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New zhong-based model
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‎epidemic_zhong_et_al_v2/generator/model_generator.py‎

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import argparse
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parser = argparse.ArgumentParser(description='Auxiliar script to generate Zhong-based CA models')
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parser.add_argument('-f', '--infected_steps', type=int, default=6, help='Number of days for the infected state')
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parser.add_argument('-r', '--recovered_steps', type=int, default=7, help='Number of days for the recovered state')
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parser.add_argument('-t', '--template_ma', type=str, default="template_sirs_zhong_ma", help='Path to zhong .ma template')
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parser.add_argument('-m', '--template_macros', type=str, default="template_sirs_zhong_macros", help='Path to zhong macros template')
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parser.add_argument('-o', '--out_ma_file', type=str, default="out.ma", help='Output path of the .ma file')
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parser.add_argument('-p', '--out_macros_file', type=str, default="sirs_zhong_macros.inc", help='Output path of the macros file')
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parser.add_argument('-v', '--virulences', type=str, default="0.6", help='Default virulence values per state')
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args = parser.parse_args()
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i = 1
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states = ["sus_0"]
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neighbors = ["(1,0)", "(0,-1)", "(0,1)", "(-1,0)"]
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steps_per_state = list(map(str, [args.infected_steps, args.recovered_steps]))
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while i <= args.infected_steps:
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states.append("inf_%d" % i)
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i += 1
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while i <= args.infected_steps + args.recovered_steps:
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states.append("rec_%d" % i)
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i += 1
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##############################
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# GENERATION OF THE .MA FILE
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##############################
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content = ""
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with open(args.template_ma, "r") as f:
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content = f.read()
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internal_vars = ["i_%s" % s for s in states] + ["v_%d" % n for n in range(1, args.infected_steps + 1)]
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content = content.replace("[[internal_vars]]", " ".join(internal_vars))
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internal_vars_values = " ".join(steps_per_state + ["1.0"] + ["0.0"] * (len(states) - 1))
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if "," in args.virulences:
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virulences = list(args.virulences.split(","))
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else:
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virulences = [args.virulences] * args.infected_steps
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internal_vars_values += " %s" % " ".join(virulences)
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content = content.replace("[[internal_vars_values]]", internal_vars_values)
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update_ports_str = " ".join(["~%s := $i_%s;" % (s, s) for s in states])
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content = content.replace("[[initial_ports_set_up]]", update_ports_str)
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content = content.replace("[[update_ports_step]]", update_ports_str)
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content = content.replace("[[ports]]", " ".join(states))
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update_rules = ""
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idx_first_rec = len(states)-args.recovered_steps
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for i in range(len(states)-1, idx_first_rec, -1):
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update_rules += "$i_%s := $i_%s;\n" % (states[i], states[i-1])
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update_rules += "$i_%s := $i_%s + #macro(local_cured);\n\n" % (states[idx_first_rec], states[idx_first_rec-1])
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for i in range(idx_first_rec-1, 1, -1):
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update_rules += "$i_%s := round(min((1 - $cured_rate) * $i_%s, 1)*100)/100;\n" % (states[i], states[i - 1])
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update_rules += "$i_%s := #macro(internal_infected) + #macro(external_infected);\n\n" % states[1]
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update_rules += "$i_%s := 1 " % states[0]
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update_rules += " ".join(["- $i_%s" % s for s in states[1:]])
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update_rules += ";\n"
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content = content.replace("[[update_vars_step]]", update_rules)
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with open(args.out_ma_file, "w") as f:
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f.write(content)
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#################################
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# GENERATION OF THE MACROS FILE
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#################################
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content = ""
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with open(args.template_macros, "r") as f:
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content = f.read()
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local_cured_rules = []
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for i in range(idx_first_rec-2, 0, -1):
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local_cured_rules.append("round(min($cured_rate * $i_%s, 1)*100)" % states[i])
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content = content.replace("[[local_cured]]", "(( %s ) / 100 )" % " +\n".join(local_cured_rules))
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content = content.replace("[[infected_vars]]", " + ".join(["i_%s" % s for s in states[idx_first_rec:0]]))
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external_infected_comp = \
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"""( round(min((
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$connection * $movement * $i_sus_0 * (
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[[external_infected]]
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)), 1)*100) / 100 )"""
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internal_infected_comp = \
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"""( round(min((
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$i_sus_0 * (
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[[internal_infected]]
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)), 1)*100) / 100 )"""
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external_infected_rules = []
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for nei in neighbors:
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lines = []
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for s in states[args.infected_steps:0:-1]:
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v = "$v_%s" % s.split("_")[-1]
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line = "(%s~pop / $population) * %s * %s~%s" % (nei, v, nei, s)
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lines.append(line)
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ext_comp = external_infected_comp.replace("[[external_infected]]", " +\n".join(lines))
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external_infected_rules.append(ext_comp)
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content = content.replace("[[external_infected]]", " +\n".join(external_infected_rules))
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lines = []
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for s in states[args.infected_steps:0:-1]:
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v = "$v_%s" % s.split("_")[-1]
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line = "(%s * $i_%s)" % (v, s)
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lines.append(line)
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internal_infected_rule = internal_infected_comp.replace("[[internal_infected]]", " +\n".join(lines))
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content = content.replace("[[internal_infected]]", internal_infected_rule)
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with open(args.out_macros_file, "w") as f:
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f.write(content)

