Implement simple compartmental models

PoonLab / Kaphi

Kernel-embedded ABC-SMC for phylodynamic inference

GNU Affero General Public License v3.0

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Implement simple compartmental models #52

Closed ArtPoon closed 7 years ago

ArtPoon commented 7 years ago

For starters:

[x] susceptible-infected (SI) model
[x] susceptible-infected-removed (SIR) model (dynamic and non-dynamic)
[x] susceptible-exposed-infected-removed (SEIR) model
[x] susceptible-infected-susceptible (SIS) model

See rcolgem-wrappers.R for an initial example.

ArtPoon commented 7 years ago

@artpoon to provide references explaining these models and implementation in rcolgem

ArtPoon commented 7 years ago

Wikipedia Original paper More recent work from Tanja Stadler

ArtPoon commented 7 years ago

@gtng92 has implemented some standard compartmental models as wrapper functions (writing the ODE expressions) but they don't yet call the deSolve package for numerical solution of the ODE, and to pass this solution to the coalescent tree simulating function of rcolgem.

Actions:

[x] write calling function to deSolve
[x] write calling function to rcolgem

ArtPoon commented 7 years ago

rcolgem-wrappers.R is not a complete example, you may want to refer to Kaphi/drivers/simulate.SI.R

ArtPoon commented 7 years ago

Closing - make unit testing and validation separate issues.