asymptor

The asymptor R package allows you to estimate the lower and upper bound of asymptomatic cases in an epidemic using the capture/recapture methods from Böhning et al. (2020) and Rocchetti et al. (2020).

Installation

You can install the stable version of this package from CRAN:

install.packages("asymptor")

or the development version from GitHub, via my r-universe:

install.packages("asymptor", repos = "https://bisaloo.r-universe.dev")

Example

Let’s start by loading some example data from the COVID-19 epidemic in Italy:

d <- readRDS(system.file("extdata", "covid19_italy.rds", package = "asymptor"))
head(d)
#>         date new_cases new_deaths
#> 1 2020-01-02         0          0
#> 2 2020-01-03         0          0
#> 3 2020-01-04         0          0
#> 4 2020-01-05         0          0
#> 5 2020-01-06         0          0
#> 6 2020-01-07         0          0

We can estimate the lower and upper bound of asymptomatic cases with:

library(asymptor)
estimate_asympto(d$date, d$new_cases, d$new_deaths)

Or, with a tidyverse-compatible syntax:

library(dplyr)
d %>%
  mutate(asympto_cases = estimate_asympto(date, new_cases, new_deaths))

Please refer to the vignette for a detailed example using the COVID-19 data from Italy.