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

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 · JSON representation ·

Repository

[UNDER DEVELOPMENT] R package implementing the DAEDALUS model for projecting and optimising health, social, and economic costs of a pandemic.

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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


[![Project Status: Concept – Minimal or no implementation has been done yet, or the repository is only intended to be a limited example, demo, or proof-of-concept.](https://www.repostatus.org/badges/latest/concept.svg)](https://www.repostatus.org/#concept)
[![R build status](https://github.com/jameel-institute/daedalus/workflows/R-CMD-check/badge.svg)](https://github.com/jameel-institute/daedalus/actions/workflows/R-CMD-check.yaml)
[![Codecov test coverage](https://codecov.io/gh/jameel-institute/daedalus/branch/main/graph/badge.svg)](https://app.codecov.io/gh/jameel-institute/daedalus?branch=main)
[![CRAN status](https://www.r-pkg.org/badges/version/daedalus)](https://CRAN.R-project.org/package=daedalus)


_daedalus_ implements the integrated epidemiological and economic model in @haw2022.

![](vignettes/figures/daedalus.png)

## 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

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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  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  url: https://www.R-project.org/
  authors:
  - name: R Core Team
  institution:
    name: R Foundation for Statistical Computing
    address: Vienna, Austria
  year: '2025'
  version: '>= 3.5'
- type: software
  title: checkmate
  abstract: 'checkmate: Fast and Versatile Argument Checks'
  notes: Imports
  url: https://mllg.github.io/checkmate/
  repository: https://CRAN.R-project.org/package=checkmate
  authors:
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    given-names: Michel
    email: michellang@gmail.com
    orcid: https://orcid.org/0000-0001-9754-0393
  year: '2025'
  doi: 10.32614/CRAN.package.checkmate
- type: software
  title: cli
  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:
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    given-names: Pablo
    email: p.perez-guzman@imperial.ac.uk
    orcid: https://orcid.org/0000-0002-5277-5196
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    given-names: Pratik
    email: pratik.gupte@lshtm.ac.uk
    orcid: https://orcid.org/0000-0001-5294-7819
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  abstract: 'data.table: Extension of `data.frame`'
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- type: software
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  abstract: 'dust2: Next Generation dust'
  notes: Imports
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  abstract: 'Rcpp: Seamless R and C++ Integration'
  notes: Imports
  url: https://www.rcpp.org
  repository: https://CRAN.R-project.org/package=Rcpp
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    given-names: Dirk
    email: edd@debian.org
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  abstract: 'R: A Language and Environment for Statistical Computing'
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    address: Vienna, Austria
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  abstract: 'countrycode: Convert Country Names and Country Codes'
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    given-names: Matthew
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  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Suggests
  url: https://ggplot2.tidyverse.org
  repository: https://CRAN.R-project.org/package=ggplot2
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  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  url: https://yihui.org/knitr/
  repository: https://CRAN.R-project.org/package=knitr
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    given-names: Yihui
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  year: '2025'
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- type: software
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  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Suggests
  url: https://pkgs.rstudio.com/rmarkdown/
  repository: https://CRAN.R-project.org/package=rmarkdown
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    given-names: JJ
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    orcid: https://orcid.org/0000-0003-0645-5666
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  repository: https://CRAN.R-project.org/package=bookdown
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  - family-names: Xie
    given-names: Yihui
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    given-names: Rich
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  repository: https://CRAN.R-project.org/package=RcppEigen
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    given-names: Yixuan
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  year: '2025'
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  • 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 actions
  • actions/checkout v4 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.5.0 composite
  • actions/checkout v4 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v4 composite
  • actions/upload-artifact v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/lint-changed-files.yaml actions
  • actions/checkout v4 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/update-citation-cff.yaml actions
  • actions/checkout v4 composite
  • peter-evans/create-pull-request v6 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite