Merge pull request #1 from SimulationEverywhere/epidemic_hoya_et_al

Epidemic hoya et al

Author: romancardenas

epidemic_hoya_et_al/SIR_Hoya.ma

@@ -1,24 +1,43 @@
-[top]
-components : population
-
-[population]
-type : cell
-dim : (100,100)
-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 : SIR_Hoya.val
-
-localtransition : infections
-
-[infections]
-
-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)
+#include(SIR_Hoya_macros.inc)
+[top]
+components : area
+
+[area]
+type : cell
+width : 50
+height : 50
+delay : transport
+defaultDelayTime : 1
+border : wrapped
+neighbors : 			area(-1,0) 
+neighbors : area(0,-1)  area(0,0)  area(0,1)
+neighbors : 			area(1,0) 
+initialvalue : -1
+
+
+localtransition : sir-hoya-rule
+
+statevariables: population virulence connection movement i_sus i_infec i_rec 
+statevalues: 100 0.6 1.0 0.5 1.0 0.0 0.0
+initialvariablesvalue: SIR_Hoya.var
+
+neighborports : initial infec rec pop sus
+
+[sir-hoya-rule]
+rule : {~initial := 0; ~pop := $population; ~infec := $i_infec; ~sus := $i_sus; ~rec := $i_rec; }
+ 1 {(0,0)~initial = -1}
+
+rule : {~pop := $population; ~infec := $i_infec; ~sus := $i_sus; ~rec := $i_rec; }
+{$i_infec:= trunc(min((1 - #macro(e)) * (0,0)~infec + $virulence*(0,0)~sus*(0,0)~infec + (0,0)~sus*#macro(effect_neighbours),1)*100)/100;
+$i_rec := trunc(min((0,0)~rec + #macro(e)*(0,0)~infec,1)*100)/100;
+$i_sus := 1 - $i_rec - $i_infec;} 
+1 { (0,0)~initial != -1 }
+
+
+
+
+
+
+
+
+

epidemic_hoya_et_al/SIR_Hoya.pal

@@ -0,0 +1,7 @@
+[-100; -0.001] 255 0 0
+[0; 0.200] 0 0 0
+[0.201; 0.400] 50 50 50
+[0.401; 0.600] 100 100 100
+[0.601; 0.800] 150 150 150
+[0.801; 1.00] 200 200 200
+[1.001;100] 255 0 0

epidemic_hoya_et_al/SIR_Hoya.var

@@ -0,0 +1 @@
+(25,25) = 10 0.6 1 1 0.3 0.7 0.0

epidemic_hoya_et_al/SIR_Hoya_macros.inc

@@ -0,0 +1,12 @@
+#BeginMacro(e) 
+0.4
+#EndMacro
+
+
+#BeginMacro(effect_neighbours) 
+( ((1,0)~pop / $population) * (1,0)~infec * $virulence * $connection * $movement  + 
+((0,-1)~pop / $population) * (0,-1)~infec * $virulence * $connection * $movement + 
+((0,1)~pop / $population) * (0,1)~infec * $virulence * $connection * $movement +
+((-1,0)~pop / $population) * (-1,0)~infec * $virulence * $connection * $movement )
+#EndMacro
+