‎epidemic_zhong_et_al_v2/generator/template_sirs_zhong_ma‎

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#include(sirs_zhong_macros.inc)
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[top]
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components : area
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[area]
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type : cell
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width : 50
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height : 50
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delay : transport
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defaultDelayTime : 1
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border : wrapped
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neighbors : area(-1,0)
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neighbors : area(0,-1) area(0,0) area(0,1)
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neighbors : area(1,0)
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initialvalue : -1
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localtransition : sirs-zhong-rule
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statevariables: population connection movement cured_rate t_i t_r [[internal_vars]]
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statevalues: 100 1 0.6 0.0 [[internal_vars_values]]
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initialvariablesvalue: sirs_zhong.var
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neighborports : initial pop [[ports]]
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[sirs-zhong-rule]
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rule : {~initial := 0; ~pop := $population; [[initial_ports_set_up]]}
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1 {(0,0)~initial = -1}
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rule : {
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~pop := $population; [[update_ports_step]]
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}
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{
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[[update_vars_step]]
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}
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1 { (0,0)~initial != -1 }
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‎epidemic_zhong_et_al_v2/generator/template_sirs_zhong_macros‎

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#BeginMacro(local_cured)
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[[local_cured]]
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#EndMacro
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#BeginMacro(internal_infected)
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[[internal_infected]]
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#EndMacro
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#BeginMacro(external_infected)
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[[external_infected]]
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#EndMacro

‎epidemic_zhong_et_al_v2/sirs_zhong.ma‎

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#include(sirs_zhong_macros.inc)
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[top]
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components : area
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[area]
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type : cell
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width : 50
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height : 50
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delay : transport
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defaultDelayTime : 1
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border : wrapped
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neighbors : area(-1,0)
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neighbors : area(0,-1) area(0,0) area(0,1)
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neighbors : area(1,0)
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initialvalue : -1
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localtransition : sirs-zhong-rule
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statevariables: population connection movement cured_rate t_i t_r i_sus_0 i_inf_1 i_inf_2 i_inf_3 i_inf_4 i_inf_5 i_inf_6 i_rec_7 i_rec_8 i_rec_9 i_rec_10 i_rec_11 i_rec_12 i_rec_13 v_1 v_2 v_3 v_4 v_5 v_6
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statevalues: 100 1 0.1 0.0 6 7 1.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.6 0.6 0.6 0.6 0.6 0.6
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initialvariablesvalue: sirs_zhong.var
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neighborports : initial pop sus_0 inf_1 inf_2 inf_3 inf_4 inf_5 inf_6 rec_7 rec_8 rec_9 rec_10 rec_11 rec_12 rec_13
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[sirs-zhong-rule]
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rule : {~initial := 0; ~pop := $population; ~sus_0 := $i_sus_0; ~inf_1 := $i_inf_1; ~inf_2 := $i_inf_2; ~inf_3 := $i_inf_3; ~inf_4 := $i_inf_4; ~inf_5 := $i_inf_5; ~inf_6 := $i_inf_6; ~rec_7 := $i_rec_7; ~rec_8 := $i_rec_8; ~rec_9 := $i_rec_9; ~rec_10 := $i_rec_10; ~rec_11 := $i_rec_11; ~rec_12 := $i_rec_12; ~rec_13 := $i_rec_13;}
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1 {(0,0)~initial = -1}
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rule : {
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~pop := $population; ~sus_0 := $i_sus_0; ~inf_1 := $i_inf_1; ~inf_2 := $i_inf_2; ~inf_3 := $i_inf_3; ~inf_4 := $i_inf_4; ~inf_5 := $i_inf_5; ~inf_6 := $i_inf_6; ~rec_7 := $i_rec_7; ~rec_8 := $i_rec_8; ~rec_9 := $i_rec_9; ~rec_10 := $i_rec_10; ~rec_11 := $i_rec_11; ~rec_12 := $i_rec_12; ~rec_13 := $i_rec_13;
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}
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{
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$i_rec_13 := $i_rec_12;
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$i_rec_12 := $i_rec_11;
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$i_rec_11 := $i_rec_10;
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$i_rec_10 := $i_rec_9;
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$i_rec_9 := $i_rec_8;
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$i_rec_8 := $i_rec_7;
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$i_rec_7 := $i_inf_6 + #macro(local_cured);
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$i_inf_6 := round(min((1 - $cured_rate) * $i_inf_5, 1)*100)/100;
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$i_inf_5 := round(min((1 - $cured_rate) * $i_inf_4, 1)*100)/100;
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$i_inf_4 := round(min((1 - $cured_rate) * $i_inf_3, 1)*100)/100;
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$i_inf_3 := round(min((1 - $cured_rate) * $i_inf_2, 1)*100)/100;
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$i_inf_2 := round(min((1 - $cured_rate) * $i_inf_1, 1)*100)/100;
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$i_inf_1 := #macro(internal_infected) + #macro(external_infected);
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$i_sus_0 := 1 - $i_inf_1 - $i_inf_2 - $i_inf_3 - $i_inf_4 - $i_inf_5 - $i_inf_6 - $i_rec_7 - $i_rec_8 - $i_rec_9 - $i_rec_10 - $i_rec_11 - $i_rec_12 - $i_rec_13;
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}
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1 { (0,0)~initial != -1 }
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‎epidemic_zhong_et_al_v2/sirs_zhong.pal‎

