salmonella enterica","Campylobacter unknown; Salmonella unknown","Campylobacter; Campylobacter","Campylobacter; Campylobacter jejuni","Campylobacter; Cryptosporidium","Campylobacter; Salmonella enterica","Campylobacter; Salmonella enterica; Escherichia coli, Shiga toxin-producing","Campylobacter; Shigella sonnei","Chloramines","Chlordane","Chlordane; Heptachlor; Toxaphene; Kerosene"],"n":[1,3,2,1,1,1,1,1,1,1,1,1,1,1,1,2,14,1,1,1,1,30,4,380,1,1,157,1,2,1,1,2,49,1,1,1,2,1,1,1,1,1,1,5,78,21,1,1,1,1,2,535,1,5,1,1,1,3,1,1,1,3,1,1,1,1,1,1,1,5,1,1,1,1,1,1,1,5,1,1,1,1,237,1,3,1,1,1,1,1,1,2,1,1,1,1,1,16,3,1]},"columns":[{"id":"etiology","name":"etiology","type":"character","maxWidth":400,"align":"left"},{"id":"n","name":"n","type":"numeric","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows (Total: 679)"},"dataKey":"7bc5d6084b2e1d5e111c6d2cbfccd112"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- ## Solution 4 ```r outbreaks %>% count(etiology) ``` <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-976c84ac72a9422948cd" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-976c84ac72a9422948cd">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"etiology":["Acanthamoeba unknown","Adenovirus","Adenovirus B","Adenovirus F; Escherichia coli, Enteroaggregative","Adenovirus F; Escherichia coli, Enteropathogenic","Adenovirus F; Escherichia coli, Enteropathogenic; Clostridium difficile","Adenovirus other; Adenovirus","Adenovirus unknown","Adenovirus; Clostridium","Adenovirus; Norovirus Genogroup II","Adenovirus; Norovirus Genogroup II; Clostridium other","Alkaline Water","Amnesic shellfish poison","Anatoxin-a; Other - Chemical/Toxin","Anisakis","Arsenic","Astrovirus","Astrovirus; Norovirus","Astrovirus; Norovirus unknown","Astrovirus; Salmonella unknown","Astrovirus; Sapovirus unknown","Avian schistosomes","Bacillus","Bacillus cereus","Bacillus cereus; Bacillus other","Bacillus cereus; Bacillus subtilus; Bacillus stearothermophilus","Bacillus cereus; Clostridium perfringens","Bacillus cereus; Clostridium perfringens; Other - Bacterium","Bacillus cereus; Clostridium perfringens; Staphylococcus aureus","Bacillus cereus; Clostridium perfringens; Staphylococcus aureus; Norovirus Genogroup II","Bacillus cereus; Norovirus","Bacillus cereus; Norovirus Genogroup I","Bacillus cereus; Staphylococcus aureus","Bacillus cereus; Staphylococcus other","Bacillus other","Bacillus unknown","Bacillus; Clostridium","Bacillus; Clostridium perfringens","Bacillus; Other - Chemical/Toxin","Bacillus; Staphylococcus","Bromate; Disinfection byproducts","Bromine","Brucella","Brucella unknown","Campylobacter","Campylobacter coli","Campylobacter coli; Campylobacter jejuni","Campylobacter coli; Campylobacter jejuni; Campylobacter unknown","Campylobacter coli; Campylobacter unknown","Campylobacter coli; Escherichia coli, Enteropathogenic","Campylobacter fetus","Campylobacter jejuni","Campylobacter jejuni; Bacillus cereus","Campylobacter jejuni; Campylobacter coli","Campylobacter jejuni; Campylobacter jejuni","Campylobacter jejuni; Campylobacter lari; Cryptosporidium unknown; Helicobacter canadensis","Campylobacter jejuni; Campylobacter other","Campylobacter jejuni; Campylobacter unknown","Campylobacter jejuni; Clostridium perfringens","Campylobacter jejuni; Cryptosporidium parvum","Campylobacter jejuni; Entamoeba unknown; Giardia unknown","Campylobacter jejuni; Escherichia coli, Shiga toxin-producing","Campylobacter jejuni; Escherichia coli, Shiga toxin-producing; Escherichia coli, Shiga toxin-producing; Cryptosporidium","Campylobacter jejuni; Escherichia coli, Shiga toxin-producing; Giardia","Campylobacter jejuni; Giardia unknown","Campylobacter jejuni; Listeria monocytogenes","Campylobacter jejuni; Norovirus other; Giardia duodenalis","Campylobacter jejuni; Norovirus unknown","Campylobacter jejuni; Plesiomonas shigelloides","Campylobacter jejuni; Salmonella enterica","Campylobacter jejuni; Salmonella enterica; Salmonella enterica","Campylobacter jejuni; Shigella unknown","Campylobacter jejuni; Shigella unknown; Blastocystis hominis; Endolimax nana; Norovirus Genogroup I","Campylobacter jejuni; Staphylococcus aureus","Campylobacter jejuni; Yersinia enterocolitica","Campylobacter lari","Campylobacter lari; Campylobacter jejuni","Campylobacter other","Campylobacter other; Campylobacter coli","Campylobacter other; Campylobacter other","Campylobacter other; Norovirus Genogroup II","Campylobacter other; Vibrio other; Vibrio cholerae","Campylobacter unknown","Campylobacter unknown; Campylobacter coli; Campylobacter jejuni","Campylobacter unknown; Campylobacter jejuni","Campylobacter unknown; Campylobacter unknown","Campylobacter unknown; Escherichia coli, Shiga toxin-producing","Campylobacter unknown; Giardia duodenalis","Campylobacter unknown; Giardia unknown","Campylobacter unknown; Salmonella enterica","Campylobacter unknown; Salmonella unknown","Campylobacter; Campylobacter","Campylobacter; Campylobacter jejuni","Campylobacter; Cryptosporidium","Campylobacter; Salmonella enterica","Campylobacter; Salmonella enterica; Escherichia coli, Shiga toxin-producing","Campylobacter; Shigella sonnei","Chloramines","Chlordane","Chlordane; Heptachlor; Toxaphene; Kerosene"],"n":[1,3,2,1,1,1,1,1,1,1,1,1,1,1,1,2,14,1,1,1,1,30,4,380,1,1,157,1,2,1,1,2,49,1,1,1,2,1,1,1,1,1,1,5,78,21,1,1,1,1,2,535,1,5,1,1,1,3,1,1,1,3,1,1,1,1,1,1,1,5,1,1,1,1,1,1,1,5,1,1,1,1,237,1,3,1,1,1,1,1,1,2,1,1,1,1,1,16,3,1]},"columns":[{"id":"etiology","name":"etiology","type":"character","maxWidth":400,"align":"left"},{"id":"n","name":"n","type":"numeric","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows (Total: 679)"},"dataKey":"7bc5d6084b2e1d5e111c6d2cbfccd112"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- class: your-turn # Your Turn 5 Let's turn our attention to only observations where the primary mode of infection is Food. Using that criterion, can you reproduce the table below? **Note:** `ifsac_category` refers to food category (IFSAC = Interagency Food Safety Analytics Collaboration, part of the CDC) <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-8215c3b2654f2247051b" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-8215c3b2654f2247051b">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"ifsac_category":["Beef","Chicken","Crustaceans","Dairy","Eggs","Fish","Fruits","Fungi","Game","Grains-Beans","Herbs","Invalid","Mollusks","Multiple","Nuts-Seeds","Oils-Sugars","Other","Other Aquatic Animals","Other Meat","Other Poultry","Pork","Root/Underground","Seeded Vegetables","Sprouts","Turkey","Unclassifiable","Vegetable Row Crops",null],"n":[723,571,111,356,197,1019,268,45,36,203,79,7,412,5984,32,12,190,12,19,12,350,86,147,54,210,440,245,11285]},"columns":[{"id":"ifsac_category","name":"ifsac_category","type":"character","maxWidth":400,"align":"left"},{"id":"n","name":"n","type":"numeric","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows"},"dataKey":"816dea2f7b3c275f2cff2d29f2fef835"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> ??? --- ## Solution 5 ```r outbreaks %>% filter(primary_mode == "Food") %>% count(ifsac_category) ``` <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-16b20034f09bff1e996e" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-16b20034f09bff1e996e">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"ifsac_category":["Beef","Chicken","Crustaceans","Dairy","Eggs","Fish","Fruits","Fungi","Game","Grains-Beans","Herbs","Invalid","Mollusks","Multiple","Nuts-Seeds","Oils-Sugars","Other","Other Aquatic Animals","Other Meat","Other Poultry","Pork","Root/Underground","Seeded Vegetables","Sprouts","Turkey","Unclassifiable","Vegetable Row Crops",null],"n":[723,571,111,356,197,1019,268,45,36,203,79,7,412,5984,32,12,190,12,19,12,350,86,147,54,210,440,245,11285]},"columns":[{"id":"ifsac_category","name":"ifsac_category","type":"character","maxWidth":400,"align":"left"},{"id":"n","name":"n","type":"numeric","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows"},"dataKey":"816dea2f7b3c275f2cff2d29f2fef835"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- class: your-turn # Your Turn 6 .pull-left[ Explore the relationship between `month` and the number of illnesses with a series of **boxplots** like the one to the right. Can you recreate it? **Hint:** Try using the `group` aesthetic to tell R that you'd like to create a boxplot for each unique value of `month`. ] .pull-right[ <img src="session01-practice-slides_files/figure-html/sol-6-1.png" width="504" /> ] ??? Check documentation for use of the argument that allows you to create a new boxplot for each grouping. --- ## Solution 6 .wide-left[ ```r outbreaks %>% ggplot(aes(x = month, y = illnesses)) + * geom_boxplot(aes(group = month)) ``` The outlier here makes it hard to see what's going on. Let's modify this. ] .narrow-right[ <img src="session01-practice-slides_files/figure-html/unnamed-chunk-17-1.png" width="504" /> ] ??? But the outlier here makes it hard to see what's going on. Let's modify this. --- class: your-turn # Your Turn 7 The outlier we just observed represents the outbreak associated with the highest number of illnesses. Which observation is this? 1. Display **only** this observation in a table. 2. Then, recreate the boxplots **without** this observation. Here is the code we just used to make the boxplots in the last exercise: ```r outbreaks %>% ggplot(aes(x = month, y = illnesses)) + geom_boxplot(aes(group = month)) ``` --- class: space-saver ## Solution 7 .pull-left[ ```r outbreaks %>% filter(illnesses == max(illnesses)) ``` ] .pull-right[ <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-3f15bcd93dfbd1ccb425" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-3f15bcd93dfbd1ccb425">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"year":[1993],"month":[3],"state":["Wisconsin"],"primary_mode":["Water"],"etiology":["Cryptosporidium parvum"],"serotype_or_genotype":[null],"etiology_status":["Confirmed"],"setting":["Community/Municipality"],"illnesses":[403000],"hospitalizations":["NA"],"info_on_hospitalizations":["NA"],"deaths":[50],"info_on_deaths":["NA"],"food_vehicle":[null],"food_contaminated_ingredient":[null],"ifsac_category":[null],"water_exposure":["Drinking water"],"water_type":["Community"],"animal_type":[null],"animal_type_specify":[null],"water_status":["Reviewed"]},"columns":[{"id":"year","name":"year","type":"numeric","maxWidth":400,"align":"left"},{"id":"month","name":"month","type":"numeric","maxWidth":400,"align":"left"},{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"primary_mode","name":"primary_mode","type":"character","maxWidth":400,"align":"left"},{"id":"etiology","name":"etiology","type":"character","maxWidth":400,"align":"left"},{"id":"serotype_or_genotype","name":"serotype_or_genotype","type":"character","maxWidth":400,"align":"left"},{"id":"etiology_status","name":"etiology_status","type":"character","maxWidth":400,"align":"left"},{"id":"setting","name":"setting","type":"character","maxWidth":400,"align":"left"},{"id":"illnesses","name":"illnesses","type":"numeric","maxWidth":400,"align":"left"},{"id":"hospitalizations","name":"hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_hospitalizations","name":"info_on_hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"deaths","name":"deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_deaths","name":"info_on_deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"food_vehicle","name":"food_vehicle","type":"character","maxWidth":400,"align":"left"},{"id":"food_contaminated_ingredient","name":"food_contaminated_ingredient","type":"character","maxWidth":400,"align":"left"},{"id":"ifsac_category","name":"ifsac_category","type":"character","maxWidth":400,"align":"left"},{"id":"water_exposure","name":"water_exposure","type":"character","maxWidth":400,"align":"left"},{"id":"water_type","name":"water_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type","name":"animal_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type_specify","name":"animal_type_specify","type":"character","maxWidth":400,"align":"left"},{"id":"water_status","name":"water_status","type":"character","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows"},"dataKey":"29afbfedb8441495d5cae72f09a4fc4b"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> <br> ] -- .pull-left[ ```r outbreaks %>% * filter(illnesses != max(illnesses)) %>% ggplot(aes(x = month, y = illnesses)) + geom_boxplot(aes(group = month)) ``` ] .pull-right[ <img src="session01-practice-slides_files/figure-html/unnamed-chunk-21-1.png" width="504" /> ] --- class: your-turn # Your Turn 8 Which outbreaks lead to the highest number of illnesses? Display these observations in a table from greatest to fewest illnesses: <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-4dbc34c85e8a9369e192" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-4dbc34c85e8a9369e192">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"year":[1993,1987,1983,1991,1980,2007,1995,1978,1987,1975,1974,1971,1979,1983,1978,1996,1992,1980,2013,2005,1976,2008,1979,2007,1980,2010,1987,1981,2007,2006,2008,1980,1997,2004,1995,1975,1998,1987,2013,1991,2008,1983,2006,2018,1974,1979,2020,2018,2014,2017,1975,1990,1983,1980,2003,2002,2003,1998,2015,1989,1975,1988,2001,2003,2005,1983,2020,2001,2015,2007,2009,1998,2017,1980,1999,1980,2020,2002,2006,1978,1977,1971,1976,1983,2011,2006,2005,1980,2000,2007,2006,2008,2016,2004,1985,2002,1989,2003,2000,2012],"month":[3,1,6,8,6,5,7,3,9,8,11,7,10,8,5,8,2,7,4,6,7,6,6,7,12,2,10,3,9,5,4,8,12,7,12,4,7,7,7,6,3,7,4,1,1,10,6,1,3,4,6,5,8,6,1,9,8,6,7,4,6,5,5,11,4,5,2,1,6,6,11,4,1,9,8,6,5,7,11,5,4,11,3,7,10,3,3,8,7,6,8,9,2,1,11,3,9,7,6,5],"state":["Wisconsin","Georgia","Pennsylvania","Puerto Rico","Texas","Utah","Georgia","Colorado","Multistate","Pennsylvania","New York","California","Pennsylvania","Texas","Vermont","California","Oregon","Texas","Alaska","New York","Puerto Rico","Texas","Arizona","Idaho","Pennsylvania","Multistate","Puerto Rico","Colorado","Florida","California","Multistate","Georgia","New York","Ohio","New York","Indiana","Texas","Puerto Rico","Illinois","Michigan","Colorado","Utah","Colorado","Wisconsin","Florida","Oregon","Multistate","Massachusetts","Indiana","Nevada","Oregon","Tennessee","West Virginia","Vermont","Texas","Illinois","Multistate","Illinois","Multistate","Arizona","California","Texas","New York","Louisiana","California","Florida","Multistate","Tennessee","Missouri","Illinois","Louisiana","Ohio","Illinois","Connecticut","New York","Montana","Multistate","Massachusetts","New York","Missouri","New Hampshire","New York","New York","Washington","Georgia","Alabama","Illinois","Ohio","Wisconsin","Pennsylvania","Multistate","Multistate","Virginia","Texas","Massachusetts","Texas","Alabama","Kansas","Ohio","Texas"],"primary_mode":["Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Person-to-person","Water","Water","Water","Water","Water","Water","Food","Water","Water","Water","Food","Food","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Water","Food","Person-to-person","Water","Water","Food","Person-to-person","Person-to-person","Person-to-person","Water","Water","Water","Water","Food","Food","Food","Food","Food","Water","Water","Water","Food","Food","Food","Water","Animal Contact","Food","Person-to-person","Food","Food","Food","Person-to-person","Water","Water","Water","Food","Water","Food","Water","Water","Water","Water","Water","Person-to-person","Food","Food","Water","Food","Water","Food","Food","Person-to-person","Food","Water","Food","Water","Water","Water","Person-to-person"],"etiology":["Cryptosporidium parvum","Cryptosporidium parvum","Unknown","Unknown","Unknown","Cryptosporidium unknown","Cryptosporidium parvum; Giardia duodenalis; Unknown; Unknown","Giardia duodenalis","Norovirus other","Unknown","Giardia duodenalis","Unknown","Giardia duodenalis","Unknown","Campylobacter jejuni","Cryptosporidium parvum; Giardia duodenalis","Cryptosporidium parvum","Unknown","Norovirus Genogroup I","Cryptosporidium hominis; Cryptosporidium hominis","Shigella sonnei","Cryptosporidium hominis","Giardia duodenalis","Cryptosporidium hominis","Chlordane; Heptachlor; Toxaphene; Kerosene","Salmonella enterica","Shigella sonnei","Rotavirus","Unknown","Campylobacter jejuni","Salmonella enterica","Norovirus other","Norovirus other","Campylobacter jejuni; Norovirus other; Giardia duodenalis","Giardia duodenalis","Unknown","Cryptosporidium parvum","Escherichia coli, Enteropathogenic","Plant/Herbal toxins","Unknown","Salmonella enterica","Giardia duodenalis","Norovirus Genogroup I","Norovirus","Shigella sonnei","Unknown","Salmonella enterica","Norovirus","Shigella sonnei","Norovirus Genogroup II; Norovirus Genogroup I; Norovirus Genogroup II; Astrovirus","Escherichia coli, Enterotoxigenic","Unknown","Unknown","Unknown","Shigella sonnei","Clostridium perfringens","Hepatitis A","Escherichia coli, Enterotoxigenic","Salmonella enterica","Norovirus other","Unknown","Shigella sonnei","Shigella flexneri","Clostridium perfringens",null,"Campylobacter jejuni","Salmonella enterica","Norovirus Genogroup II","Shigella sonnei","Salmonella enterica","Clostridium perfringens",null,"Norovirus Genogroup II","Campylobacter jejuni","Escherichia coli, Shiga toxin-producing; Campylobacter jejuni","Giardia duodenalis","Cyclospora cayetanensis","Cryptosporidium unknown","Norovirus unknown","Unknown","Giardia duodenalis","Unknown","Salmonella unknown","Salmonella enterica","Shigella sonnei","Clostridium perfringens",null,"Unknown","Escherichia coli, Shiga toxin-producing","Cryptosporidium parvum","Salmonella enterica","Salmonella enterica","Norovirus",null,"Giardia duodenalis","Salmonella enterica","Unknown","Cryptosporidium hominis; Cryptosporidium hominis","Cryptosporidium parvum","Norovirus Genogroup II"],"serotype_or_genotype":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"unknown",null,null,null,null,null,null,"Enteritidis",null,null,null,null,"Saintpaul",null,null,null,null,null,null,null,null,null,"Typhimurium",null,null,null,null,null,"Newport",null,"subgroup D","GII.2; unknown - ; GII.3;","O6:H16",null,null,null,null,null,null,"O6","Poona",null,null,null,"serotype 2a",null,null,null,"Hadar","unknown",null,"Heidelberg",null,null,"unknown",null,"O157:H7;",null,null,null,null,null,null,null,null,"Enteritidis",null,null,null,null,"O157:H7",null,"Tennessee","Typhimurium",null,null,null,"Enteritidis",null,null,null,"unknown"],"etiology_status":["Confirmed","Confirmed","Suspected","Suspected","Suspected","Confirmed","Confirmed; Confirmed; Suspected; Suspected","Confirmed","Confirmed","Suspected","Confirmed","Suspected","Confirmed","Suspected","Confirmed","Confirmed; Confirmed","Confirmed","Suspected","Confirmed","Confirmed; Suspected","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed; Confirmed; Suspected; Suspected","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed; Confirmed; Confirmed","Confirmed","Suspected","Confirmed","Confirmed","Suspected","Suspected","Confirmed","Confirmed","Confirmed","Suspected","Confirmed","Suspected","Confirmed","Suspected","Confirmed","Confirmed; Confirmed; Confirmed; Confirmed","Confirmed","Suspected","Suspected","Suspected","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Suspected","Confirmed","Confirmed","Confirmed",null,"Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Suspected",null,"Confirmed","Confirmed","Confirmed; Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Suspected","Confirmed","Suspected","Confirmed","Confirmed","Confirmed","Suspected",null,"Suspected","Confirmed","Confirmed","Confirmed","Confirmed","Suspected",null,"Confirmed","Confirmed","Suspected","Confirmed; Suspected","Confirmed","Suspected"],"setting":["Community/Municipality","Community/Municipality","Camp/Cabin Setting","Community/Municipality","Community/Municipality","Community/Municipality","Park - Waterpark","Community/Municipality","School/College/University; Other","Community/Municipality","Community/Municipality","Community/Municipality","Community/Municipality","Community/Municipality","Community/Municipality","Park - Waterpark; Other","Community/Municipality","Community/Municipality","School/college/university","Park - State Park","Community/Municipality","Community/Municipality","Camp/Cabin Setting","Community/Municipality","Community/Municipality","Restaurant - Sit-down dining; Restaurant - other or unknown type; Private home/residence; Banquet Facility (food prepared and served on-site); Caterer (food prepared off-site from where served)","Community/Municipality","Community/Municipality","Community/Municipality","Prison/jail",null,"Community/Municipality","Resort","Restaurant/Cafeteria; Camp/Cabin Setting; Other","Other","Community/Municipality","Subdivision/Neighborhood","Community/Municipality","Other","Camp/Cabin Setting","Community/Municipality","Community/Municipality",null,"School/college/university","Community/Municipality","Community/Municipality","Restaurant - \"Fast-food\"(drive up service or pay at counter); Restaurant - Sit-down dining; Restaurant - other or unknown type; Private home/residence; Grocery store; Long-term care/nursing home/assisted living facility; Camp; Farm/dairy","School/college/university","Other, specify","School/college/university","Park - National Park","Club (Requires Membership)","Community/Municipality","Community/Municipality","Unknown","Prison/jail","Restaurant - other or unknown type","Caterer (food prepared off-site from where served)",null,"Resort","Resort","Restaurant/Cafeteria","Restaurant - other or unknown type","Prison/jail","Prison/jail","Community/Municipality",null,"Restaurant - other or unknown type","Other, specify","Restaurant - other or unknown type; Fair, festival, other temp or mobile services",null,"Restaurant - other or unknown type","School/college/university","School/College/University","Festival/Fair","Community/Municipality","Other","Club (Requires Membership)","Restaurant - other or unknown type","Restaurant/Cafeteria","Community/Municipality","Restaurant/Cafeteria","Resort","Restaurant/Cafeteria","Other, specify","Prison/jail","School/college/university","Community/Municipality","Restaurant - other or unknown type","Community/Municipality","Other",null,"School/college/university","Unknown","Community/Municipality","Restaurant - other or unknown type","Community/Municipality","Community/Municipality","Club (Requires Membership)",null],"illnesses":[403000,13000,11400,9847,8000,5697,5449,5000,5000,5000,4800,3500,3500,3400,3000,3000,2760,2550,2500,2307,2150,2050,2000,2000,2000,1939,1800,1761,1663,1644,1500,1500,1450,1450,1449,1400,1400,1400,1341,1320,1300,1272,1200,1200,1200,1200,1132,1126,1101,1000,1000,1000,1000,990,964,950,935,916,907,900,900,900,886,880,872,871,848,811,809,802,800,800,800,800,781,780,771,767,766,750,750,750,750,750,742,741,738,738,736,730,715,714,708,707,703,700,700,700,700,699],"hospitalizations":["NA","NA",2,12,"NA",0,2,"NA","NA","NA","NA","NA","NA",2,"NA","NA","NA","NA",0,25,"NA",5,"NA","NA","NA","NA",30,"NA",0,7,308,"NA","NA",21,"NA","NA",23,9,0,"NA","NA",13,1,0,"NA","NA",167,"NA",53,0,"NA",5,"NA","NA","NA",1,"NA",7,204,1,"NA",0,22,35,0,4,179,0,0,29,0,4,0,"NA",71,"NA",39,"NA",27,"NA","NA","NA","NA",18,1,"NA",0,2,23,11,129,166,0,"NA","NA",3,1,3,0,0],"info_on_hospitalizations":["NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA",2500,"NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA",0,"NA","NA",705,0,1075,279,"NA","NA","NA","NA","NA","NA","NA","NA",720,"NA","NA","NA","NA","NA","NA","NA",524,"NA",0,"NA",800,"NA",800,"NA","NA","NA",763,"NA","NA","NA","NA","NA","NA","NA",742,"NA","NA","NA","NA","NA","NA","NA",708,"NA","NA","NA","NA","NA","NA",0],"deaths":[50,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,"NA",0,0,0,0,0,0,0,0,"NA",0,0,0,0,2,0,0,0,0,0,0,0,0,"NA",1,0,0,0,0,0,0,0,0,0,0,0,0,0,"NA",0,"NA",0,6,0,0,0,"NA",0,0,0,0,0,0,0,0,0,0,0,2,0,"NA","NA",0,0,0,0,0,0,0,"NA",0,0,1,0,0,9,0,"NA",0,0,0,0,0,0],"info_on_deaths":["NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA",2500,"NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA",0,"NA","NA",708,112,1075,279,"NA","NA","NA","NA","NA","NA","NA","NA",720,"NA","NA","NA","NA","NA","NA","NA",509,"NA",0,"NA",800,"NA",800,"NA","NA","NA",0,"NA","NA","NA","NA","NA","NA","NA",742,"NA","NA","NA","NA","NA","NA","NA",708,"NA","NA","NA","NA","NA","NA",0],"food_vehicle":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"shell egg, other",null,null,null,"other milk, pasteurized","peppers, jalapeno; tomato, unspecified; peppers, serrano",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"red onion",null,null,null,null,null,null,null,null,"gravy, beef; roast beef, unspecified; potato, mashed","green onion/scallion","potato salad; macaroni salad","cucumber",null,null,null,"tomato, unspecified","corn, unspecified",null,null,null,null,null,"hummus",null,"unspecified vegetables",null,null,null,null,"salad mix, bagged",null,null,null,null,null,null,null,null,"chicken, baked",null,null,"watermelon",null,"peanut butter","peanut butter; peanut paste",null,null,null,"salsa, 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Pool",null],"animal_type":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Baby chick or duckling",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"animal_type_specify":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"duck, chicken",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_status":["Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed",null,"Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed",null,"Reviewed","Reviewed","Reviewed",null,null,"Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed","Reviewed",null,null,"Reviewed","Reviewed",null,null,null,null,"Reviewed","Reviewed","Reviewed","Reviewed",null,null,null,null,null,"Reviewed","Reviewed","Reviewed",null,null,null,"Reviewed",null,null,null,null,null,null,null,"Reviewed","Reviewed","Reviewed",null,"Reviewed",null,"Reviewed","Reviewed","Reviewed","Reviewed","Reviewed",null,null,null,"Reviewed",null,"Reviewed",null,null,null,null,"Reviewed",null,"Reviewed","Reviewed","Reviewed",null]},"columns":[{"id":"year","name":"year","type":"numeric","maxWidth":400,"align":"left"},{"id":"month","name":"month","type":"numeric","maxWidth":400,"align":"left"},{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"primary_mode","name":"primary_mode","type":"character","maxWidth":400,"align":"left"},{"id":"etiology","name":"etiology","type":"character","maxWidth":400,"align":"left"},{"id":"serotype_or_genotype","name":"serotype_or_genotype","type":"character","maxWidth":400,"align":"left"},{"id":"etiology_status","name":"etiology_status","type":"character","maxWidth":400,"align":"left"},{"id":"setting","name":"setting","type":"character","maxWidth":400,"align":"left"},{"id":"illnesses","name":"illnesses","type":"numeric","maxWidth":400,"align":"left"},{"id":"hospitalizations","name":"hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_hospitalizations","name":"info_on_hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"deaths","name":"deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_deaths","name":"info_on_deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"food_vehicle","name":"food_vehicle","type":"character","maxWidth":400,"align":"left"},{"id":"food_contaminated_ingredient","name":"food_contaminated_ingredient","type":"character","maxWidth":400,"align":"left"},{"id":"ifsac_category","name":"ifsac_category","type":"character","maxWidth":400,"align":"left"},{"id":"water_exposure","name":"water_exposure","type":"character","maxWidth":400,"align":"left"},{"id":"water_type","name":"water_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type","name":"animal_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type_specify","name":"animal_type_specify","type":"character","maxWidth":400,"align":"left"},{"id":"water_status","name":"water_status","type":"character","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows (Total: 57,649)"},"dataKey":"f4f68f23f8665a88a73b148a39014d69"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- class: your-turn # Your Turn 9 How many different primary modes of illness are in this data set? How often does each appear in the data? Order the rows so that the most common primary mode appears at the top. --- ## Solution 9 ```r outbreaks %>% count(primary_mode, sort = TRUE) ``` or... ```r outbreaks %>% count(primary_mode) %>% arrange(desc(n)) ``` <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-2d61f4cc14070f598e7c" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-2d61f4cc14070f598e7c">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"primary_mode":["Person-to-person","Food","Indeterminate/Other/Unknown","Water","Animal Contact","Environmental contamination other than