epireview contains the latest open access pathogen data from the Pathogen Epidemiology Review Group (PERG), who aim to extract modelling parameters for nine priority pathogens as defined by WHO. This R package contains tools to update pathogen databases with new peer-reviewed data as it becomes available, and to summarise the latest data using tables and figures.
There are several vignettes available:
Pathogen database options which lists the options for each model, outbreak, or parameter field and describes how to access them using a function in the package.
How to update the database with new article data to explain the process of updating the database with new article, model, outbreak, or pathogen data.
In addition to this, the github repo has a wiki which provides details on the data extraction process together with examples and an overview of the quality assessment measures.
We also provide an empty access database file which can be used as a starting point for any new pathogens which are not already covered by this review. For updates to the existing datasets please follow the How to update the database with new article data guide.