Network-based interactions

[ptheywood]

Implements network-based interactions and other changes/fixes:

• Implements Random household generation
  • Households are of a randomised size based on model parameters
  • Age demographics within a household are random, to match the target global population age demographics.
  • Note: Demographics within a household may be unrealistic, see Realistic household age-distributions #29.
• Implements workplaces and workplace interactions
  • Individuals are assigned to a workplace network, based on their age demographic and for adults parameters controlling the adult to non-adult ratios for non-adult workplaces
  • 5 work place categories:
    • Schools for 0-9 year olds, with a target ratio of adults to children
    • Schools for 10-19 year olds, with a target ratio of adults to children
    • General adult (20-69) workplace population
    • Retirement network for 70-79, with a target ratio of adults
    • Elderly network for 80+, with a target ratio of adults
  • Each workplace network is constructed as a Watts-Strogatz small world network, with individuals
    interacting with a subset of their neighbours per day, and networks designed to achieve a target number of interactions based on the network type
• Random daily interactions
  • Re-generated per day (in serial on the host, so costly)
  • Fixed upper limit defined at compile time due to FLAME GPU 2 limitations on agent varable arrays (they are std::array-like rather than std::vector)
  • Individuals have a target number of daily interactions, sampled from a random distribution based on their age demographic
  • Generation is potentailyl somewhat unrealistic, deferred to Random Network generation Improvements #30
• Significant increase in model parameters, to allow control of new behaviours
• Adds optional per-individual file output, controlled by CLI parameter
  • Adds associated simple script showing use of post processing data
• Identified several bugs in FLAME GPU 2, which have been worked-around for now
  • 1 fixed upstream, 1 fix in review
• Addresses compatibility with GCC 8
• Includes refactoring and additional testing
• Visualisation adjusted to be household centric

Closes #4
Closes #6
Closes #7
Closes #12

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Hosuehold-centric Visualisation:

Per-individual plotting demonstration for arbitrary model input:

Time-series demo plots for arbitrary model input: