Compute the Monthly Death Tolls from the JHU CSSE COVID-19 Time-Series Data

COVID19MonthlyDeathToll.csv

COVID19MonthlyDeathToll.R

library(tidyverse)
library(lubridate)

raw <- read_csv('https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Deaths.csv')

processed <- raw %>%
  mutate(Location = ifelse(is.na(`Province/State`), `Country/Region`, paste(`Province/State`, `Country/Region`, sep = ', '))) %>%
  select(Location, `1/22/20`:`3/21/20`) %>%
  pivot_longer(cols = `1/22/20`:`3/21/20`, names_to = 'Date', values_to = "Deaths") %>%
  mutate(Date = mdy(Date)) %>%
  group_by(Date) %>%
  summarise(Deaths = sum(Deaths)) %>%
  mutate(month = month(Date)) %>%
  group_by(month) %>%
  summarise(Deaths = max(Deaths)) %>%
  mutate(newDeaths = Deaths - lag(Deaths))

processed$newDeaths[1] <- processed$Deaths[1]

write_csv(processed, "COVID19MonthlyDeathToll.csv")

NewYorkDeathsOverTime.R

library(tidyverse)
library(lubridate)

theDates <- mdy('03-21-2020'):mdy('01-22-2020') %>%
  as.Date(origin=ymd('1970-01-01')) %>%
  as.character(format="%m-%d-%Y")

for(theDate in theDates){
  temp <- read_csv(paste0('https://github.com/CSSEGISandData/COVID-19/raw/master/csse_covid_19_data/csse_covid_19_daily_reports/', theDate, '.csv'))
  write_csv(temp, paste0(theDate,'.csv'))
}

for(theDate in theDates){
  temp <- read_csv(paste0(theDate, '.csv')) %>%
    select(`Province/State`, Deaths) %>%
    mutate(date = theDate)
  if(theDate == theDates[1]){
    raw <- temp
  } else {
    raw <- raw %>%
      bind_rows(temp)
  }
}

theDates <- mdy('03-27-2020'):mdy('03-22-2020') %>%
  as.Date(origin=ymd('1970-01-01')) %>%
  as.character(format="%m-%d-%Y")

for(theDate in theDates){
  temp <- read_csv(paste0(theDate, '.csv')) %>%
    select(`Province/State` = `Province_State`, Deaths) %>%
    mutate(date = theDate)
  raw <- raw %>%
    bind_rows(temp)
}

processed <- raw %>%
  filter(`Province/State` == "New York") %>%
  #filter(`Country/Region` == 'US') %>%
  select(date, Deaths) %>%
  group_by(date) %>%
  summarize(deaths = sum(Deaths)) %>%
  View