Retrieve pathogen-specific data
Arguments
- pathogen
name of pathogen. 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 a suffix to distinguish them.
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.
Details
The data extracted in the systematic review has been stored in three
files - one each for articles, parameters, and transmission models.
Data in the three files can be linked using article identifier.
This function will read in the pathogen-specific articles and
parameters 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.