SIYR_Aparicio_Poisson.st

siyrConcern := KEModelPart new.
siyrConcern attributes: 
	{#status->#(#S #I #Y #R)}.
siyrConcern addParameters: 
    {#lambda. #gamma. #sigma}.
	 
siyrConcern
	addTransitionFrom: {(#status -> #S)}
	to: {(#status -> #I)}
	probability: 'lambda'.
siyrConcern changeParameter: #lambda 
	value: 'itgen*taugen*alphagen'.
siyrConcern
	addTransitionFrom: {(#status -> #I)} 
	to: {(#status -> #Y)}
	probability: 'gamma'.
	
siyrConcern
	addTransitionFrom: {(#status -> #Y)} 
	to: {(#status -> #R)}
	probability: 'sigma'.
		
aparicioConcern := KEModelPart new.	
aparicioConcern addParameter: #alphagen
	value: 'tau+gamma'.
aparicioConcern addParameter: #itgen
	value: 'I/N'.
aparicioConcern
		addParameter: #taugen
		value: 'R0'.	

model := siyrConcern + aparicioConcern.
		
model atCompartment: {(#status -> #S)} put: 9950.
model atCompartment: {(#status -> #I)} put: 30.
model atCompartment: {(#status -> #Y)} put: 20.
model atCompartment: {(#status -> #R)} put: 0.

model atParameter: #R0 
	 assignValue: 'tau*(meank2 - meank)/(meank*(tau+gamma))'.	
model atParameter: #tau assignValue: 0.025.
model atParameter: #gamma assignValue: 0.1.
model atParameter: #sigma assignValue: 1.
model atParameter: #meank assignValue: 10.
"for Poisson network, meank2 = meank * (meank + 1)"
model atParameter: #meank2 assignValue: 110.
	
simulator := KESimulator
	new: #RungeKutta
	from: 0.0
	to: 200
	step: 0.1.
 simulator executeOn: model.

chart := KEChart new.
chart addDataFrame: 
    ((simulator timeSeriesOutputsAt:
         {(#status -> #I)})/10000).
chart yLabel: 'New infections per day'.
chart legendTitle: 'Aparicio on Poisson network'.
chart plot.

df := simulator timeSeriesOutputs.
file := ('Aparicio_Poisson', DateAndTime now asString,  '.csv') asFileReference.
df writeToCsv: file.