v0.9.1

v0.9.1 check changelog.md

v0.9.0

All graphs in publication (title pending) generated with this stable version.

v0.2.6

v0.2.6 check changelog.md

v0.2.5

v0.2.5 check changelog.md

v0.2.4

See changelog.md

v0.2.3

See changelog.md

v0.2.2

See changelog for more info

v0.2.1

v0.2.1

1 June 2021

• Update version tags

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

v0.1.7

Corrected bugs that caused hosts/vectors to become less infectious over time because total infection fitness wasn't amended upon recovery, and new pathogen genomes weren't correctly checked upon addition in some cases. Also changed contacts so that now a contact is one-way only (behavior closer to Gillespie algorithm assumptions).