antigen
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trvrb
Simulating virus evolution and epidemiology
## Description Emit daily case counts per deme to support models like @marlinfiggins's [Rt frequency dynamics models](https://github.com/blab/rt-from-frequency-dynamics). These models consume real case counts from the CDC that have been processed...
## Description Building on the work in issue #22, output the number of cases per day, deme, and variant to support models like @marlinfiggins's Rt frequency dynamics models. Example output...
Each timestep look at genetic diversity, quit simulation if greater than some number.
When extinction occurs, reseed rather restarting. Not clear how to do this best.
Output tree imbalance statistic. Also, decide on which imbalance statistic to use.
When there is a coinfection event, there is a certain probability (which could be 100%) at which "recombination" occurs. This mutates the viral phenotypes of both infecting strains. This mutation...
Currently, [each Host references a single virus](https://github.com/trvrb/antigen/blob/master/Host.java#L10). Refactor to have each Host reference an array of viruses, which can be empty. Then, allow new infections to occur at a rate...