Waffle plots to illustrate the importance of base rates

vaxx-waffle.R

library(tidyverse)
# Sys.unsetenv('GITHUB_PAT')
# remotes::install_github('https://github.com/hrbrmstr/waffle')
library(waffle)


## <https://www.npr.org/sections/goatsandsoda/2021/08/20/1029628471/highly-vaccinated-israel-is-seeing-a-dramatic-surge-in-new-covid-cases-heres-why>
## "half of Israel's seriously ill patients who are currently hospitalized were fully vaccinated at least five months ago"

# vaxx rate: 78%
# unvaxxed serious case rate: 178.7 per 100,000
# vaxxed serious case rate:  178.7/9

n = 500
vaxx_rate = .80
cases_uv = 200/1000
cases_vx = cases_uv / 5

vaxx_total = round(n*vaxx_rate)
vaxx_cases = round(n*vaxx_rate*cases_vx)
unvaxx_total = round(n*(1-vaxx_rate))
unvaxx_cases = round(n*(1-vaxx_rate)*cases_uv)

## Almost 50% of cases are in vaccinated people oh no! 
vaxx_cases / (unvaxx_cases + vaxx_cases)

dataf = tribble(
    ~ vaxx, ~ disease, ~ n, 
    'vaccinated', 'healthy', vaxx_total - vaxx_cases, 
    'vaccinated', 'sick', vaxx_cases,
    'unvaccinated', 'healthy', unvaxx_total - unvaxx_cases,
    'unvaccinated', 'sick', unvaxx_cases
)

dataf |>
    filter(disease == 'sick') |>
    ggplot(aes(fill = vaxx, values = n)) +
    geom_waffle(n_rows = 6) +
    scale_fill_viridis_d(option = 'C', 
                         name = '') +
    coord_equal() +
    theme_enhance_waffle() +
    theme_void() +
    theme(legend.position = 'bottom') +
    labs(title = '44% of cases are in vaccinated people', 
         caption = 'Made up data to illustrate base rates')
ggsave('base_rate1.png', 
       height = 3, width = 5)

dataf |>
    ggplot(aes(fill = disease, values = n)) +
    geom_waffle() +
    scale_fill_brewer(palette = 'Set1',
                       direction = -1, 
                      name = '') +
    facet_wrap(vars(vaxx), ncol = 1) +
    coord_equal() +
    theme_enhance_waffle() +
    theme_void() +
    theme(legend.position = 'bottom') +
    labs(title = 'But vaccinated people are much less likely to get sick', 
         caption = 'Made up data to illustrate base rates')

ggsave('base_rate2.png', 
       height = 3, width = 5)