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DAEDALUS data

daedalus.data is a package and repository to handle input data files for daedalus, Jameel Institute’s combined economic-epidemiological model of emerging respiratory pandemic diseases.

daedalus.data prepares data objects to be used by the daedalus (see here) model.

Installation

You can install the development version of daedalus.data from the Jameel Institute R-universe with:

installation from R-universe
install.packages(
 "daedalus.data",
 repos = c(
   "https://jameel-institute.r-universe.dev", "https://cloud.r-project.org"
 )
)

or from GitHub GitHub with:

install.packages("pak")
pak::pak("jameel-institute/daedalus.data")

Installation notes

Both daedalus.data and daedalus are under active development. To use them, always ensure you have the latest versions on main branch.

Adding or modifying data

Follow these basic principles. Refer to the Data chapter in R Packages for guidance.

  1. Add raw data (such as CSV files) under inst/extdata.

  2. Add scripts that process raw data under data-raw. See existing scripts for guidance. In these scripts, use usethis::use_data() to save processed data into data as .rda files, which will be made available as package data.

    • To regenerate data, rerun these scripts.

  3. Add documentation for package data under R/<data_name>.R See existing files such as R/country_data.R for guidance.

  4. Document changes in the changelog NEWS.md.

Quick start

This package contains the following data sets:

data(package = "daedalus.data")

Infections data

Users can select infection parameters from among seven epidemics caused by directly-transmitted viral respiratory pathogens, which are stored in the package as daedalus.data::infection_data, with epidemic identifiers stored as daedalus.data::epidemic_names.

  1. daedalus: Ingests daedalus.data data to create S3 class objects representing infections, populations, and epidemic mitigation measures.
  2. daedalus.compare: Ingests daedalus outputs to help compare epidemic scenarios.