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CompartmentalModeling

Guides

  • Compartmental Modeling

Tech Notes

  • Vertical Transmission Models

Symbols

  • DynamicTransmissionModel
  • ForceOfInfection
  • Incidence
  • NextGenerationMatrix
  • CollectModel
  • CompartmentalModelGraph
  • CompetitiveInhibitorKinetics
  • DefinePropensityFunction
  • DeriveTransitions
  • DynamicTransmissionModel
  • EnzymeReaction
  • EpidemiologyModelData
  • EpidemiologyModel
  • ExpandModel
  • ForceOfInfection
  • HillKinetics
  • Incidence
  • KineticCompartmentalModel
  • KineticReactionNetworkModel
  • MichaelisMentenKinetics
  • NextGenerationMatrix
  • NoncompetitiveInhibitorKinetics
  • NullCompartment
  • ResolveCompartmentalModel
  • StochasticSolve
  • StoichiometryTable
  • StratifyModel
  • Transition
  • UncompetitiveInhibitorKinetics
  • VitalDemographicsModel
  • $C
  • $CompartmentalModelingVersion
  • $EpidemiologyColor
  • $EpidemiologyModelingVersion
  • $R
  • $SystemsBiologyModelingVersion
RobertNachbar`EpidemiologyModeling`
DynamicTransmissionModel
​
DynamicTransmissionModel
[{
tr
1
,
tr
2
,…},t]
returns an association of model data for the input transitions in
tr
i
and time symbol
t
.
​
Details and Options

Examples  
(27)
Basic Examples  
(1)
Generate the model data
Association
for an SIR model:
In[1]:=
modelData=
DynamicTransmissionModel

βλ[t]
→
ℐ,ℐ
γ
→
ℛ,t,"ForceOfInfection"{λ,ℐ}
Out[1]=
Variables{ℐ,ℛ,},ComponentTransitionsℐ
γ
→
ℛ,
βλ[t]
→
ℐ,StoichiometricMatrix{{-1,1,0},{1,0,-1}},Rates{γℐ[t],β[t]λ[t]},Equations{
′
ℐ
[t]-γℐ[t]+β[t]λ[t],
′
ℛ
[t]γℐ[t],
′

[t]-β[t]λ[t]},TimeSymbolt,ForceOfInfection{λ[t]ℐ[t]}
The compartments and transitions can be visualized with
CompartmentalModelGraph
:
In[2]:=
CompartmentalModelGraph
modelData["ComponentTransitions"],"CompartmentColors"
$EpidemiologyColor
["Susceptible"],ℐ
$EpidemiologyColor
["Infected"],ℛ
$EpidemiologyColor
["Recovered"],
options

Out[2]=
Options  
(23)

Applications  
(2)

Possible Issues  
(1)

SeeAlso
VitalDemographicsModel
 
▪
StratifyModel
 
▪
ForceOfInfection
 
▪
KineticCompartmentalModel
 
▪
CompartmentalModelGraph
RelatedGuides
▪
Compartmental Modeling
""

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