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 sdg-3

Last synced: 28 days 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 (7 months ago)
• Default Branch: main
• Last Pushed: 2024-10-29T09:46:25.000Z (3 months ago)
• Last Synced: 2024-10-29T11:49:23.705Z (3 months ago)
• Topics: decision-support, epidemiological-models, health-economics, pandemic-preparedness, public-health, r-package, sdg-3
• Language: R
• Homepage: https://jameel-institute.github.io/daedalus/
• Size: 6.39 MB
• Stars: 3
• Watchers: 2
• Forks: 0
• Open Issues: 5
• 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: Optimise economic, social and health trade-offs in 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.

## 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"

  )

)

```

## 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 package as `daedalus::infection_data`, with epidemic identifiers are stored as `daedalus::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).

## References