food/water"],"n":[26561,23105,4647,2713,512,111]},"columns":[{"id":"primary_mode","name":"primary_mode","type":"character","maxWidth":400,"align":"left"},{"id":"n","name":"n","type":"numeric","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows"},"dataKey":"e17482ca74d9c611a3b0053e5d016982"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> ??? Looks like the most common primary mode for outbreaks in this particular data set is person-to-person. --- class: your-turn # Your Turn 10 .pull-left[Can you recreate this visualization of the **primary modes** of infection? _Hint:_ Look up the help page for `coord_flip()`. ] .pull-right[ <img src="session01-practice-slides_files/figure-html/unnamed-chunk-28-1.png" width="504" /> ] ??? --- ## Solution 10 .pull-left[ ```r outbreaks %>% ggplot(aes(x = primary_mode)) + geom_bar() + * coord_flip() ``` ] .pull-right[ <img src="session01-practice-slides_files/figure-html/unnamed-chunk-29-1.png" width="504" /> ] ??? Notice coord_flip() If your first inclination was to use count() then you might have come up with an answer like... --- ## Solution 10 - alternative .wide-left[ ```r outbreaks %>% * count(primary_mode, name = "count") %>% ggplot(aes(x = primary_mode, y = count)) + * geom_col() + coord_flip() ``` ] .narrow-right[ <img src="session01-practice-slides_files/figure-html/unnamed-chunk-30-1.png" width="504" /> ] ??? This one, but it's a little less efficient code-wise. --- class: your-turn # Your Turn 11 Let's take a closer look at outbreaks for which the primary mode of infection is **Animal Contact**. How many Animal Contact outbreaks has each _individual_ state had? Recreate the table below. <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-291d5580f426671fcf3c" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-291d5580f426671fcf3c">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"state":["Ohio","Minnesota","Idaho","Colorado","Pennsylvania","Utah","Wisconsin","Illinois","Michigan","New Hampshire","Oregon","Wyoming","Nebraska","Iowa","Kansas","Virginia","Washington","Missouri","North Carolina","Tennessee","Indiana","Massachusetts","Montana","Kentucky","West Virginia","Alaska","Arizona","Maine","Maryland","South Carolina","South Dakota","Texas","Alabama","Arkansas","Oklahoma","Vermont","Connecticut","Hawaii","Louisiana","New Mexico","New York","North Dakota","Rhode Island"],"n":[53,42,24,19,17,17,17,15,14,13,13,10,9,8,7,7,7,6,6,6,5,5,5,4,4,3,3,3,3,3,3,3,2,2,2,2,1,1,1,1,1,1,1]},"columns":[{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"n","name":"n","type":"numeric","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows"},"dataKey":"68deb848cb0ec52862568ebf08da7973"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> _Hint_: You will need to remove observations where `state` is equal to "Multistate". --- ## Solution 11 ```r outbreaks %>% filter( primary_mode == "Animal Contact", state != "Multistate" ) %>% count(state, sort = TRUE) ``` <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-3a6528a088338f788ede" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-3a6528a088338f788ede">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"state":["Ohio","Minnesota","Idaho","Colorado","Pennsylvania","Utah","Wisconsin","Illinois","Michigan","New Hampshire","Oregon","Wyoming","Nebraska","Iowa","Kansas","Virginia","Washington","Missouri","North Carolina","Tennessee","Indiana","Massachusetts","Montana","Kentucky","West Virginia","Alaska","Arizona","Maine","Maryland","South Carolina","South Dakota","Texas","Alabama","Arkansas","Oklahoma","Vermont","Connecticut","Hawaii","Louisiana","New Mexico","New York","North Dakota","Rhode Island"],"n":[53,42,24,19,17,17,17,15,14,13,13,10,9,8,7,7,7,6,6,6,5,5,5,4,4,3,3,3,3,3,3,3,2,2,2,2,1,1,1,1,1,1,1]},"columns":[{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"n","name":"n","type":"numeric","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows"},"dataKey":"68deb848cb0ec52862568ebf08da7973"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- class: your-turn # Your Turn 12 .left-column35[ Now that we know the top 3 states are **Ohio**, **Minnesota**, and **Idaho**, recreate this table: * Has only the Animal Contact outbreaks for those locations * Column names with "animal" appear after `state` * Drop the `primary_mode` column ] .right-column63.space-saver[ <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-947262bc7e89cbd65f6e" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-947262bc7e89cbd65f6e">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"year":[2009,2009,2009,2009,2009,2009,2009,2010,2010,2010,2011,2011,2011,2011,2012,2012,2012,2012,2012,2012,2012,2012,2013,2013,2013,2013,2013,2013,2013,2014,2013,2012,2014,2014,2014,2014,2014,2014,2014,2014,2014,2014,2014,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2017,2016,2017,2017,2017,2017,2017,2017,2018,2018,2017,2017,2017,2017,2017,2018,2018,2018,2018,2018,2018,2018,2018,2018,2018,2018,2019,2018,2018,2019,2019,2019,2019],"month":[1,4,5,5,5,8,8,3,4,8,7,8,9,9,1,2,4,5,7,7,8,11,5,6,8,6,10,10,10,1,12,7,6,7,5,7,8,9,7,10,10,6,12,3,3,4,8,8,8,9,9,7,12,11,11,3,4,4,4,5,5,6,7,7,8,6,9,3,4,3,4,7,8,9,9,1,1,11,8,5,6,5,4,6,7,6,7,6,8,8,9,11,9,2,11,11,4,5,4,5],"state":["Ohio","Ohio","Ohio","Ohio","Idaho","Minnesota","Minnesota","Ohio","Minnesota","Minnesota","Minnesota","Minnesota","Idaho","Ohio","Ohio","Ohio","Minnesota","Ohio","Minnesota","Minnesota","Minnesota","Minnesota","Ohio","Minnesota","Minnesota","Minnesota","Ohio","Minnesota","Minnesota","Ohio","Ohio","Idaho","Ohio","Minnesota","Minnesota","Minnesota","Minnesota","Ohio","Minnesota","Minnesota","Ohio","Ohio","Ohio","Ohio","Ohio","Minnesota","Minnesota","Minnesota","Ohio","Ohio","Minnesota","Ohio","Ohio","Minnesota","Ohio","Ohio","Ohio","Ohio","Ohio","Minnesota","Minnesota","Ohio","Ohio","Minnesota","Minnesota","Ohio","Minnesota","Ohio","Idaho","Ohio","Ohio","Minnesota","Ohio","Ohio","Idaho","Ohio","Ohio","Idaho","Idaho","Idaho","Idaho","Idaho","Ohio","Ohio","Ohio","Minnesota","Minnesota","Minnesota","Ohio","Minnesota","Ohio","Ohio","Idaho","Ohio","Ohio","Minnesota","Ohio","Ohio","Ohio","Minnesota"],"animal_type":["Cattle","Pet fish","Cattle","Sheep or goats","Cat or kitten","Cattle","Cattle","Cattle","Cattle","Other poultry",null,"Sheep or goats",null,"Pet fish","Dog or Puppy","Cattle","Cattle","Other poultry","Cattle","Cattle; Sheep or goats","Other poultry","Cattle","Dog or Puppy","Cattle; Sheep or goats","Cattle","Other (specify)","Dog or Puppy","Cattle","Sheep or goats","Cattle","Turtle","Lizard","Cattle","Sheep or goats","Other small mammalian household pet","Cattle","Cattle","Pig","Other poultry","Cattle","Other reptile","Dog or Puppy","Other small mammalian household pet","Cattle","Cattle","Cattle","Cattle","Other (specify); Pig; Sheep or goats; Other small mammalian household pet; Cattle","Dog or Puppy","Cattle","Cattle","Cat or kitten","Cattle","Cattle","Cattle","Cattle","Cattle","Baby chick or duckling; Baby chick or duckling","Other small mammalian household pet","Cattle","Cattle","Other poultry","Sheep or goats","Other reptile; Baby chick or duckling","Other poultry","Cattle; Other poultry","Other small mammalian household pet",null,"Dog or Puppy","Sheep or goats",null,"Sheep or goats; Other (specify); Sheep or goats","Cattle","Cattle","Cattle","Cattle","Cattle","Dog or Puppy","Cattle","Cattle","Baby chick or duckling","Sheep or goats","Pig","Dog or Puppy",null,"Sheep or goats","Cattle","Dog or Puppy","Dog or Puppy",null,"Cattle","Cattle","Cattle","Sheep or goats","Dog or Puppy","Dog or Puppy","Dog or Puppy; Other poultry","Cattle","Other (specify)","Cattle"],"animal_type_specify":["Cattle, calf","Fish","Cattle, calf","Goat, kid","Cat, kitten","Cattle, calf","Cattle, calf","Cattle, calf","Cattle, calf","Chicken",null,"Goat",null,"Fish","Dog, puppy","Cattle, calf","Cattle, calf","Chicken","Cattle, calf","Cattle, calf; Goat","Turkey","Cattle, calf","Dog, puppy","Cattle, calf; Goat","Calf","Raccoon","Dog, puppy","Cattle, calf","Goat","Cattle, calf","Turtle","Bearded dragon","Cattle, calf","Goat","Mouse","Cattle, calf","Cattle, calf","Pig/hog (domestic)","Turkey","Cattle, calf","Reptile, other","Dog, puppy","Guinea pig","Cattle","Cattle, calf","Cattle, calf","Cattle, calf","Yaks; Pigs; Goats; Rabbits; Calves","Dog, puppy","Cattle, calf","Cattle, calf","Cat","Cattle, calf","Cattle, calf","Cattle, calf","Cattle, calf","Cattle, calf","Chick, baby chick; Duck, duckling","Hedgehog","Cattle, calf","Cattle, calf","Chicken","Goat","Black roughneck monitor lizard; Frozen chicks fed to reptile","Turkey","Cattle, calf; Chicken","Hedgehog",null,"Shelter dog","Goat",null,"angora goats; alpacas; sheep","Calf","Calves","calves",null,null,"puppy, strays","Cattle and Goats: Custom Slaughter workers","calves","ducklings","sheep, lambing shed",null,"animal shelter",null,"Sheep","beef calves","puppies","puppies",null,"calf","Holstein and Jersey","calves","Goats","dog","puppies","Blood Hound; Chickens","Two week old calf","calves","Calves"],"etiology":["Cryptosporidium unknown","Salmonella enterica","Cryptosporidium unknown","Cryptosporidium unknown","Campylobacter jejuni","Cryptosporidium parvum","Escherichia coli, Shiga toxin-producing","Cryptosporidium unknown","Cryptosporidium parvum","Campylobacter jejuni","Campylobacter jejuni","Escherichia coli, Shiga toxin-producing","Escherichia coli, Shiga toxin-producing","Salmonella enterica","Campylobacter unknown","Cryptosporidium unknown","Cryptosporidium parvum","Campylobacter unknown","Escherichia coli, Shiga toxin-producing; Cryptosporidium parvum","Escherichia coli, Shiga toxin-producing","Campylobacter jejuni","Cryptosporidium","Campylobacter jejuni","Cryptosporidium parvum","Cryptosporidium parvum","Campylobacter jejuni","Salmonella enterica; Campylobacter","Escherichia coli, Shiga