add cholera challenge for Rt and CFR based on case study

[avallecam]

This can include missingness in recovery data, to show why simple calculation doesn't work, and a frequent situation for cholera.

Example dataset:

library(outbreaks)
library(tidyverse)

outbreaks::ebola_sim_clean$linelist %>%
  as_tibble() %>% 
  count(outcome)
#> # A tibble: 3 × 2
#>   outcome     n
#>   <fct>   <int>
#> 1 Death    2564
#> 2 Recover  1963
#> 3 <NA>     1302

to explore:

• data in https://cran.r-project.org/web/packages/cholera/index.html
• use simulist
• Global.health data also has examples for Marburg