README.Rmd

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output: github_document
bibliography: vignettes/resources/references.json
link-citations: true
---

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```{r, include = FALSE}
knitr::opts_chunk$set(
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# daedalus: Optimise economic, social and health trade-offs in a pandemic

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_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