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Implemented tracking multiple diseases #47

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@debog debog commented May 13, 2024

Implemented the tracking of multiple diseases (comorbidity and "co-immunity" not yet implemented). The major change is as follows:

  • Disease-specific agent attributes (Real-type and int-type) are now available for each disease. Therefore, they are now runtime SoA attributes; the number of these attributes depends on the number of diseases being tracked. This has consequences for how the attributes are accessed in the code.
  • The demographic attributes are untouched (age_group, home, work, etc.).
  • Disease attributes like hospitalization timer and withdrawn are unique (if an agent withdraws from society due to a symptomatic infection of one disease, they'll not go around spreading other diseases as well).

The changes to input file are as follows:

  • Specify the number of diseases by agent.number_of_diseases. (Default: 1)
  • Specify disease names by `agent.disease_names'. (Default: "default00", "default01", ...).
  • agent.initial_case_type should now have as many entries ("random" or "file") as the number of diseases.
  • For multiple diseases, the initial case filename or number of initial cases should be specified by:
    • `agent.case_filename_[disease name]'
    • agent.num_initial_cases_[disease name]

(For a single disease, agent.case_filename and agent.num_initial_cases still work).

For specifying the disease parameters in the input file, anything that is common for all/some diseases can be specified as

  • disease.[key] = [value]

Parameters that are different for a specific disease can be specified as:

  • disease_[disease name].[key] = [value]

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