toxin-producing","Escherichia coli, Shiga toxin-producing","Cryptosporidium unknown","Salmonella enterica","Salmonella enterica","Campylobacter; Salmonella enterica; Escherichia coli, Shiga toxin-producing","Escherichia coli, Shiga toxin-producing","Salmonella enterica","Cryptosporidium parvum","Cryptosporidium parvum","Salmonella enterica","Salmonella enterica","Cryptosporidium parvum","Salmonella enterica","Campylobacter unknown","Salmonella enterica","Salmonella enterica","Cryptosporidium unknown","Cryptosporidium parvum","Escherichia coli, Shiga toxin-producing","Escherichia coli, Shiga toxin-producing","Campylobacter unknown","Cryptosporidium unknown","Cryptosporidium unknown; Cryptosporidium parvum; Cryptosporidium parvum; Cryptosporidium other","Campylobacter unknown","Cryptosporidium unknown","Cryptosporidium parvum","Cryptosporidium unknown","Cryptosporidium unknown","Cryptosporidium unknown","Campylobacter unknown","Salmonella enterica","Cryptosporidium parvum","Escherichia coli, Shiga toxin-producing","Campylobacter","Escherichia coli, Shiga toxin-producing","Salmonella enterica","Salmonella enterica","Escherichia coli, Shiga toxin-producing; Campylobacter jejuni","Salmonella enterica; Salmonella enterica","Cryptosporidium","Campylobacter jejuni; Campylobacter jejuni","Cryptosporidium","Cryptosporidium parvum","Escherichia coli, Shiga toxin-producing; Escherichia coli, Shiga toxin-producing","Cryptosporidium parvum","Cryptosporidium","Cryptosporidium unknown","Cryptosporidium unknown","Cryptosporidium unknown; Campylobacter unknown","Campylobacter unknown","Salmonella enterica","Escherichia coli, Shiga toxin-producing","Campylobacter","Campylobacter","Salmonella enterica","Campylobacter jejuni","Cryptosporidium unknown","Escherichia coli, Shiga toxin-producing; Escherichia coli, Shiga toxin-producing","Cryptosporidium parvum","Campylobacter jejuni","Campylobacter jejuni","Cryptosporidium parvum","Cryptosporidium parvum; Cryptosporidium unknown; Salmonella enterica","Salmonella enterica; Giardia unknown; Cryptosporidium unknown","Salmonella enterica","Campylobacter jejuni","Campylobacter unknown","Campylobacter jejuni","Campylobacter jejuni","Cryptosporidium unknown","Cryptosporidium unknown","Cryptosporidium parvum"],"serotype_or_genotype":[null,"Paratyphi B",null,null,null,null,"O157:H7",null,null,null,null,"O157:H7","O26:H11","Paratyphi B",null,null,null,null,"O111:NM; IIaA15G2R2","O157:H7",null,null,null,null,null,null,"Typhimurium;","O157:H7","O157:H7",null,"Typhimurium","Cotham","Typhimurium; O111","O157:H7","Enteritidis",null,"IIaA15G2R1","I 4,[5],12:i:-","I 4,[5],12:i:-",null,"Pomona",null,"Braenderup","Typhimurium",null,"IIaA15G2R1","O157:H7","O157:H7",null,null,"other; ;",null,null,"IIaA15G2R1",null,null,null,null,"Typhimurium","IIaA15G2R1","O145",null,"O157:H7","Heidelberg","Uganda","O157:H7;","Typhimurium; Typhimurium",null,null,null,"IIaA15G2R1","O111; O26","IIaA15G2R1",null,null,null,null,null,"I 4,[5],12:i:-","O26",null,null,"I 4,[5],12:i:-",null,null,"O111; O111","IIaA15G2R2",null,null,"unknown","IIaA15G2R1; ; unknown","Typhimurium; ;","Heidelberg",null,null,null,null,null,null,"other"],"etiology_status":["Confirmed","Confirmed","Confirmed","Confirmed","Suspected","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Suspected","Confirmed","Confirmed","Suspected; Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed; Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed; Confirmed; Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Confirmed","Suspected","Suspected","Confirmed","Confirmed","Confirmed","Suspected","Confirmed","Confirmed","Confirmed","Suspected","Suspected; Suspected; Suspected; Confirmed","Confirmed","Suspected","Confirmed","Confirmed","Confirmed","Suspected","Suspected","Suspected","Confirmed","Confirmed","Suspected","Confirmed","Confirmed","Confirmed","Suspected; Suspected","Confirmed; Confirmed","Confirmed","Confirmed; 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specify","Private 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of {rows} rows (Total: 119)"},"dataKey":"0e1324c7fae74d7ba342df04084c3535"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> ] --- class: space-saver ## Solution 12 ```r outbreaks %>% filter( primary_mode == "Animal Contact", state %in% c("Ohio", "Minnesota", "Idaho") ) %>% relocate( contains("animal"), .after = state ) %>% select(-primary_mode) ``` <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-035a0ccabb6d3a99d8f4" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-035a0ccabb6d3a99d8f4">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"year":[2009,2009,2009,2009,2009,2009,2009,2010,2010,2010,2011,2011,2011,2011,2012,2012,2012,2012,2012,2012,2012,2012,2013,2013,2013,2013,2013,2013,2013,2014,2013,2012,2014,2014,2014,2014,2014,2014,2014,2014,2014,2014,2014,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2015,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2016,2017,2016,2017,2017,2017,2017,2017,2017,2018,2018,2017,2017,2017,2017,2017,2018,2018,2018,2018,2018,2018,2018,2018,2018,2018,2018,2019,2018,2018,2019,2019,2019,2019],"month":[1,4,5,5,5,8,8,3,4,8,7,8,9,9,1,2,4,5,7,7,8,11,5,6,8,6,10,10,10,1,12,7,6,7,5,7,8,9,7,10,10,6,12,3,3,4,8,8,8,9,9,7,12,11,11,3,4,4,4,5,5,6,7,7,8,6,9,3,4,3,4,7,8,9,9,1,1,11,8,5,6,5,4,6,7,6,7,6,8,8,9,11,9,2,11,11,4,5,4,5],"state":["Ohio","Ohio","Ohio","Ohio","Idaho","Minnesota","Minnesota","Ohio","Minnesota","Minnesota","Minnesota","Minnesota","Idaho","Ohio","Ohio","Ohio","Minnesota","Ohio","Minnesota","Minnesota","Minnesota","Minnesota","Ohio","Minnesota","Minnesota","Minnesota","Ohio","Minnesota","Minnesota","Ohio","Ohio","Idaho","Ohio","Minnesota","Minnesota","Minnesota","Minnesota","Ohio","Minnesota","Minnesota","Ohio","Ohio","Ohio","Ohio","Ohio","Minnesota","Minnesota","Minnesota","Ohio","Ohio","Minnesota","Ohio","Ohio","Minnesota","Ohio","Ohio","Ohio","Ohio","Ohio","Minnesota","Minnesota","Ohio","Ohio","Minnesota","Minnesota","Ohio","Minnesota","Ohio","Idaho","Ohio","Ohio","Minnesota","Ohio","Ohio","Idaho","Ohio","Ohio","Idaho","Idaho","Idaho","Idaho","Idaho","Ohio","Ohio","Ohio","Minnesota","Minnesota","Minnesota","Ohio","Minnesota","Ohio","Ohio","Idaho","Ohio","Ohio","Minnesota","Ohio","Ohio","Ohio","Minnesota"],"animal_type":["Cattle","Pet 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specify","Private home/residence",null,null,null,null,null,null,null,null,null,null,null,null,null],"illnesses":[4,2,3,3,2,4,3,2,9,2,2,2,2,2,3,5,31,27,10,52,2,3,11,2,4,18,6,7,2,4,2,3,6,15,2,2,7,4,12,13,4,3,3,3,4,3,4,2,2,19,17,2,2,6,3,9,3,5,4,72,2,4,4,2,6,2,2,6,2,6,2,21,6,5,5,4,22,3,2,2,3,2,2,3,4,5,3,2,2,2,4,3,2,7,4,2,2,12,2,5],"hospitalizations":[1,2,0,2,0,0,2,0,0,0,0,0,0,2,0,0,0,6,1,2,0,0,0,0,1,0,0,2,2,1,0,1,1,0,1,0,1,0,0,2,0,1,0,1,0,0,1,1,0,1,0,0,0,0,0,0,1,0,1,0,0,0,1,0,0,0,0,0,0,0,0,2,0,0,0,1,3,0,0,0,0,0,0,0,1,2,0,0,0,2,0,0,0,0,0,0,0,2,0,0],"info_on_hospitalizations":[4,2,0,3,2,4,3,2,9,2,2,2,2,2,3,5,31,24,10,5,2,3,9,0,4,18,6,7,2,4,2,3,6,15,2,2,7,4,12,13,4,3,3,3,4,3,4,2,2,19,17,2,2,6,0,9,3,5,4,71,2,4,4,0,6,2,2,6,2,6,2,20,6,5,5,4,22,3,2,2,3,2,2,3,3,5,3,2,2,2,4,0,2,7,4,2,2,4,0,5],"deaths":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"info_on_deaths":[4,2,3,3,2,4,3,2,9,2,2,2,2,2,3,5,31,27,10,5,2,3,9,0,4,18,6,7,2,4,2,3,6,15,2,2,7,4,12,13,4,3,3,3,4,3,4,2,2,19,17,2,2,6,0,9,0,5,4,71,2,4,4,2,6,2,2,6,2,6,2,21,6,5,5,4,22,3,2,2,3,2,2,3,4,5,3,2,2,2,4,0,2,7,4,2,2,4,0,5],"food_vehicle":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"food_contaminated_ingredient":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"ifsac_category":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_exposure":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_type":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_status":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"year","name":"year","type":"numeric","maxWidth":400,"align":"left"},{"id":"month","name":"month","type":"numeric","maxWidth":400,"align":"left"},{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type","name":"animal_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type_specify","name":"animal_type_specify","type":"character","maxWidth":400,"align":"left"},{"id":"etiology","name":"etiology","type":"character","maxWidth":400,"align":"left"},{"id":"serotype_or_genotype","name":"serotype_or_genotype","type":"character","maxWidth":400,"align":"left"},{"id":"etiology_status","name":"etiology_status","type":"character","maxWidth":400,"align":"left"},{"id":"setting","name":"setting","type":"character","maxWidth":400,"align":"left"},{"id":"illnesses","name":"illnesses","type":"numeric","maxWidth":400,"align":"left"},{"id":"hospitalizations","name":"hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_hospitalizations","name":"info_on_hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"deaths","name":"deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_deaths","name":"info_on_deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"food_vehicle","name":"food_vehicle","type":"character","maxWidth":400,"align":"left"},{"id":"food_contaminated_ingredient","name":"food_contaminated_ingredient","type":"character","maxWidth":400,"align":"left"},{"id":"ifsac_category","name":"ifsac_category","type":"character","maxWidth":400,"align":"left"},{"id":"water_exposure","name":"water_exposure","type":"character","maxWidth":400,"align":"left"},{"id":"water_type","name":"water_type","type":"character","maxWidth":400,"align":"left"},{"id":"water_status","name":"water_status","type":"character","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows (Total: 119)"},"dataKey":"0e1324c7fae74d7ba342df04084c3535"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- class: your-turn # Your Turn 13 .pull-left[Visualize the relationship between **year** and number of **illnesses** with a smooth line plot: * Before you plot, exclude the outlier we previously identified (the outbreak with the max number of illnesses). * Color each line by its primary mode.] .pull-right[ <img src="session01-practice-slides_files/figure-html/unnamed-chunk-36-1.png" width="504" /> ] --- ## Solution 13 .pull-left[ ```r outbreaks %>% filter(illnesses != max(illnesses)) %>% ggplot(aes(y = illnesses, x = year, color = primary_mode)) + geom_smooth(se = FALSE) ``` ] .pull-right[ <img src="session01-practice-slides_files/figure-html/unnamed-chunk-37-1.png" width="504" /> ] --- class: your-turn # Your Turn 14 Visualize the number of illnesses in **Washington DC**, grouped by **primary mode** of infection using a "violin plot". *Hint:* You may need to investigate `geom_violin()`. (Don't worry if your plot dimensions look different than the plot below.) ``` ## Warning: Groups with fewer than two data points have been dropped. ``` <img src="session01-practice-slides_files/figure-html/sol-14-1.png" width="70%" /> --- ## Solution 14 ```r outbreaks %>% filter(state == "Washington DC") %>% ggplot(aes(x = primary_mode, y = illnesses)) + geom_violin(aes(color = primary_mode)) + geom_point(alpha = 0.3) # any alpha value < 1 is OK ``` <img src="session01-practice-slides_files/figure-html/unnamed-chunk-39-1.png" width="75%" /> --- class: your-turn # Your Turn 15 Let's focus only on **Washington DC** and **food borne illnesses**. Show the most recent outbreaks in a table from most recent to least recent. _Hint_: Which two columns contain date information? <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-56cebad7b819c9a71f51" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-56cebad7b819c9a71f51">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"year":[2019,2019,2019,2018,2018,2018,2018,2017,2016,2015,2015,2008,2008,2007,2007,2007,2004,2004,2004,2004,2004,2004,2004,2004,2004,2003,2003,2003,2003,2002,2002,2002,2002,2002,2002,2002,2002,2002,2002,2001,2000,2000,1998,1998],"month":[6,5,3,9,3,3,3,12,2,9,8,10,9,11,6,5,10,8,4,3,3,3,2,1,1,6,6,6,4,11,10,10,6,6,5,5,5,4,2,6,11,3,10,9],"state":["Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC"],"primary_mode":["Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food"],"etiology":["Cyclospora cayetanensis","Norovirus Genogroup II",null,null,"Norovirus Genogroup II","Norovirus Genogroup II","Norovirus unknown","Norovirus Genogroup II",null,"Salmonella enterica","Ciguatoxin","Norovirus Genogroup I",null,null,"Salmonella enterica","Ciguatoxin","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I; Norovirus Genogroup II","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I; Adenovirus","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus unknown; Norovirus Genogroup II",null,"Salmonella enterica; Escherichia coli, Enteropathogenic","Scombroid toxin",null,"Salmonella enterica",null,"Salmonella enterica","Norovirus Genogroup I; Campylobacter other","Staphylococcus aureus","Norovirus Genogroup I","Salmonella enterica",null,"Rotavirus",null,"Cryptosporidium parvum"],"serotype_or_genotype":[null,"unknown - unknown",null,null,"unknown - unknown",null,null,"unknown - unknown",null,"Enteritidis",null,"GI.1",null,null,"Newport",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Muenchen",null,null,null,null,null,"Braenderup",null,null,null,null],"etiology_status":["Confirmed","Suspected",null,null,"Confirmed","Suspected","Suspected","Confirmed",null,"Confirmed","Suspected","Confirmed",null,null,"Confirmed","Confirmed","Confirmed","Suspected","Suspected; Suspected","Confirmed","Confirmed","Suspected","Suspected","Suspected","Suspected","Suspected; Suspected","Suspected","Confirmed","Confirmed; Confirmed",null,"Confirmed; Confirmed","Suspected",null,"Confirmed",null,"Confirmed","Confirmed; Confirmed","Confirmed","Suspected","Confirmed",null,"Confirmed",null,"Confirmed"],"setting":["Restaurant - \"Fast-food\"(drive up service or pay at counter); Restaurant - Sit-down dining","Private home/residence","Restaurant - Sit-down dining","Restaurant - Buffet","Restaurant - Sit-down dining","Restaurant - Sit-down dining","Restaurant - Sit-down dining","Caterer (food prepared off-site from where served)","School/college/university","Restaurant - Sit-down dining","Office/indoor workplace",null,"School/college/university","Caterer (food prepared off-site from where served)","Restaurant - other or unknown type; Private home/residence","Private home/residence","Unknown","Restaurant - other or unknown type","Other","Unknown","Unknown","Unknown","Unknown","Hospital","Unknown","Restaurant - other or unknown type; Caterer (food prepared off-site from where served)","Restaurant - other or unknown type; Private home/residence; Caterer (food prepared off-site from where served)","Caterer (food prepared off-site from where served)","Caterer (food prepared off-site from where served); Other","School/college/university","Caterer (food prepared off-site from where served)","Restaurant - other or unknown type","Grocery store","Restaurant - other or unknown type","Restaurant - other or unknown type","Caterer (food prepared off-site from where served)","Long-term care/nursing home/assisted living facility","Other","Other","Restaurant - other or unknown type","Private home/residence","School/college/university","Restaurant - other or unknown type","Other"],"illnesses":[3,4,16,4,6,12,3,52,49,160,6,27,110,42,46,9,22,6,65,35,69,15,19,16,35,48,44,47,181,5,29,2,11,57,3,14,88,8,23,21,15,108,7,88],"hospitalizations":[0,0,0,0,0,0,0,1,0,9,"NA","NA",0,"NA","NA",0,"NA","NA",1,"NA","NA","NA","NA","NA","NA",0,"NA","NA",0,0,3,0,0,3,0,1,0,0,0,"NA",0,"NA",0,0],"info_on_hospitalizations":[3,4,14,4,5,12,3,51,0,9,"NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA"],"deaths":[0,0,0,0,0,0,0,0,0,0,"NA",0,0,"NA","NA",0,"NA","NA",0,"NA","NA","NA","NA","NA","NA",0,"NA","NA",0,0,0,0,0,0,0,0,0,0,0,"NA",0,"NA",0,0],"info_on_deaths":[3,4,16,4,5,12,3,51,0,0,"NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA"],"food_vehicle":["basil mayo",null,null,null,null,null,null,null,null,null,"fish, amberjack",null,null,"pasta-based salads unspecified","tomato, unspecified; avocado, unspecified; guacamole, unspecified; cilantro, unspecified","fish",null,"chicken, grilled; green salad","chicken, other; potato, mashed; caesar salad",null,null,null,null,null,null,"ice","onion, tart; mixed vegetables, unspecified; green salad","pastry, paris-brest; tomato, basil and mozzarella salad","water","quesadilla, chicken",null,"tuna, unspecified","strawberries; watermelon","pasta salad","sandwich, chicken; pork, roasted","sandwich, chicken",null,"other cheese, pasteurized; honeydew melon; potato, fried",null,"sandwich, other specialty","deviled eggs","sandwich, tuna salad; sandwich, chicken salad",null,null],"food_contaminated_ingredient":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"cheese; melon; root (eg. potato)",null,null,"egg",null,null,null],"ifsac_category":["Multiple",null,null,null,null,null,null,null,null,null,"Fish",null,null,"Multiple","Multiple","Fish",null,"Multiple","Multiple",null,null,null,null,null,null,"Other","Multiple","Multiple","Other","Multiple",null,"Fish","Fruits","Multiple","Multiple","Multiple",null,"Multiple",null,"Multiple","Eggs","Multiple",null,null],"water_exposure":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_type":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"animal_type":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"animal_type_specify":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_status":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"year","name":"year","type":"numeric","maxWidth":400,"align":"left"},{"id":"month","name":"month","type":"numeric","maxWidth":400,"align":"left"},{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"primary_mode","name":"primary_mode","type":"character","maxWidth":400,"align":"left"},{"id":"etiology","name":"etiology","type":"character","maxWidth":400,"align":"left"},{"id":"serotype_or_genotype","name":"serotype_or_genotype","type":"character","maxWidth":400,"align":"left"},{"id":"etiology_status","name":"etiology_status","type":"character","maxWidth":400,"align":"left"},{"id":"setting","name":"setting","type":"character","maxWidth":400,"align":"left"},{"id":"illnesses","name":"illnesses","type":"numeric","maxWidth":400,"align":"left"},{"id":"hospitalizations","name":"hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_hospitalizations","name":"info_on_hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"deaths","name":"deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_deaths","name":"info_on_deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"food_vehicle","name":"food_vehicle","type":"character","maxWidth":400,"align":"left"},{"id":"food_contaminated_ingredient","name":"food_contaminated_ingredient","type":"character","maxWidth":400,"align":"left"},{"id":"ifsac_category","name":"ifsac_category","type":"character","maxWidth":400,"align":"left"},{"id":"water_exposure","name":"water_exposure","type":"character","maxWidth":400,"align":"left"},{"id":"water_type","name":"water_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type","name":"animal_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type_specify","name":"animal_type_specify","type":"character","maxWidth":400,"align":"left"},{"id":"water_status","name":"water_status","type":"character","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows"},"dataKey":"325302bcca7ff94c2e7775f8219b0412"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- ## Solution 15 .left-column40[ ```r outbreaks %>% filter( state == "Washington DC" & primary_mode == "Food" ) %>% arrange(desc(year), desc(month)) ``` ] .right-column55[ <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-5fd2d934ddc9bca3a9a7" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-5fd2d934ddc9bca3a9a7">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"year":[2019,2019,2019,2018,2018,2018,2018,2017,2016,2015,2015,2008,2008,2007,2007,2007,2004,2004,2004,2004,2004,2004,2004,2004,2004,2003,2003,2003,2003,2002,2002,2002,2002,2002,2002,2002,2002,2002,2002,2001,2000,2000,1998,1998],"month":[6,5,3,9,3,3,3,12,2,9,8,10,9,11,6,5,10,8,4,3,3,3,2,1,1,6,6,6,4,11,10,10,6,6,5,5,5,4,2,6,11,3,10,9],"state":["Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC"],"primary_mode":["Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food"],"etiology":["Cyclospora cayetanensis","Norovirus Genogroup II",null,null,"Norovirus Genogroup II","Norovirus Genogroup II","Norovirus unknown","Norovirus Genogroup II",null,"Salmonella enterica","Ciguatoxin","Norovirus Genogroup I",null,null,"Salmonella enterica","Ciguatoxin","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I; Norovirus Genogroup II","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus Genogroup I; Adenovirus","Norovirus Genogroup I","Norovirus Genogroup I","Norovirus unknown; Norovirus Genogroup II",null,"Salmonella enterica; Escherichia coli, Enteropathogenic","Scombroid toxin",null,"Salmonella enterica",null,"Salmonella enterica","Norovirus Genogroup I; Campylobacter other","Staphylococcus aureus","Norovirus Genogroup I","Salmonella enterica",null,"Rotavirus",null,"Cryptosporidium parvum"],"serotype_or_genotype":[null,"unknown - unknown",null,null,"unknown - unknown",null,null,"unknown - unknown",null,"Enteritidis",null,"GI.1",null,null,"Newport",null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"Muenchen",null,null,null,null,null,"Braenderup",null,null,null,null],"etiology_status":["Confirmed","Suspected",null,null,"Confirmed","Suspected","Suspected","Confirmed",null,"Confirmed","Suspected","Confirmed",null,null,"Confirmed","Confirmed","Confirmed","Suspected","Suspected; Suspected","Confirmed","Confirmed","Suspected","Suspected","Suspected","Suspected","Suspected; Suspected","Suspected","Confirmed","Confirmed; Confirmed",null,"Confirmed; Confirmed","Suspected",null,"Confirmed",null,"Confirmed","Confirmed; Confirmed","Confirmed","Suspected","Confirmed",null,"Confirmed",null,"Confirmed"],"setting":["Restaurant - \"Fast-food\"(drive up service or pay at counter); Restaurant - Sit-down dining","Private home/residence","Restaurant - Sit-down dining","Restaurant - Buffet","Restaurant - Sit-down dining","Restaurant - Sit-down dining","Restaurant - Sit-down dining","Caterer (food prepared off-site from where served)","School/college/university","Restaurant - Sit-down dining","Office/indoor workplace",null,"School/college/university","Caterer (food prepared off-site from where served)","Restaurant - other or unknown type; Private home/residence","Private home/residence","Unknown","Restaurant - other or unknown type","Other","Unknown","Unknown","Unknown","Unknown","Hospital","Unknown","Restaurant - other or unknown type; Caterer (food prepared off-site from where served)","Restaurant - other or unknown type; Private home/residence; Caterer (food prepared off-site from where served)","Caterer (food prepared off-site from where served)","Caterer (food prepared off-site from where served); Other","School/college/university","Caterer (food prepared off-site from where served)","Restaurant - other or unknown type","Grocery store","Restaurant - other or unknown type","Restaurant - other or unknown type","Caterer (food prepared off-site from where served)","Long-term care/nursing home/assisted living facility","Other","Other","Restaurant - other or unknown type","Private home/residence","School/college/university","Restaurant - other or unknown type","Other"],"illnesses":[3,4,16,4,6,12,3,52,49,160,6,27,110,42,46,9,22,6,65,35,69,15,19,16,35,48,44,47,181,5,29,2,11,57,3,14,88,8,23,21,15,108,7,88],"hospitalizations":[0,0,0,0,0,0,0,1,0,9,"NA","NA",0,"NA","NA",0,"NA","NA",1,"NA","NA","NA","NA","NA","NA",0,"NA","NA",0,0,3,0,0,3,0,1,0,0,0,"NA",0,"NA",0,0],"info_on_hospitalizations":[3,4,14,4,5,12,3,51,0,9,"NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA"],"deaths":[0,0,0,0,0,0,0,0,0,0,"NA",0,0,"NA","NA",0,"NA","NA",0,"NA","NA","NA","NA","NA","NA",0,"NA","NA",0,0,0,0,0,0,0,0,0,0,0,"NA",0,"NA",0,0],"info_on_deaths":[3,4,16,4,5,12,3,51,0,0,"NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA","NA"],"food_vehicle":["basil mayo",null,null,null,null,null,null,null,null,null,"fish, amberjack",null,null,"pasta-based salads unspecified","tomato, unspecified; avocado, unspecified; guacamole, unspecified; cilantro, unspecified","fish",null,"chicken, grilled; green salad","chicken, other; potato, mashed; caesar salad",null,null,null,null,null,null,"ice","onion, tart; mixed vegetables, unspecified; green salad","pastry, paris-brest; tomato, basil and mozzarella salad","water","quesadilla, chicken",null,"tuna, unspecified","strawberries; watermelon","pasta salad","sandwich, chicken; pork, roasted","sandwich, chicken",null,"other cheese, pasteurized; honeydew melon; potato, fried",null,"sandwich, other specialty","deviled eggs","sandwich, tuna salad; sandwich, chicken salad",null,null],"food_contaminated_ingredient":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,"cheese; melon; root (eg. potato)",null,null,"egg",null,null,null],"ifsac_category":["Multiple",null,null,null,null,null,null,null,null,null,"Fish",null,null,"Multiple","Multiple","Fish",null,"Multiple","Multiple",null,null,null,null,null,null,"Other","Multiple","Multiple","Other","Multiple",null,"Fish","Fruits","Multiple","Multiple","Multiple",null,"Multiple",null,"Multiple","Eggs","Multiple",null,null],"water_exposure":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_type":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"animal_type":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"animal_type_specify":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null],"water_status":[null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null,null]},"columns":[{"id":"year","name":"year","type":"numeric","maxWidth":400,"align":"left"},{"id":"month","name":"month","type":"numeric","maxWidth":400,"align":"left"},{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"primary_mode","name":"primary_mode","type":"character","maxWidth":400,"align":"left"},{"id":"etiology","name":"etiology","type":"character","maxWidth":400,"align":"left"},{"id":"serotype_or_genotype","name":"serotype_or_genotype","type":"character","maxWidth":400,"align":"left"},{"id":"etiology_status","name":"etiology_status","type":"character","maxWidth":400,"align":"left"},{"id":"setting","name":"setting","type":"character","maxWidth":400,"align":"left"},{"id":"illnesses","name":"illnesses","type":"numeric","maxWidth":400,"align":"left"},{"id":"hospitalizations","name":"hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_hospitalizations","name":"info_on_hospitalizations","type":"numeric","maxWidth":400,"align":"left"},{"id":"deaths","name":"deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"info_on_deaths","name":"info_on_deaths","type":"numeric","maxWidth":400,"align":"left"},{"id":"food_vehicle","name":"food_vehicle","type":"character","maxWidth":400,"align":"left"},{"id":"food_contaminated_ingredient","name":"food_contaminated_ingredient","type":"character","maxWidth":400,"align":"left"},{"id":"ifsac_category","name":"ifsac_category","type":"character","maxWidth":400,"align":"left"},{"id":"water_exposure","name":"water_exposure","type":"character","maxWidth":400,"align":"left"},{"id":"water_type","name":"water_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type","name":"animal_type","type":"character","maxWidth":400,"align":"left"},{"id":"animal_type_specify","name":"animal_type_specify","type":"character","maxWidth":400,"align":"left"},{"id":"water_status","name":"water_status","type":"character","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows"},"dataKey":"325302bcca7ff94c2e7775f8219b0412"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> ] --- class: your-turn # Your Turn 16 Continue to focus only on **Washington DC** and **food borne illnesses**. Use tidyverse functions to display the unique values of `food_vehicle` as a vector, as shown below: ``` ## [1] NA ## [2] "deviled eggs" ## [3] "sandwich, tuna salad; sandwich, chicken salad" ## [4] "sandwich, chicken; pork, roasted" ## [5] "other cheese, pasteurized; honeydew melon; potato, fried" ## [6] "sandwich, chicken" ## [7] "strawberries; watermelon" ## [8] "pasta salad" ## [9] "sandwich, other specialty" ## [10] "quesadilla, chicken" ## [11] "tuna, unspecified" ## [12] "ice" ## [13] "onion, tart; mixed vegetables, unspecified; green salad" ## [14] "water" ## [15] "pastry, paris-brest; tomato, basil and mozzarella salad" ## [16] "chicken, other; potato, mashed; caesar salad" ## [17] "chicken, grilled; green salad" ## [18] "fish" ## [19] "tomato, unspecified; avocado, unspecified; guacamole, unspecified; cilantro, unspecified" ## [20] "pasta-based salads unspecified" ## [21] "fish, amberjack" ## [22] "basil mayo" ``` --- ## Solution 16 .left-column1[ ```r outbreaks %>% filter( state == "Washington DC", primary_mode == "Food" ) %>% distinct(food_vehicle) %>% pull() ``` ] .right-column55[ ``` ## [1] NA ## [2] "deviled eggs" ## [3] "sandwich, tuna