epiparameter

{epiparameter} is an R package that contains a library of epidemiological parameters for infectious diseases and a set classes and helper functions to be able to work with the data. It also includes functions to extract and convert parameters from reported summary statistics.

{epiparameter} 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

The easiest way to install the development version of {epiparameter} is to use the {pak} package:

# check whether {pak} is installed
if(!require("pak")) install.packages("pak")
pak::pak("epiverse-trace/epiparameter")

Quick start

library(epiparameter)

To load the library of epidemiological parameters into R:

epidists <- epidist_db()
#> Returning 122 results that match the criteria (99 are parameterised). 
#> Use subset to filter by entry variables or single_epidist to return a single entry. 
#> To retrieve the citation for each use the 'get_citation' function
epidists
#> List of <epidist> objects
#>   Number of entries in library: 122
#>   Number of studies in library: 47
#>   Number of diseases: 23
#>   Number of delay distributions: 112
#>   Number of offspring distributions: 10

This results a list of database entries. Each entry of the library is an <epidist> object.

The results can be filtered by disease and epidemiological distribution. Here we set single_epidist = TRUE as we only want a single database entry returned, and by default (single_epidist = FALSE) it will return all database entries that match the disease (disease) and epidemiological distribution (epi_dist).

influenza_incubation <- epidist_db(
  disease = "influenza",
  epi_dist = "incubation period",
  single_epidist = TRUE
)
#> Using Virlogeux V, Li M, Tsang T, Feng L, Fang V, Jiang H, Wu P, Zheng J, Lau
#> E, Cao Y, Qin Y, Liao Q, Yu H, Cowling B (2015). "Estimating the
#> Distribution of the Incubation Periods of Human Avian Influenza A(H7N9)
#> Virus Infections." _American Journal of Epidemiology_.
#> doi:10.1093/aje/kwv115 <https://doi.org/10.1093/aje/kwv115>.. 
#> To retrieve the citation use the 'get_citation' function
influenza_incubation
#> Disease: Influenza
#> Pathogen: Influenza-A-H7N9
#> Epi Distribution: incubation period
#> Study: Virlogeux V, Li M, Tsang T, Feng L, Fang V, Jiang H, Wu P, Zheng J, Lau
#> E, Cao Y, Qin Y, Liao Q, Yu H, Cowling B (2015). "Estimating the
#> Distribution of the Incubation Periods of Human Avian Influenza A(H7N9)
#> Virus Infections." _American Journal of Epidemiology_.
#> doi:10.1093/aje/kwv115 <https://doi.org/10.1093/aje/kwv115>.
#> Distribution: weibull
#> Parameters:
#>   shape: 2.101
#>   scale: 3.839

The <epidist> object can be plotted.

plot(influenza_incubation)

Parameter conversion and extraction

The parameters of a distribution can be converted to and from mean and standard deviation. In {epiparameter} we implement this for a variety of distributions:

• gamma
• lognormal
• Weibull
• negative binomial
• geometric

The parameters of a probability distribution can also be extracted from other summary statistics, for example, percentiles of the distribution, or the median and range of the data. This can be done for:

• gamma
• lognormal
• Weibull
• normal

Contributing to library of epidemiological parameters

If you would like to contribute to the different epidemiological parameters stored in the {epiparameter} package, you can add data to a public google sheet. This spreadsheet contains two example entries as a guide to what fields can accept. We are monitoring this sheet for new entries that will subsequently be included in the package.

Alternatively, 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.

Help

To report a bug please open an issue

Contribute

Contributions to {epiparameter} are welcomed. package contributing guide.

Code of Conduct

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

Citing this package

citation("epiparameter")
#> To cite package 'epiparameter' in publications use:
#> 
#>   Lambert J, Kucharski A, Tamayo C (2024). _epiparameter: Library of
#>   Epidemiological Parameters with Helper Functions and Classes_.
#>   doi:10.5281/zenodo.11110881
#>   <https://doi.org/10.5281/zenodo.11110881>,
#>   <https://github.com/epiverse-trace/epiparameter/,https://epiverse-trace.github.io/epiparameter/>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {epiparameter: Library of Epidemiological Parameters with Helper Functions and Classes},
#>     author = {Joshua W. Lambert and Adam Kucharski and Carmen Tamayo},
#>     year = {2024},
#>     doi = {10.5281/zenodo.11110881},
#>     url = {https://github.com/epiverse-trace/epiparameter/,
#> https://epiverse-trace.github.io/epiparameter/},
#>   }