USA daily deaths with and without NY, highlighting weekends

coviddeaths.R

library(COVID19)
library(dplyr)
library(zoo) # rollmean
library(ggplot2)
library(ggeasy) # easy_add_legend_title

#### deaths ####

## gather USA data at state level and identify weekends
us <- covid19("USA", level = 2) %>% 
    select(id, date, deaths) %>% 
    mutate(day = weekdays(date), 
           weekend = day %in% c("Saturday", "Sunday", "Monday"))

## sum deaths by date across all states
all <- us %>% 
    group_by(id) %>% 
    arrange(date) %>% 
    mutate(newdeaths = deaths - lag(deaths, default = 0)) %>% 
    group_by(date) %>% 
    summarise(totalnewdeaths = sum(newdeaths), day = unique(day), weekend = unique(weekend)) %>% 
    mutate(roll = c(rep(0, 6), rollmean(totalnewdeaths, 7, align = "right"))) %>% 
    mutate(id = "USA, total") 

## sum deaths in NY 
ny <- us %>% 
    filter(id == "USA, NY") %>% 
    mutate(totalnewdeaths = deaths - lag(deaths, default = 0)) %>% 
    mutate(roll = c(rep(0, 6), rollmean(totalnewdeaths, 7, align = "right"))) %>% 
    ungroup() %>% 
    mutate(id = "NY")
 
## sum deaths outside of NY
notny <- us %>% 
    filter(id != "USA, NY") %>% 
    group_by(id) %>% 
    mutate(newdeaths = deaths - lag(deaths, default = 0)) %>% 
    group_by(date) %>% 
    summarise(totalnewdeaths = sum(newdeaths), day = unique(day), weekend = unique(weekend)) %>% 
    mutate(roll = c(rep(0, 6), rollmean(totalnewdeaths, 7, align = "right"))) %>% 
    mutate(id = "USA - NY") 

## combine into one data.frame for plotting
d <- bind_rows(all, notny, ny)

ggplot(d, aes(date, totalnewdeaths)) +
    geom_col(aes(fill = weekend), alpha = 0.4) +
    geom_line(aes(y = roll), lwd = 1) +
    theme_light() +
    facet_wrap(~id, nrow = 1) +
    scale_x_date(limits = c(as.Date("2020-03-15"), Sys.Date()), 
                 date_breaks = "2 weeks", 
                 date_minor_breaks = "1 day") +
    labs(x = "Date", 
         y = "Daily Deaths (linear)", 
         title = "USA with and without NY", 
         subtitle = "Solid line indicates 7-day rolling mean. Weekends: Sat/Sun/Mon",
         caption = "Data source: {COVID19} (https://cran.r-project.org/package=COVID19)") +
    easy_add_legend_title("Weekend?")

#### cases ####

## gather USA data at state level and identify weekends
us <- covid19("USA", level = 2) %>% 
    select(id, date, cases = confirmed) %>% 
    mutate(day = weekdays(date), 
           weekend = day %in% c("Saturday", "Sunday", "Monday"))

## sum deaths by date across all states
all <- us %>% 
    group_by(id) %>% 
    arrange(date) %>% 
    mutate(newcases = cases - lag(cases, default = 0)) %>% 
    group_by(date) %>% 
    summarise(totalnewcases = sum(newcases), day = unique(day), weekend = unique(weekend)) %>% 
    mutate(roll = c(rep(0, 6), rollmean(totalnewcases, 7, align = "right"))) %>% 
    mutate(id = "USA, total") 

## sum cases in NY 
ny <- us %>% 
    filter(id == "USA, NY") %>% 
    mutate(totalnewcases = cases - lag(cases, default = 0)) %>% 
    mutate(roll = c(rep(0, 6), rollmean(totalnewcases, 7, align = "right"))) %>% 
    ungroup() %>% 
    mutate(id = "NY")

## sum cases outside of NY
notny <- us %>% 
    filter(id != "USA, NY") %>% 
    group_by(id) %>% 
    mutate(newcases = cases - lag(cases, default = 0)) %>% 
    group_by(date) %>% 
    summarise(totalnewcases = sum(newcases), day = unique(day), weekend = unique(weekend)) %>% 
    mutate(roll = c(rep(0, 6), rollmean(totalnewcases, 7, align = "right"))) %>% 
    mutate(id = "USA - NY") 

## combine into one data.frame for plotting
d <- bind_rows(all, notny, ny)

ggplot(d, aes(date, totalnewcases)) +
    geom_col(aes(fill = weekend), alpha = 0.4) +
    geom_line(aes(y = roll), lwd = 1) +
    theme_light() +
    facet_wrap(~id, nrow = 1) +
    scale_x_date(limits = c(as.Date("2020-03-15"), Sys.Date()), 
                 date_breaks = "2 weeks", 
                 date_minor_breaks = "1 day") +
    labs(x = "Date", 
         y = "Daily cases (linear)", 
         title = "USA with and without NY", 
         subtitle = "Solid line indicates 7-day rolling mean. Weekends: Sat/Sun/Mon",
         caption = "Data source: {COVID19} (https://cran.r-project.org/package=COVID19)") +
    easy_add_legend_title("Weekend?")