daedalus
[UNDER DEVELOPMENT] R package implementing the DAEDALUS model for projecting and optimising health, social, and economic costs of a pandemic.
Science Score: 52.0%
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Keywords
decision-support
epidemiological-models
health-economics
pandemic-preparedness
public-health
r-package
rcpp
sdg-3
Last synced: 6 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.
Basic Info
- Host: GitHub
- Owner: jameel-institute
- License: other
- Language: R
- Default Branch: main
- Homepage: https://jameel-institute.github.io/daedalus/
- Size: 14.7 MB
Statistics
- Stars: 6
- Watchers: 1
- Forks: 0
- Open Issues: 26
- Releases: 3
Topics
decision-support
epidemiological-models
health-economics
pandemic-preparedness
public-health
r-package
rcpp
sdg-3
Created over 1 year ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
License
Citation
README.Rmd
---
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
Owner
- Name: Jameel Institute
- Login: jameel-institute
- Kind: organization
- Location: Imperial College London
- Website: http://www.imperial.ac.uk/jameel-institute/
- Repositories: 1
- Profile: https://github.com/jameel-institute
Jameel Institute
Citation (CITATION.cff)
# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
cff-version: 1.2.0
message: 'To cite package "daedalus" in publications use:'
type: software
license: MIT
title: 'daedalus: Model Health, Social, and Economic Costs of a Pandemic'
version: 0.2.25
abstract: Model the health, education, and economic costs of directly transmitted
respiratory virus pandemics, under different scenarios of prior vaccine investment
and reactive interventions, using the 'DAEDALUS' integrated health-economics model
adapted from Haw et al. (2022) <doi.org/10.1038/s43588-022-00233-0>.
authors:
- family-names: Gupte
given-names: Pratik
email: p.gupte24@imperial.ac.uk
orcid: https://orcid.org/0000-0001-5294-7819
- family-names: Doohan
given-names: Patrick
orcid: https://orcid.org/0000-0001-8076-1106
- family-names: Johnson
given-names: Robert
orcid: https://orcid.org/0000-0002-7365-0042
- family-names: Perez-Guzman
given-names: Pablo
orcid: https://orcid.org/0000-0002-5277-5196
- family-names: FitzJohn
given-names: Rich
orcid: https://orcid.org/0000-0001-8888-3837
- family-names: Russell
given-names: Emma
- family-names: Mears
given-names: David
- family-names: Hauck
given-names: Katharina
orcid: https://orcid.org/0000-0003-3138-4169
repository-code: https://github.com/jameel-institute/daedalus
url: https://jameel-institute.github.io/daedalus/
contact:
- family-names: Gupte
given-names: Pratik
email: p.gupte24@imperial.ac.uk
orcid: https://orcid.org/0000-0001-5294-7819
keywords:
- decision-support
- epidemiological-models
- health-economics
- pandemic-preparedness
- public-health
- r-package
- rcpp
- sdg-3
references:
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notes: Depends
url: https://www.R-project.org/
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address: Vienna, Austria
year: '2025'
version: '>= 3.5'
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authors:
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given-names: Michel
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year: '2025'
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abstract: 'cli: Helpers for Developing Command Line Interfaces'
notes: Imports
url: https://cli.r-lib.org
repository: https://CRAN.R-project.org/package=cli
authors:
- family-names: Csárdi
given-names: Gábor
email: gabor@posit.co
year: '2025'
doi: 10.32614/CRAN.package.cli
- type: software
title: daedalus.data
abstract: 'daedalus.data: DAEDALUS Data'
notes: Imports
url: https://jameel-institute.github.io/daedalus.data/
authors:
- family-names: Perez-Guzman
given-names: Pablo
email: p.perez-guzman@imperial.ac.uk
orcid: https://orcid.org/0000-0002-5277-5196
- family-names: Gupte
given-names: Pratik
email: pratik.gupte@lshtm.ac.uk
orcid: https://orcid.org/0000-0001-5294-7819
- family-names: Doohan
given-names: Patrick
orcid: https://orcid.org/0000-0001-8076-1106
- family-names: Johnson
given-names: Robert
orcid: https://orcid.org/0000-0002-7365-0042
year: '2025'
- type: software
title: data.table
abstract: 'data.table: Extension of `data.frame`'
notes: Imports
url: https://r-datatable.com
repository: https://CRAN.R-project.org/package=data.table
authors:
- family-names: Barrett
given-names: Tyson
email: t.barrett88@gmail.com
orcid: https://orcid.org/0000-0002-2137-1391
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email: mattjdowle@gmail.com
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email: asrini@pm.me
- family-names: Gorecki
given-names: Jan
- family-names: Chirico
given-names: Michael
orcid: https://orcid.org/0000-0003-0787-087X
- family-names: Hocking
given-names: Toby
orcid: https://orcid.org/0000-0002-3146-0865
- family-names: Schwendinger
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- family-names: Krylov
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email: rich.fitzjohn@gmail.com
year: '2025'
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abstract: 'RcppEigen: ''Rcpp'' Integration for the ''Eigen'' Templated Linear Algebra
Library'
notes: LinkingTo
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GitHub Events
Total
- Create event: 44
- Release event: 1
- Issues event: 9
- Watch event: 3
- Delete event: 4
- Issue comment event: 167
- Push event: 336
- Pull request review comment event: 161
- Pull request review event: 165
- Pull request event: 102
Last Year
- Create event: 44
- Release event: 1
- Issues event: 9
- Watch event: 3
- Delete event: 4
- Issue comment event: 167
- Push event: 336
- Pull request review comment event: 161
- Pull request review event: 165
- Pull request event: 102
Dependencies
DESCRIPTION
cran
- testthat >= 3.0.0 suggests
.github/workflows/R-CMD-check.yaml
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