Contagious disease data for US states

library("dslabs")

## Warning: package 'dslabs' was built under R version 3.6.1

data(package="dslabs")
list.files(system.file("script", package = "dslabs"))

##  [1] "make-admissions.R"                   
##  [2] "make-brca.R"                         
##  [3] "make-brexit_polls.R"                 
##  [4] "make-death_prob.R"                   
##  [5] "make-divorce_margarine.R"            
##  [6] "make-gapminder-rdas.R"               
##  [7] "make-greenhouse_gases.R"             
##  [8] "make-historic_co2.R"                 
##  [9] "make-mnist_27.R"                     
## [10] "make-movielens.R"                    
## [11] "make-murders-rda.R"                  
## [12] "make-na_example-rda.R"               
## [13] "make-nyc_regents_scores.R"           
## [14] "make-olive.R"                        
## [15] "make-outlier_example.R"              
## [16] "make-polls_2008.R"                   
## [17] "make-polls_us_election_2016.R"       
## [18] "make-reported_heights-rda.R"         
## [19] "make-research_funding_rates.R"       
## [20] "make-stars.R"                        
## [21] "make-temp_carbon.R"                  
## [22] "make-tissue-gene-expression.R"       
## [23] "make-trump_tweets.R"                 
## [24] "make-weekly_us_contagious_diseases.R"
## [25] "save-gapminder-example-csv.R"

library(RColorBrewer)
library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(ggplot2)

## Registered S3 methods overwritten by 'ggplot2':
##   method         from 
##   [.quosures     rlang
##   c.quosures     rlang
##   print.quosures rlang

library(plotly)

## Warning: package 'plotly' was built under R version 3.6.1

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
## 
##     last_plot

## The following object is masked from 'package:stats':
## 
##     filter

## The following object is masked from 'package:graphics':
## 
##     layout

library(gapminder)

## Warning: package 'gapminder' was built under R version 3.6.1

## 
## Attaching package: 'gapminder'

## The following object is masked from 'package:dslabs':
## 
##     gapminder

library(gganimate)

## Warning: package 'gganimate' was built under R version 3.6.1

data("us_contagious_diseases")
the_disease <- "Measles"
us_contagious_diseases <- us_contagious_diseases %>% 
  filter(!state %in% c("Hawaii","Alaska") & disease ==  the_disease) %>%
  mutate(rate = count / population * 10000 * 52 / weeks_reporting) %>%
  mutate(state = reorder(state, rate))

us_contagious_diseases1 <- ggplot(us_contagious_diseases, aes(x = year, y = state, fill = rate)) +
      geom_tile(color = "grey50") +
      scale_x_continuous(expand=c(0,0)) +
      scale_fill_gradientn(colors = brewer.pal(9, "Reds"), trans = "sqrt") +
      geom_vline(xintercept=1963, col = "blue") +
      theme_minimal() +  theme(panel.grid = element_blank()) +
      ggtitle(the_disease, "US States") +
      ylab("State") +
      xlab("Year")
us_contagious_diseases1

us_contagious_diseases2 <- ggplot(us_contagious_diseases, 
                                  aes(x = rate, y = state, frame = year, color = rate)) +
                        geom_point(aes(colour = rate, 
                         text = 
                           paste(paste("Rate: ", us_contagious_diseases$rate),
                           paste("Year: ", us_contagious_diseases$year),
                           paste("State: ", us_contagious_diseases$state),
                           paste("Count: ", us_contagious_diseases$count),
                           paste("population: ", us_contagious_diseases$population),
                           paste("Weeks reported: ", us_contagious_diseases$weeks_reporting),
                           sep = "<br />")
                           , alpha = 10)) +
                        ggtitle("Measles: US States") +
                        xlab("Rate") +
                        ylab("State") +
                        theme_minimal(base_size = 10) +
                        theme(legend.position="Rate") +
                        scale_x_log10() +
                        scale_colour_gradientn(colours=rainbow(4))

## Warning: Ignoring unknown aesthetics: text

us_contagious_diseases2 <- ggplotly(us_contagious_diseases2,
                                    height = 900, width = 700,
                                    tooltip = "text") %>%
                        animation_opts(frame = 200,
                                    redraw = FALSE)

## Warning: Transformation introduced infinite values in continuous x-axis

us_contagious_diseases2