salad; sandwich, chicken salad" ## [4] "sandwich, chicken; pork, roasted" ## [5] "other cheese, pasteurized; honeydew melon; potato, fried" ## [6] "sandwich, chicken" ## [7] "strawberries; watermelon" ## [8] "pasta salad" ## [9] "sandwich, other specialty" ## [10] "quesadilla, chicken" ## [11] "tuna, unspecified" ## [12] "ice" ## [13] "onion, tart; mixed vegetables, unspecified; green salad" ## [14] "water" ## [15] "pastry, paris-brest; tomato, basil and mozzarella salad" ## [16] "chicken, other; potato, mashed; caesar salad" ## [17] "chicken, grilled; green salad" ## [18] "fish" ## [19] "tomato, unspecified; avocado, unspecified; guacamole, unspecified; cilantro, unspecified" ## [20] "pasta-based salads unspecified" ## [21] "fish, amberjack" ## [22] "basil mayo" ``` ] --- class: your-turn # Your Turn 17 Find **food borne** outbreaks that resulted in at least 1 **death**. Display the results in a table that contains only the columns `year`, `primary_mode`, `state`, and `deaths`. <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-7dc2e7a33b483b667277" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-7dc2e7a33b483b667277">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"year":[2009,2009,2010,2010,2010,2010,2011,2009,2009,2010,2009,2011,2011,2011,2010,2011,2011,2011,2010,2011,2012,2012,2012,2011,2012,2012,2012,2011,2011,2012,2012,2013,2013,2012,2012,2012,2013,2013,2013,2013,2013,2013,2013,2013,2014,2014,2014,2014,2014,2014,2013,2014,2014,2014,2013,2015,2013,2014,2014,2005,1999,1999,1999,1998,1998,1999,1999,1999,1998,1998,1999,2000,2000,2000,2000,2000,2000,2000,2000,2000,2000,2000,2000,1998,1998,1998,1998,1999,2001,2002,2001,2002,2001,2001,2001,2002,2003,2003,2003,2003],"primary_mode":["Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food"],"state":["Michigan","West Virginia","Illinois","Louisiana","New York","Colorado","Rhode Island","Multistate","Multistate","Texas","Multistate","New York","Pennsylvania","Oregon","Texas","Louisiana","Georgia","Michigan","Multistate","North Carolina","Connecticut","Massachusetts","Oregon","Multistate","Louisiana","North Carolina","Ohio","Multistate","Multistate","New York","California","Oregon","Maryland","Multistate","Multistate","Multistate","Multistate","Multistate","Idaho","South Carolina","Kentucky","New Mexico","Multistate","Multistate","California","New York","Massachusetts","Utah","Alaska","Multistate","Multistate","Multistate","Oregon","Oregon","Rhode Island","Kansas","Multistate","Multistate","Multistate","Colorado","New York","New Mexico","Minnesota","Multistate","Multistate","Maryland","Iowa","Hawaii","Florida","Florida","Florida","Wisconsin","South Dakota","Ohio","Multistate","Illinois","Florida","Florida","Colorado","California","California","California","California","California","New Jersey","Ohio","Texas","Ohio","Georgia","Tennessee","Florida","Florida","Texas","Louisiana","Oklahoma","California","Nevada","Florida","Florida","California"],"deaths":[1,2,1,3,1,1,2,1,2,5,1,1,1,2,1,1,1,1,1,1,1,1,1,33,1,1,1,1,1,1,4,1,1,3,1,5,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,2,1,1,2,7,1,1,2,1,21,3,2,1,1,2,2,1,1,2,1,7,1,1,3,1,1,1,1,1,1,2,1,1,1,1,1,1,1,4,1,2,1,1,1,7,1]},"columns":[{"id":"year","name":"year","type":"numeric","maxWidth":400,"align":"left"},{"id":"primary_mode","name":"primary_mode","type":"character","maxWidth":400,"align":"left"},{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"deaths","name":"deaths","type":"numeric","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows (Total: 265)"},"dataKey":"b0ff06522a93dea6f96a25d930b0e412"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- ## Solution ```r outbreaks %>% filter( primary_mode == "Food", deaths >= 1 ) %>% select(year, primary_mode, state, deaths) ``` <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-222e92a01eceebb59b41" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-222e92a01eceebb59b41">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"year":[2009,2009,2010,2010,2010,2010,2011,2009,2009,2010,2009,2011,2011,2011,2010,2011,2011,2011,2010,2011,2012,2012,2012,2011,2012,2012,2012,2011,2011,2012,2012,2013,2013,2012,2012,2012,2013,2013,2013,2013,2013,2013,2013,2013,2014,2014,2014,2014,2014,2014,2013,2014,2014,2014,2013,2015,2013,2014,2014,2005,1999,1999,1999,1998,1998,1999,1999,1999,1998,1998,1999,2000,2000,2000,2000,2000,2000,2000,2000,2000,2000,2000,2000,1998,1998,1998,1998,1999,2001,2002,2001,2002,2001,2001,2001,2002,2003,2003,2003,2003],"primary_mode":["Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food","Food"],"state":["Michigan","West Virginia","Illinois","Louisiana","New York","Colorado","Rhode Island","Multistate","Multistate","Texas","Multistate","New York","Pennsylvania","Oregon","Texas","Louisiana","Georgia","Michigan","Multistate","North Carolina","Connecticut","Massachusetts","Oregon","Multistate","Louisiana","North Carolina","Ohio","Multistate","Multistate","New York","California","Oregon","Maryland","Multistate","Multistate","Multistate","Multistate","Multistate","Idaho","South Carolina","Kentucky","New Mexico","Multistate","Multistate","California","New York","Massachusetts","Utah","Alaska","Multistate","Multistate","Multistate","Oregon","Oregon","Rhode Island","Kansas","Multistate","Multistate","Multistate","Colorado","New York","New Mexico","Minnesota","Multistate","Multistate","Maryland","Iowa","Hawaii","Florida","Florida","Florida","Wisconsin","South Dakota","Ohio","Multistate","Illinois","Florida","Florida","Colorado","California","California","California","California","California","New Jersey","Ohio","Texas","Ohio","Georgia","Tennessee","Florida","Florida","Texas","Louisiana","Oklahoma","California","Nevada","Florida","Florida","California"],"deaths":[1,2,1,3,1,1,2,1,2,5,1,1,1,2,1,1,1,1,1,1,1,1,1,33,1,1,1,1,1,1,4,1,1,3,1,5,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,2,1,1,2,7,1,1,2,1,21,3,2,1,1,2,2,1,1,2,1,7,1,1,3,1,1,1,1,1,1,2,1,1,1,1,1,1,1,4,1,2,1,1,1,7,1]},"columns":[{"id":"year","name":"year","type":"numeric","maxWidth":400,"align":"left"},{"id":"primary_mode","name":"primary_mode","type":"character","maxWidth":400,"align":"left"},{"id":"state","name":"state","type":"character","maxWidth":400,"align":"left"},{"id":"deaths","name":"deaths","type":"numeric","maxWidth":400,"align":"left"}],"sortable":false,"defaultPageSize":8,"showPageInfo":true,"striped":true,"compact":true,"nowrap":true,"language":{"pageInfo":"{rowStart}-{rowEnd} of {rows} rows (Total: 265)"},"dataKey":"b0ff06522a93dea6f96a25d930b0e412"},"children":[]},"class":"reactR_markup"},"evals":[],"jsHooks":[]}</script> --- class: your-turn # Your Turn 18 Calculate new variable for each outbreak: **`fatality_rate`** (the number of deaths / the number of illnesses, multiplied by 100). Then visualize the distribution of the fatality rate with a histogram. <img src="session01-practice-slides_files/figure-html/unnamed-chunk-48-1.png" width="35%" /> --- ## Solution 18 .pull-left[ ```r outbreaks %>% mutate( fatality_rate = deaths / illnesses * 100 ) %>% ggplot(aes(x = fatality_rate)) + geom_histogram() ``` ``` ## Warning: Removed 7154 rows containing non-finite values (`stat_bin()`). ``` ] .pull-right[ <img src="session01-practice-slides_files/figure-html/unnamed-chunk-49-1.png" width="504" /> ] --- class: your-turn # Your Turn 19 * Remove outbreaks that have a fatality rate of zero. * What is the distribution of the fatality rate for the remaining outbreaks as shown by a histogram? <img src="session01-practice-slides_files/figure-html/unnamed-chunk-50-1.png" width="35%" /> --- ## Solution 19 .pull-left[ ```r outbreaks %>% mutate( fatality_rate = deaths / illnesses * 100 ) %>% filter(fatality_rate > 0) %>% ggplot(aes(x = fatality_rate)) + geom_histogram() ``` ] .pull-right[ <img src="session01-practice-slides_files/figure-html/unnamed-chunk-51-1.png" width="504" /> ] --- class: your-turn # Your Turn 20 - last one! Find Washington DC's worst outbreak as defined by its **`hospitalization_rate`** (the number of hospitalizations / the number of illnesses, multiplied by 100). * Subset the data so you display observations that are at least 1.5 times greater than DC's mean hopsitalization rate. * Your answer should be a tibble with the highest hospitalization rates shown at the top. * Any ties should be broken by outbreaks that happened more recently. --- ## Solution 20 ```r outbreaks %>% filter(state == "Washington DC") %>% mutate(hospitalization_rate = hospitalizations / illnesses * 100) %>% filter(hospitalization_rate >= 1.60 * mean(hospitalization_rate, na.rm = TRUE)) %>% arrange(desc(hospitalization_rate), desc(year)) ``` <div class="reactable html-widget html-fill-item-overflow-hidden html-fill-item" id="htmlwidget-77106bb36c9c53d39bfc" style="width:auto;height:auto;"></div> <script type="application/json" data-for="htmlwidget-77106bb36c9c53d39bfc">{"x":{"tag":{"name":"Reactable","attribs":{"data":{"year":[2019,2015,2014,2009,2010,2019,2014,2002,2009,2010,2009,2002],"month":[3,3,2,2,12,7,2,10,3,12,2,5],"state":["Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC","Washington DC"],"primary_mode":["Environmental contamination other than food/water","Environmental contamination other than food/water","Indeterminate/Other/Unknown","Indeterminate/Other/Unknown","Person-to-person","Indeterminate/Other/Unknown","Indeterminate/Other/Unknown","Food","Indeterminate/Other/Unknown","Person-to-person","Indeterminate/Other/Unknown","Food"],"etiology":["Norovirus Genogroup II","Norovirus unknown","Norovirus Genogroup II",null,"Norovirus unknown","Norovirus unknown","Norovirus Genogroup II","Salmonella enterica; 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