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epirecipes / sir-julia

Various implementations of the classical SIR model in Julia
MIT License
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phylogenies from SIR #71

Open slwu89 opened 1 year ago

slwu89 commented 1 year ago

Hi @sdwfrost I saw the paper you linked to (https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.14038), I'm just putting this here as an interesting project for myself later. It seems like it wouldn't be too hard to do this in the DifferentialEquations.jl system. Perhaps using InfiniteArrays.jl to store things too, for generality if the population isn't closed.

sdwfrost commented 1 year ago

Hi @slwu89 - this is a fun one. For ODEs, the first package to implement this kind of approach is @emvolz phydynR, implementing the theory from Volz (2012). More recently, there's @kingaa phylopomp package - the paper linked is really nice. For stochastic models, there's MASTER. All of these packages have a common theme; you write the model in terms of the processes, not the states, then split the processes into those that have a direct impact on the phylogeny and those that don't. Ping me if you need feedback!