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# load packages
library(pacman)
pacman::p_load("tidyverse","lubridate","ggrepel","paletteer","scales","prismatic")
pacman::p_load_gh("markushlang/spanishflu")
# prepare cumulative counts
flu_curve <- deaths_registered_in_certain_cities %>%
select(date,city,deaths) %>%
group_by(city) %>%
arrange(date) %>%
mutate(deaths = ifelse(is.na(deaths),0,deaths)) %>%
mutate(cu_deaths = cumsum(deaths)) %>%
filter(cu_deaths > 9) %>%
mutate(days_elapsed = date - min(date),
end_label = ifelse(date == max(date), city, NA))
# create cumulative deaths plot
flu_curve %>%
filter(city %in% c("New York","Philadelphia","Chicago",
"Boston","Pittsburgh")) %>%
ggplot(mapping = aes(x = days_elapsed, y = cu_deaths,
color = city, label = end_label,
group = city)) +
geom_line(size = 0.8) +
geom_text_repel(nudge_x = 1.1,
nudge_y = 0.1,
segment.color = NA) +
guides(color = FALSE) +
theme_minimal() +
scale_color_manual(values = prismatic::clr_darken(paletteer_d("jcolors::default"), 0.2)) +
scale_y_continuous(labels = scales::comma_format(accuracy = 1),
trans = "log2") +
labs(x = "Days Since 10th Confirmed Death",
y = "Cumulative Number of Deaths (log scale)",
title = "Cumulative Deaths from the Spanish Flu, Selected U.S. Cities") +
theme(plot.title = element_text(size = rel(1), face = "bold"),
axis.text.y = element_text(size = rel(1)),
axis.title.x = element_text(size = rel(0.75)),
axis.title.y = element_text(size = rel(0.75)),
axis.text.x = element_text(size = rel(1)),
legend.text = element_text(size = rel(1))
)
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