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mrc-ide / covid-vaccine-impact-orderly

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death curves for si plot #1

Closed OJWatson closed 2 years ago

OJWatson commented 2 years ago

In src/compile_plots_si/script.R just need to make the death curves that have been fitted to. I have quickly done it for the SI, but copy something like the following into this task:


  data = tibble(
    deaths = c(
      118, 378, 813, 935, 656, 331, 173, 88, 46, 24, 19, 33, 44, 40, 38, 62,
      114, 191, 263, 305, 348, 473, 659, 737, 606, 368, 183, 82, 36, 23, 24,
      21, 18, 43, 87, 148, 225, 298, 388, 467, 387, 309, 259, 218, 164
    )
  ) %>%
    mutate(
      week_start = as_date("2021-12-01") - 7 * rev(seq_along(deaths)),
      week_end = week_start + 7
    )

  population = c(
    19676332, 20045152, 21089487, 21242908, 22258745, 23835330, 23052479,
    21615791, 20294599, 20053798, 20577807, 21542270, 20669143, 17819027,
    14354863, 9727734, 13147182
  )

  data2 = tibble(
    deaths = c(14506, 50601, 62041, 83553, 110407, 137149, 133691, 98801, 82238, 81455, 64927, 63541, 65007, 63094, 55199, 34818, 36804, 49677, 51421,
               64591, 163419, 271734, 600103, 624699, 407582, 140985, 126373, 129763, 136651, 118683, 101090, 92772, 94338, 94087, 90210, 81653, 76853, 43591)
  ) %>%
    mutate(
      week_start = as_date("2021-12-01") - 7 * rev(seq_along(deaths)),
      week_end = week_start + 7
    )

  population2 = c(
    116879507, 117982127, 126155952, 126045566, 122504804, 117397269, 112176098, 103460178, 90219894, 79440280, 68875962, 59256268,
    48890528, 38260283, 24091443, 15083955, 13284271
  )

gg1 <- ggplot(data, aes(week_start, deaths/sum(population)*(sum(population)/1e5))) + 
  geomtextpath::geom_textvline(label = "Delta Introduction", xintercept = as.Date("2021-07-01"), hjust = 0.2, linetype = 2) +
  geom_step(color = "red") +
  theme_bw() + ylab("Weekly Deaths per 100,000\n") + xlab("")  +
  ggpubr::theme_pubr()

gg2 <- ggplot(data2, aes(week_start, deaths/sum(population2)*(sum(population2)/1e5))) + geom_step(color = "purple") + 
  geomtextpath::geom_textvline(label = "Delta Introduction", xintercept = as.Date("2021-07-01"), hjust = 0.2, linetype = 2) +
  theme_bw() + ylab("Weekly Deaths per 100,000\n") + xlab("") +
  ggpubr::theme_pubr()

gg <- cowplot::plot_grid(gg1, gg2, labels = c("c", "d"))
cowplot::save_plot("test.png", gg, base_height = 4, base_width = 10)
GBarnsley commented 2 years ago

Added