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https://github.com/bisaloo/asymptor
R package to estimate asymptomatic cases via capture/recapture methods
https://github.com/bisaloo/asymptor
epidemiology r-package
Last synced: 2 months ago
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R package to estimate asymptomatic cases via capture/recapture methods
- Host: GitHub
- URL: https://github.com/bisaloo/asymptor
- Owner: Bisaloo
- License: gpl-3.0
- Created: 2020-09-29T12:07:16.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2022-10-05T08:32:59.000Z (about 2 years ago)
- Last Synced: 2024-10-10T20:33:45.001Z (2 months ago)
- Topics: epidemiology, r-package
- Language: R
- Homepage: https://bisaloo.github.io/asymptor
- Size: 2.25 MB
- Stars: 3
- Watchers: 3
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE.md
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# asymptor 
[](https://CRAN.R-project.org/package=asymptor)
[](https://github.com/Bisaloo/asymptor/actions)
[](https://lifecycle.r-lib.org/articles/stages.html#maturing)
[](https://app.codecov.io/gh/Bisaloo/asymptor?branch=main)
The asymptor R package allows you to estimate the lower and upper bound of
asymptomatic cases in an epidemic using the capture/recapture methods from
[Böhning et al. (2020)](https://doi.org/10.1016/j.ijid.2020.06.009) and
[Rocchetti et al. (2020)](https://doi.org/10.1101/2020.07.14.20153445).
**Please note there is currently some discussion about the validity of the
methods implemented in this package. You should read carefully the original
articles, alongside this answer from [Li et al.
(2022)](https://doi.org/10.48550/arXiv.2209.11334) before using this package in
your project.**
## Installation
You can install the stable version of this package from CRAN:
```{r, eval = FALSE}
install.packages("asymptor")
```
or the development version from [GitHub](https://github.com/bisaloo), via my
[r-universe](https://bisaloo.r-universe.dev/):
```{r, eval = FALSE}
install.packages("asymptor", repos = "https://bisaloo.r-universe.dev")
```
## Example
Let's start by loading some example data from the COVID-19 epidemic in Italy:
```{r}
d <- readRDS(system.file("extdata", "covid19_italy.rds", package = "asymptor"))
head(d)
```
We can estimate the lower and upper bound of asymptomatic cases with:
```{r eval = FALSE}
library(asymptor)
estimate_asympto(d$date, d$new_cases, d$new_deaths)
```
Or, with a tidyverse-compatible syntax:
```{r eval = FALSE}
library(dplyr)
d %>%
mutate(asympto_cases = estimate_asympto(date, new_cases, new_deaths))
```
Please refer to the
[vignette](https://hugogruson.fr/asymptor/articles/example.html) for a
detailed example using the COVID-19 data from Italy.
