Simple SIR model example. Implemented in basic CD++. No ports. No state variables

Author: cruizm

tr_0.4_dr_0.05_cd++/README.md

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+#Disease Spread Model
+
+New rule added for the Incubation period where people are Asymptomatic. 
+People cannot die during Asymptomatic incubation (they have no even symptoms...)
+
+##Parameters:
+Von Neumann Neighborhood
+Transport Delays
+Death Rate:0.05
+Transmission Rate:0.4
+
+##How to run the model:
+
+In the linux terminal, type:  
+
+> ./../cd++ -mcovid.ma -lresults/covid.log

tr_0.4_dr_0.05_cd++/VN.inc

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+#BeginMacro(susceptible) 
+0 
+#EndMacro
+
+#BeginMacro(infected)   
+  1	 
+#EndMacro % asymptomatic
+
+#BeginMacro(sick)   	    
+  8	 
+#EndMacro % separate asymptomatic 
+
+#BeginMacro(recovered)  
+16 
+#EndMacro
+
+#BeginMacro(dead)	   
+-1 
+#EndMacro
+
+#BeginMacro(imAsymp)   
+  ( ((0,0)>=1) and ((0,0) < 8))  
+#EndMacro
+
+#BeginMacro(imInfected)   
+((0,0)>=1 and (0,0)<16)   
+#EndMacro
+
+#BeginMacro(imRecovered)
+  ((0,0)=16 ) %(((0,0) > 8) and not ((0,0)>0 and (0,0)<16))
+#EndMacro
+
+#BeginMacro(anyNeighborIsInfected)
+( ( (-1,0)>0 and (-1,0)<16 ) or ( (0,-1)>0 and (0,-1)<16) or  
+  ( (0,0)>0  and (0,0)<16  ) or ( (0,1)> 0 and (0,1)<16 ) or
+  ( (1,0)>0 and (1,0)<16   )  
+)
+#EndMacro
+
+#BeginMacro(gotInfected)   
+   (uniform(0,1) <= 0.4)
+#EndMacro
+
+%#BeginMacro(asymp)         
+%   (uniform(0,1) <= 0.5)   
+%#EndMacro
+
+#BeginMacro(died)          
+   (uniform(0,1) <= 0.05) 
+#EndMacro

tr_0.4_dr_0.05_cd++/covid.ma

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+#include(VN.inc)
+[top]
+components : population
+
+[population]
+type : cell
+dim : (200,200)
+delay : transport
+defaultDelayTime : 1
+border : nowrapped
+neighbors : population(0,-1) population(0,0) population(0,1) 
+neighbors :                  population(-1,0) 
+neighbors :                  population(1,0) 
+
+initialvalue : 0
+InitialCellsValue : covid.val
+
+localtransition : infections
+
+[infections]
+rule : {if( #macro(gotInfected), #macro(infected), (0,0))} 1 
+     { (0,0)=0 and #macro(anyNeighborIsInfected)}
+
+rule : { #macro(sick) }  7   { #macro(imAsymp) }
+
+rule : {if( #macro(died), #macro(dead), (0,0)+1)} 1 
+            {#macro(imInfected)}
+
+rule : {(0,0)} 1000 { t }  
+
+% neighbors : population(-1,-1) population(-1,0) population(-1,1) 
+% neighbors : population(1,-1) population(1,0) population(1,1)

tr_0.4_dr_0.05_cd++/covid.pal

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+[-1.5;-0.5] 0 0 0
+[-0.5;0.5] 255 255 255
+[0.5;7.5] 255 255 0
+[7.5;15.5] 255 0 0
+[15.5;16.5] 0 255 0
+[16.5;100] 128 128 128

tr_0.4_dr_0.05_cd++/covid.val

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+(19,10) = 1
+(159,100) = 1
+(180,190) = 1
+
+