In this PR I've added the capacity to load parameters for pathogen archetypes through the get_parameters() function. (parameters.R). The new argument has a default value of "none" and when this option is selected the parameter list returns the parameter list as usual with the specified overrides. When an archetype is selected (current options are flu, sars_cov_2, and measles, get_parameters() assigns values to each parameter as normal, then overwrites the values for the following parameters:
duration_exposed
duration_infectious
beta_household
beta_school
beta_workplace
beta_leisure
beta_community
The beta community values are selected to represent R0 values of approximately 1.5 for flu, 2.5 for sars_cov_2, and 9 for measles. There is also a test added to ensure that a recognised archetype has been specified and errors out if not. I have added some basic unit tests to check that the error catches erroneous archetype arguments as expected and that the parameter sets load as expected.
In this PR I've added the capacity to load parameters for pathogen archetypes through the
get_parameters()function. (parameters.R). The new argument has a default value of "none" and when this option is selected the parameter list returns the parameter list as usual with the specifiedoverrides. When an archetype is selected (current options areflu,sars_cov_2, andmeasles,get_parameters()assigns values to each parameter as normal, then overwrites the values for the following parameters:The beta community values are selected to represent R0 values of approximately 1.5 for flu, 2.5 for sars_cov_2, and 9 for measles. There is also a test added to ensure that a recognised archetype has been specified and errors out if not. I have added some basic unit tests to check that the error catches erroneous archetype arguments as expected and that the parameter sets load as expected.
Happy for all suggestions and recommendations!