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

‎epidemic_zhong_et_al_v2/sirs_zhong.var‎

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(25,25) = 100 1 0.1 0.0 6 7 0.7 0.3 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.6 0.6 0.6 0.6 0.6 0.6

‎epidemic_zhong_et_al_v2/sirs_zhong_macros.inc‎

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#BeginMacro(local_cured)
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(( round(min($cured_rate * $i_inf_5, 1)*100) +
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round(min($cured_rate * $i_inf_4, 1)*100) +
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round(min($cured_rate * $i_inf_3, 1)*100) +
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round(min($cured_rate * $i_inf_2, 1)*100) +
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round(min($cured_rate * $i_inf_1, 1)*100) ) / 100 )
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#EndMacro
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#BeginMacro(internal_infected)
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( round(min((
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$i_sus_0 * (
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($v_6 * $i_inf_6) +
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($v_5 * $i_inf_5) +
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($v_4 * $i_inf_4) +
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($v_3 * $i_inf_3) +
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($v_2 * $i_inf_2) +
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($v_1 * $i_inf_1)
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)), 1)*100) / 100 )
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#EndMacro
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#BeginMacro(external_infected)
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( round(min((
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$connection * $movement * $i_sus_0 * (
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((1,0)~pop / $population) * $v_6 * (1,0)~inf_6 +
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((1,0)~pop / $population) * $v_5 * (1,0)~inf_5 +
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((1,0)~pop / $population) * $v_4 * (1,0)~inf_4 +
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((1,0)~pop / $population) * $v_3 * (1,0)~inf_3 +
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((1,0)~pop / $population) * $v_2 * (1,0)~inf_2 +
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((1,0)~pop / $population) * $v_1 * (1,0)~inf_1
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)), 1)*100) / 100 ) +
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( round(min((
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$connection * $movement * $i_sus_0 * (
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((0,-1)~pop / $population) * $v_6 * (0,-1)~inf_6 +
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((0,-1)~pop / $population) * $v_5 * (0,-1)~inf_5 +
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((0,-1)~pop / $population) * $v_4 * (0,-1)~inf_4 +
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((0,-1)~pop / $population) * $v_3 * (0,-1)~inf_3 +
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((0,-1)~pop / $population) * $v_2 * (0,-1)~inf_2 +
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((0,-1)~pop / $population) * $v_1 * (0,-1)~inf_1
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)), 1)*100) / 100 ) +
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( round(min((
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$connection * $movement * $i_sus_0 * (
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((0,1)~pop / $population) * $v_6 * (0,1)~inf_6 +
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((0,1)~pop / $population) * $v_5 * (0,1)~inf_5 +
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((0,1)~pop / $population) * $v_4 * (0,1)~inf_4 +
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((0,1)~pop / $population) * $v_3 * (0,1)~inf_3 +
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((0,1)~pop / $population) * $v_2 * (0,1)~inf_2 +
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((0,1)~pop / $population) * $v_1 * (0,1)~inf_1
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)), 1)*100) / 100 ) +
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( round(min((
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$connection * $movement * $i_sus_0 * (
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((-1,0)~pop / $population) * $v_6 * (-1,0)~inf_6 +
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((-1,0)~pop / $population) * $v_5 * (-1,0)~inf_5 +
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((-1,0)~pop / $population) * $v_4 * (-1,0)~inf_4 +
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((-1,0)~pop / $population) * $v_3 * (-1,0)~inf_3 +
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((-1,0)~pop / $population) * $v_2 * (-1,0)~inf_2 +
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((-1,0)~pop / $population) * $v_1 * (-1,0)~inf_1
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)), 1)*100) / 100 )
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#EndMacro

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