This is an update of an earlier post.
The two key data variables are cases and deaths. As a measure of progress of the pandemic, cases are a more timely statistic than deaths (and also a little less morbid), but there are by-now-well-understood issues with cases, such as under-reporting due to lack of symptoms, or symptoms insufficiently serious to lead to hospitalization or testing. As pointed out in the WSJ article linked to above, as testing capacity increases, we might expect to see a rise in reported cases, even if the underlying number of cases is flat.
Getting the data
Getting the data is quite easy.
library(readr)
library(lubridate)
library(dplyr, warn.conflicts = FALSE)
library(ggplot2)
library(RcppRoll)
raw <- read_csv(paste0("https://raw.githubusercontent.com/",
"nytimes/covid-19-data/master/us-states.csv"))
covid_world_raw <- read_csv(paste0("https://covid.ourworldindata.org",
"/data/owid-covid-data.csv"),
col_types = cols(.default = col_guess(),
new_tests = col_double(),
new_tests_smoothed = col_double(),
new_tests_smoothed_per_thousand = col_double(),
tests_per_case = col_double(),
positive_rate = col_double(),
total_tests = col_double(),
total_tests_per_thousand = col_double(),
new_tests_per_thousand = col_double(),
weekly_hosp_admissions = col_double(),
weekly_hosp_admissions_per_million = col_double(),
weekly_icu_admissions = col_double(),
weekly_icu_admissions_per_million = col_double(),
icu_patients = col_double(),
icu_patients_per_million = col_double(),
hosp_patients = col_double(),
hosp_patients_per_million = col_double(),
tests_units = col_character()))
covid_states <-
raw %>%
group_by(state) %>%
arrange(date) %>%
mutate(new_cases = cases - lag(cases),
new_deaths = deaths - lag(deaths)) %>%
rename(total_deaths = deaths,
total_cases = cases)Initially, I wanted to consider Australia as a US state for the purpose of comparison. For the US, I focused on a few states of interest: New York was the worst-hit state, Massachusetts is where I am now, and California is the most populous state. Pennsylvania provides an interesting comparison for Massachusetts. Apart from Australia, I also considered the United Kingdom, which was hit at about the same time as New York.
selected_states <- c("Massachusetts", "New York", "Pennsylvania", "California")
selected_countries <- c("AUS", "GBR")
covid_aus_usa <-
covid_world_raw %>%
filter(iso_code %in% selected_countries) %>%
select(location:new_deaths) %>%
rename(state = location)
covid_selected <-
covid_states %>%
filter(state %in% selected_states) %>%
union_all(covid_aus_usa)Cases
One thing I noticed initially was a definite lumpiness to the data (e.g., many more deaths on Tuesdays rather than Sundays in Pennsylvania), which I assume is down to reporting rather than actual events. Initially, I used a four-day moving average, but here I use a seven-day moving average (as the four-day one still showed clean peaks and valleys).
covid_selected %>%
group_by(state) %>%
arrange(date) %>%
mutate(new_cases = roll_meanr(new_cases, n = 7, fill = NA)) %>%
filter(!is.na(new_cases)) %>%
ggplot(aes(x = date, y = new_cases, color = state)) +
geom_line() +
scale_x_date(breaks = "8 weeks")
Deaths
# So use a seven-day rolling average
covid_selected %>%
group_by(state) %>%
arrange(date) %>%
mutate(new_deaths = roll_meanr(new_deaths, n = 7, fill = NA)) %>%
filter(!is.na(new_deaths)) %>%
ggplot(aes(x = date, y = new_deaths, color = state)) +
geom_line() +
scale_x_date(breaks = "8 weeks")