Yet another COVID 19 map - Chicago area cases, hospitalizations, and deaths (normalized for peak)

chicovidcasevsothers.R

## Author Gene Leynes
## Date: Oct 27, 2020

## Best run with R (Free) in R Studio (Free)
## Download R and R Studio to reproduce. 
## Available for windows, mac, linux

## If you don't have these packages you can install them with this code:
## install.packages("data.table")
## install.packages("magrittr")
## install.packages("plotly")
## install.packages("devtools")
## devtools::install_github("geneorama::geneorama")
##
## They are free, free, free, free, and free.  They also install several 
## dependencies... which are free. 


library(data.table)
library(magrittr)
library(plotly, warn.conflicts = F, quietly = TRUE)
library(geneorama)

## Download from the data portal
## Link to human readable page: https://data.cityofchicago.org/resource/naz8-j4nc
dat <- fread("https://data.cityofchicago.org/api/views/naz8-j4nc/rows.csv?accessType=DOWNLOAD")

## Convert column names to be R friendly
colnames(dat) %>% 
    gsub(" - ","_", .) %>% 
    gsub(" ","_", .) %>% 
    gsub("-","_", .) %>% 
    gsub("/","_", .) %>% 
    tolower() %>% 
    setnames(dat, .) %>% 
    .[ , date := as.IDate(date, "%m/%d/%Y")]

## Define rolling average period
period <- 7

## Create plot data... order the data, remove na dates, calculate MA's
plotdata <- dat %>% 
    .[order(date)] %>% 
    .[ , list(date, 
              cases = ma(cases_total, p = period),
              hospitalizations = ma(hospitalizations_total, p = period),
              deaths = ma(deaths_total, p = period))] %>% 
    .[date>"2020-03-16"]

## The normalization part
plotdata[ , cases := cases / max(cases, na.rm = TRUE)]
plotdata[ , hospitalizations := hospitalizations / max(hospitalizations, na.rm = TRUE)]
plotdata[ , deaths := deaths / max(deaths, na.rm = TRUE)]

## Create and print the figure
fig <- plot_ly() %>%
    add_lines(x = plotdata$date, y = plotdata$cases, name = "Cases") %>%
    add_lines(x = plotdata$date, y = plotdata$hospitalizations, name = "Hospitalizations") %>%
    add_lines(x = plotdata$date, y = plotdata$deaths, name = "Deaths") %>%
    layout(title = "Chicago COVID Cases, Deaths, and Hospitalizations")
fig