version simulating. Not tested

Author: cruizm

epidemic_hoya_et_al/SIR_Hoya.ma

@@ -1,59 +1,33 @@
-#include(SIR_Hoya_macros.inc)
-[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
-
-statevariables: people %population in the cell
-statevariables: c %connectivy between cells
-% 1 - 3 ways of transportation
-% 0.6 - 2 ways of transportation
-% 0.3 - 1 way of transportation
-% 0 - no transportation
-% We are assuming same connectivity for all cell, but in the original model, we should have a c for each neighbour cell
-
-statevariables: m
-%movement factor [0, 1] probability of an infected individual from a neighbour cell moved to here. We are assuming same for all cells, but we may have a different one for each cell.
-
-statevariables: i_sus i_inf i_rec
-statevalues: 10 1 0.5 0.9 0.1 0
-
-NeighborPorts : sus inf rec pop
-
-localtransition : infections
-
-
-[infections]
-
-%IT DOES NOT WORK
-%rule : {~pop := $people;} { $i_rec := (#macro(e)+(0,1)~inf);} 1000 { t } 
-
-%IT DOES WORK
-%rule : {~pop := $people;} { $i_rec := #macro(e);} 1000 { t }
-
-%IT DOES WORK
-rule : {~pop := $i_rec;} { $i_rec := #macro(e);} 1000 { t }  
-
-%IT DOES NOT WORK
-%rule : {~pop := $i_rec+(0,1)~inf;} { $i_rec := #macro(e);} 1000 { t }  
-
-%IT DOES WORK
-rule : {~pop := $i_rec;} { $i_rec := #macro(e);} 1000 { (0,0)~pop = 10 } 
-
- 	% 
-	%~inf:= (1-#macro(e)) * (0,0)~inf + #macro(v)*(0,0)~sus*(0,0)~inf+(0,0)~sus* #macro(effect_neighbours);
-	%~sus := (0,0)~sus - #macro(v)*(0,0)~sus*(0,0)~inf - (0,0)~sus* #macro(effect_neighbours); 
-
-% 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 : 21
+height : 21
+delay : transport
+defaultDelayTime : 100
+border : wrapped
+neighbors : 			area(-1,0) 
+neighbors : area(0,-1)  area(0,0)  area(0,1)
+neighbors : 			area(1,0) 
+initialvalue : 0
+
+
+localtransition : sir-hoya-rule
+
+statevariables: population v c m
+statevalues: 10 0.5 1 0.7
+
+
+neighborports : value infec rec pop sus
+
+[sir-hoya-rule]
+rule : { ~pop := $population;
+~infec:= (1 - #macro(e)) * (0,0)~infec + $v*(0,0)~sus*(0,0)~infec + (0,0)~sus*#macro(effect_neighbours);
+~sus := (0,0)~sus - $v*(0,0)~sus*(0,0)~infec - (0,0)~sus*#macro(effect_neighbours);
+~rec := (0,0)~rec + #macro(e)*(0,0)~infec;
+} 100 { t }
+
+

epidemic_hoya_et_al/SIR_Hoya_macros.inc

@@ -1,17 +1,12 @@
-#BeginMacro(e) %recovery rate [0,1]
+#BeginMacro(e) 
 0.5
 #EndMacro
 
-#BeginMacro(v) %virulence of the epidemic [0,1]
-  0.5
-#EndMacro 
 
-#BeginMacro(effect_neighbours)
-0.45
+#BeginMacro(effect_neighbours) 
+( ((1,0)~pop / $population) * (1,0)~infec * $v * $c * $m  + 
+((0,-1)~pop / $population) * (0,-1)~infec * $v * $c * $m + 
+((0,1)~pop / $population) * (0,1)~infec * $v * $c * $m +
+((-1,0)~pop / $population) * (-1,0)~infec * $v * $c * $m )
 #EndMacro
 
-%( (((0,-1)~pop/$people)*$c*$m*#macro(v)*(0,-1)~inf) + 
-%(0,1)~pop/$people)*$c*$m*#macro(v)*(0,1)~inf) +
-%	((-1,0)~pop/$people)*$c*$m*#macro(v)*(-1,0)~inf)  +
-%	((1,0)~pop/$people)*$c*$m*#macro(v)*(1,0)~inf) 
-%	)