covidcomp_vax.Rmd

---
title: "Vaccinations vs Cases/Deaths"
output: html_notebook
---

# Data

```{r}
source("covidcomp_lib.R")
refresh <- TRUE 

vax_file <- "data/comp_data_vax.fst"

if (!fs::file_exists(vax_file) || refresh) {
  vax_dat <- fetchPrepGoogData(use_cache = FALSE, add_vax = TRUE,
                               readable_loc = FALSE, add_labels = TRUE) %>%
    pivot_wider(names_from = stat, values_from = value) %>%
    select(location, date, label, population,
           cases = new_confirmed, deaths = new_deceased,
           doses = total_vaccine_doses_administered) %>%
    # only rows with all stats available
    filter(complete.cases(.)) %>%
    # outcomes
    pivot_longer(c(cases, deaths)) %>%
    mutate(geo_level = str_count(location, "_"),
           geo = if_else(geo_level == 0, "GLOBAL",
                         str_sub(location, 1, 2))) %>%
    unite(geo, geo, geo_level) %>%
    group_by(geo) %>%
    mutate(geo_count = n_distinct(location)) %>%
    ungroup()
  fst::write_fst(vax_dat, vax_file)
} else {
  vax_dat <- fst::read_fst(vax_file)
}
```

# Plot

```{r}
geo_limit <- 250

geo_list <- vax_dat %>% filter(geo_count <= geo_limit) %>%
  pull(geo) %>% unique()

one_geo <- sample(geo_list, 1)

vax_dat  %>%
  # geo filter
  filter(one_geo == geo) %>%
  # outlier value filtering
  filter(value >= 0) %>%
  # # scale outcomes between 0 and 1
  # group_by(name, date) %>%
  # mutate(value = value / sum(value)) %>%
  # ungroup() %>%
  # fix date for frame animation
  mutate(date = as.character(date)) %>%
  # wait until at least x locations %>%
  mutate(total_locs = n_distinct(location)) %>%
  group_by(date) %>%
  filter(n_distinct(location) > total_locs / 2 &
           sum(doses > 0) >= total_locs / 2) %>%
  select(-total_locs) %>%
  # plot
  ggplot(aes(doses, value, frame = date)) +
  geom_point(aes(label = label, ids = location)) +
  ggtitle(one_geo) + 
  ylab("weekly cases per million") +
  xlab("cumulative doses per million") +
  facet_wrap(~ name, scales = "free_y", nrow = 2) -> p

ggplotly(p) %>%
  animation_opts(redraw = FALSE)
```