https://github.com/jameel-institute/daedalus
[UNDER DEVELOPMENT] R package implementing the DAEDALUS model for projecting and optimising health, social, and economic costs of a pandemic.
https://github.com/jameel-institute/daedalus
decision-support epidemiological-models health-economics pandemic-preparedness public-health r-package rcpp sdg-3
Last synced: about 2 months ago
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[UNDER DEVELOPMENT] R package implementing the DAEDALUS model for projecting and optimising health, social, and economic costs of a pandemic.
- Host: GitHub
- URL: https://github.com/jameel-institute/daedalus
- Owner: jameel-institute
- License: other
- Created: 2024-07-08T12:38:16.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-08-21T11:12:17.000Z (2 months ago)
- Last Synced: 2025-08-21T11:52:15.103Z (2 months ago)
- Topics: decision-support, epidemiological-models, health-economics, pandemic-preparedness, public-health, r-package, rcpp, sdg-3
- Language: R
- Homepage: https://jameel-institute.github.io/daedalus/
- Size: 14.6 MB
- Stars: 6
- Watchers: 1
- Forks: 0
- Open Issues: 22
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS.md
- License: LICENSE
- Citation: CITATION.cff
Awesome Lists containing this project
README
---
output: github_document
bibliography: vignettes/resources/references.json
link-citations: true
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# daedalus: Model health, social, and economic costs of a pandemic
[](https://www.repostatus.org/#concept)
[](https://github.com/jameel-institute/daedalus/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/jameel-institute/daedalus?branch=main)
[](https://CRAN.R-project.org/package=daedalus)
_daedalus_ implements the integrated epidemiological and economic model in @haw2022.
## Installation
You can install the development version of daedalus from this repository using the _pak_ package, or from the Jameel Institute R-universe.
```r
# install.packages("pak")
pak::pak("jameel-institute/daedalus", upgrade = FALSE)
# installation from R-universe
install.packages(
"daedalus",
repos = c(
"https://jameel-institute.r-universe.dev", "https://cloud.r-project.org"
)
)
```
### Installation notes
_daedalus_ is under active development. To use a version of _daedalus_ associated with major milestones, install a specific version from the list below.
- IDM Thailand 2024: `pak::pak("jameel-institute/daedalus@v0.1.0")`
- IfG workshop 2025 (with real time modelling): `pak::pak("jameel-institute/daedalus@v0.2.0")`
### Known issues
We have found the following issues with released versions:
1. `v0.1.0`: Consumer-worker contacts are not correctly handled, leading to higher and faster epidemic peaks.
2. `v0.2.0`: Consumer-worker contacts are not included in the model, leading to lower and later epidemic peaks. The 'recovered' compartment does not include recoveries from hospitalisation. Please use the helper function `get_epidemic_summary()` to get epidemic sizes.
## Quick start
The model can be run for any country or territory in the `country_names` list by passing the country name to the function.
This automatically pulls country-specific demographic and economic data, which is included in the package, into the model (see the ['Get started' vignette](https://jameel-institute.github.io/daedalus/articles/daedalus.html) for more details).
```{r libraries}
library(daedalus)
# run model for Canada
data <- daedalus("Canada", "influenza_1918")
# get pandemic costs as a total in million dollars
get_costs(data, "total")
# disaggregate total for economic, education, and health costs
get_costs(data, "domain")
```
Users can select infection parameters from among seven epidemics caused by directly-transmitted viral respiratory pathogens, which are stored in the stand-alone helper package `daedalus.data`. These can be called as `daedalus.data::infection_data`, while epidemic identifiers are stored as `daedalus.data::epidemic_names`.
Users can override default country contact data and epidemic-specific infection arguments by passing custom classes to `daedalus()`; see the package website for more details.
Users can also model the implementation of pandemic response measures: for more on this see the documentation for the main model function `daedalus()`, and the vignette on modelling interventions on the package website.
## Related projects
_daedalus_ is an R implementation of the scenario model from a [project on the economics of pandemic preparedness](https://github.com/robj411/p2_drivers).
[_daedalus.data_](https://github.com/jameel-institute/daedalus.data) is a stand-alone helper R package to handle input data for the _daedalus_ model. Its purpose is to allow users to flexibly manipulate or change epidemiological and economic data, without needing to modify the model itself.
## References