Created
June 29, 2020 19:29
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library(tidyverse) | |
library(RcppRoll) | |
library(lubridate) | |
library(broom) | |
covid <- read_csv("https://covid.ourworldindata.org/data/owid-covid-data.csv") %>% | |
filter(location != "World") | |
covid <- covid %>% | |
group_by(iso_code) %>% | |
arrange(date) %>% | |
mutate(rolling_deaths = roll_sum(new_deaths, 7, align = "right", fill = NA) / 7, | |
rolling_cases = roll_sum(new_cases, 7, align = "right", fill = NA) / 7, | |
lagged_cfr = rolling_deaths / lag(rolling_cases, 14), | |
week = week(date) - week(ymd("2020-05-01")), | |
lagged_tests = lag(new_tests_smoothed_per_thousand, 14)) %>% | |
filter(week > 0) | |
stats <- covid %>% | |
filter(!is.na(lagged_tests)) %>% | |
group_by(iso_code, location) %>% | |
nest() %>% | |
rowwise() %>% | |
mutate(mod = list(lm(lagged_cfr ~ week + lagged_tests, data)), | |
summary = list(tidy(mod)), | |
fit = list(glance(mod)) | |
) %>% | |
unnest(fit) %>% | |
select(location, summary, r.squared) %>% | |
unnest(summary) | |
countries <- covid %>% | |
filter(date == ymd("2020-06-29")) %>% | |
filter(rolling_cases > 500, | |
rolling_deaths > 10) | |
stats <- stats %>% | |
arrange(estimate) %>% | |
filter(term %in% c("week")) | |
stats$location <- fct_reorder(stats$location, rev(stats$estimate)) | |
stats %>% | |
filter(location %in% countries$location) %>% | |
mutate(lower = estimate - std.error, | |
upper = estimate + std.error) %>% | |
ggplot(aes(y = location, x = estimate, colour = r.squared)) + | |
geom_pointrange(aes(xmin = lower, xmax = upper)) + | |
scale_color_viridis_c() + | |
theme_light() + | |
scale_x_continuous(labels = scales::percent) + | |
geom_vline(xintercept = 0, alpha = 0.2) + | |
labs(title = "Weekly change in lagged CFR", | |
subtitle = "After accounting for changes in testing") + | |
ylab("Country") + | |
xlab("Average weekly change in CFR") | |
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