v0.2.0

v0.2.0

1 June 2021

Simulation mechanics

• pathogen genome influences transmission, death, recovery, migration,
  mutation probabilities. Done, tested
• independent recombination of alleles -> make chromosome separators!!
  make reassortment parameter option as related but separate to
  recombination. Done, tested
• host/vector birth/death rates in populations -> make birth event.
  Done, tested
• separate natural death into an event that doesn't log deaths. Done, tested
• make RECEIVE_CONTACT and RECEIVE_POPULATION_CONTACT coefficient columns
  in arrays, modify how these events are handled. Done, tested
• migrate vectors. Done, test
• contact between populations (without migration). Done, tested

Output

• make genome labels optional, if no labels write a file with the genomes
  in the same order for compositionPlot. Done, test
• compositionPlot – make custom groupings, eg. "genomes containing
  sequence AAA". Done, test
• make option to count only 1 fitness-dominant strain/host in
  compositionPlot. Done, test
• genomes and dates output for TDA. Done, test

Technical details

• set seed. Done, test
• make all events except mutation, recombination and recovery
  1-coefficient like contact and pop contact are. this way, coefficients are
  fraction of healthy rate. Modify dummy rows in coeff arrays to match
  this. Done, tested
• parallelizeable simulations. Done, test
• try Numba, Cython, JAX optimization

Miscellaneous

• update docs. Done
• update tutorials. Done, tested