Database of Epidemiological Parameters • epiparameterDB

epiparameterDB provides a database of epidemiological parameters. It stores the data for the epiparameter R package.

We recommend reading the epidemiological parameters via the epiparameter::epiparameter_db() function rather than using this package. epiparameter::epiparameter_db() function formats the epidemiological parameters into <epiparameter> objects and organises the object elements (e.g. into R classes like <distribution> and <bibentry>), whereas reading the parameter database (parameters.json) in this package will provide a list of information.

epiparameterDB is developed at the Centre for the Mathematical Modelling of Infectious Diseases at the London School of Hygiene and Tropical Medicine as part of Epiverse-TRACE.

Installation

You can install epiparameterDB from CRAN with:

install.packages("epiparameterDB")

You can install the development version of epiparameterDB from GitHub with:

# install.packages("pak")
pak::pak("epiverse-trace/epiparameterDB")

Usage

library(epiparameterDB)
data(package = "epiparameterDB")

Contributing to library of epidemiological parameters

Parameters can be added to the JSON file holding the data base directly via a Pull Request.

You can find explanation of accepted entries for each column in the data dictionary.

There are simpler ways to add to the epidemiological parameter database outlined in the README of the epiparameter package.

Help

To report a bug please open an issue

Contributions

Contributions to epiparameterDB are welcomed. package contributing guide.

Contributions are welcome via pull requests.

Code of Conduct

Please note that the epiparameterDB project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

This project is related to other existing projects in R or other languages, but also differs from them in the following aspects:

epireview: An R package containing epidemiological parameters for a range of priority pathogens (e.g. Ebola, Lassa and SARS). These can be read into R as tabular data. To fully utilise data stored in epireview we recommend converting the epidemiological parameter of choice into an <epiparameter> object using epiparameter::as_epiparameter(), see data_from_epireview vignette.

Citing this package

citation("epiparameterDB")
#> To cite package 'epiparameterDB' in publications use:
#> 
#>   Lambert J, Kucharski A, Tamayo C (2024). _epiparameterDB: Database of
#>   Epidemiological Parameters_. R package version 0.1.0,
#>   https://epiverse-trace.github.io/epiparameterDB/,
#>   <https://github.com/epiverse-trace/epiparameterDB/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {epiparameterDB: Database of Epidemiological Parameters},
#>     author = {Joshua W. Lambert and Adam Kucharski and Carmen Tamayo},
#>     year = {2024},
#>     note = {R package version 0.1.0, 
#> https://epiverse-trace.github.io/epiparameterDB/},
#>     url = {https://github.com/epiverse-trace/epiparameterDB/},
#>   }

{epiparameterDB}