Retrieve pathogen-specific data

Usage

load_epidata(pathogen, mark_multiple = TRUE)

Arguments

pathogen: name of pathogen. This argument is case-insensitive. Must be one of the priority pathogens You can get a list of the priority pathogens currently included in the package by calling the function priority_pathogens.
mark_multiple: logical. If TRUE, multiple studies from the same author in the same year will be marked with an numeric suffix to distinguish them. See mark_multiple_estimates for more details.

Value

a list of length 4. The first element is a data.frame called "articles" which contains all of the information about the articles extracted for this pathogen. The second element is a data.frame called "params" with articles information (authors, publication year, doi) combined with the parameters. The third element is a data.frame called "models" with all transmission models extracted for this pathogen including articles information as above. The fourth element is a data.frame called "outbreaks" which contains all of the outbreaks extracted for this pathogen, where available. If no data is available for a particular table, the corresponding element in the list will be NULL.

Details

The data extracted in the systematic review has been stored in four files - one each for articles, parameters, outbreaks, and transmission models. Data in these files can be linked using article identifier. This function will read in the pathogen-specific files and join them into a data.frame. This function also creates user-friendly short labels for the "parameter_type" column in params data.frame. See short_parameter_type for more details.