Created
July 25, 2020 20:21
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library(tidyverse) | |
library(janitor) | |
library(RcppRoll) | |
deaths <- read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_covid19_deaths_global.csv") | |
deaths <- deaths %>% | |
rename(province_state = `Province/State`, | |
country_region = `Country/Region`) %>% | |
pivot_longer(-c("province_state", "country_region", "Lat", "Long"), | |
names_to = "date", values_to = "deaths") %>% | |
mutate(date = lubridate::mdy(date)) %>% | |
janitor::clean_names() | |
deaths <- deaths %>% | |
mutate( | |
lat_group = case_when( | |
lat > 25 ~ "North", | |
lat < 25 & lat > -25 ~ "Equator", | |
TRUE ~ "South" | |
), | |
month = lubridate::month(date), | |
quarter = lubridate::quarter(date), | |
is_summer = dplyr::case_when( | |
month %in% c(10, 11, 12, 1:4) ~ FALSE, | |
TRUE ~ TRUE | |
), | |
is_summer = dplyr::case_when( | |
lat_group == "South" ~ !is_summer, | |
lat_group == "Equator" ~ TRUE, | |
lat_group == "North" ~ is_summer | |
), | |
season = case_when( | |
!is_summer ~ "not_summer", | |
is_summer ~ "summer" | |
) | |
) | |
deaths <- deaths %>% | |
filter(lat_group %in% c("North", "South")) %>% | |
group_by(country_region, date,) %>% | |
summarize(deaths = sum(deaths), | |
season = season[1], | |
is_summer = is_summer[1], | |
lat_group = lat_group[1]) %>% | |
group_by(country_region) %>% | |
mutate(daily_deaths = deaths ) %>% | |
mutate(daily_deaths = deaths - lag(deaths)) %>% | |
arrange(date) %>% | |
mutate(rolling_deaths = roll_sum(daily_deaths, 7, align = "right", fill = NA)) | |
deaths <- deaths %>% | |
mutate(mean_summer_deaths = mean(rolling_deaths[!is_summer], na.rm = TRUE)) %>% | |
mutate(deaths_norm = rolling_deaths / mean_summer_deaths) %>% | |
filter(mean_summer_deaths > 1) | |
deaths %>% | |
mutate(season = fct_rev(season)) %>% | |
ggplot(aes(x = date, y = rolling_deaths, color = season, group = country_region)) + | |
geom_point(alpha = 0.7, size = .5) + | |
facet_wrap(~lat_group, nrow = 2, scales = "free") + | |
theme_light() + | |
labs(title = "Covid Deaths", | |
y = "Seven day rolling average (free scales)", | |
x = "Date") + | |
scale_color_brewer(palette = "Set1") + | |
scale_color_manual(values = c("summer" = "maroon", "not_summer" = "dark blue")) | |
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