case_ascertainment_summary.Rmd

### Key results on case ascertainment

```{r echo = FALSE, warning = FALSE, message = FALSE}

case_at <- readr::read_csv(
    "Team.output/unformatted_summary_DeathToRepoted_14days_2020-04-05.csv"
)
case_at$country <- snakecase::to_any_case(case_at$country, case = "title")

top2_case_at <- dplyr::top_n(
    case_at, n = 2, wt = estimated_reporting_50
    ) %>%
    dplyr::mutate_if(is.numeric, ~ scales::percent(round(., 3), accuracy = 0.1))

bottom2_case_at <- dplyr::top_n(
    case_at, n = -2, wt = estimated_reporting_50
    ) %>%
    dplyr::mutate_if(is.numeric, ~ scales::percent(round(., 3), accuracy = 0.1))


top2_size <- dplyr::top_n(
    case_at, n = 2, wt = Predicted_True_case_last_week_50
    ) %>%
    dplyr::mutate_if(is.numeric, ~signif(., 3)) %>%
    dplyr::mutate_if(is.numeric, ~prettyNum(., big.mark = ","))

bottom2_size <- dplyr::top_n(
    case_at, n = -2, wt = Predicted_True_case_last_week_50
    ) %>%
    dplyr::mutate_if(is.numeric, ~signif(., 3)) %>%
    dplyr::mutate_if(is.numeric, ~prettyNum(., big.mark = ","))

```
Case ascertainment was estimated based on the deaths in the previous 2 weeks  and 
reported cases in the 10 days prior to that period.  Estimates of case
ascertainment were highly variable and, due to the underlying
assumption of perfect reporting, are likely to be an underestimate. In
particular, community deaths due to COVID-19 are likely under-reported
[@onsreport]. 
Results indicate that, assuming perfect reporting of deaths, the countries with the highest case ascertainment were:
  
* `r top2_case_at$country[2]` with an estimated median ascertainment
  of `r top2_case_at$estimated_reporting_50[2]` 
  (95% confidence interval (CI) `r top2_case_at$estimated_reporting_025[2]`  - `r top2_case_at$estimated_reporting_975[2]`), and
* `r top2_case_at$country[1]` with an estimated median ascertainment
  of `r top2_case_at$estimated_reporting_50[1]` 
  (95% CI `r top2_case_at$estimated_reporting_025[1]`  - `r top2_case_at$estimated_reporting_975[1]`).

and again assuming perfect reporting of deaths, the countries with the lowest case ascertainment were:

* `r bottom2_case_at$country[2]` with an estimated median ascertainment
  of `r bottom2_case_at$estimated_reporting_50[2]` 
  (95% CI `r bottom2_case_at$estimated_reporting_025[2]`- `r bottom2_case_at$estimated_reporting_975[2]`), and
* `r bottom2_case_at$country[1]` with an estimated median ascertainment
  of `r bottom2_case_at$estimated_reporting_50[1]` 
  (95% CI `r bottom2_case_at$estimated_reporting_025[1]`  - `r bottom2_case_at$estimated_reporting_975[1]`).


Based on the estimated ascertainment, we estimated the true size of
the epidemic in each country in the previous 7 days (week starting 22-03-2020). 
Countries with the largest true epidemic size in this period were:
  
* the `r top2_size$country[2]` with an estimated median size of
  `r top2_size$Predicted_True_case_last_week_50[2]` 
  (95% CI `r top2_size$Predicted_True_case_last_week_025[2]`  - `r top2_size$Predicted_True_case_last_week_975[2]`), and
* `r top2_size$country[1]` with an estimated median size 
  of `r top2_size$Predicted_True_case_last_week_50[1]` 
  (95% CI `r top2_size$Predicted_True_case_last_week_025[1]`  - `r top2_size$Predicted_True_case_last_week_975[1]`).

and countries with the lowest true epidemic size in this period were:
  
* `r bottom2_size$country[2]` with an estimated median size of
  of `r bottom2_size$Predicted_True_case_last_week_50[2]` 
  (95% CI `r bottom2_size$Predicted_True_case_last_week_025[2]`  - `r bottom2_size$Predicted_True_case_last_week_975[2]`), and
* `r bottom2_size$country[1]` with an estimated median size of
  of `r bottom2_size$Predicted_True_case_last_week_50[1]` 
  (95% CI `r bottom2_size$Predicted_True_case_last_week_025[1]`  - `r bottom2_size$Predicted_True_case_last_week_975[1]`).