SIIR Agent-Based Model
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globals [ b2 c3 ] turtles-own [;; Turtle characteristics infectious? ;; note: symptomatics have the virus but not infectious (since they're assumed to be quarantined) infection_state ;; presymptomatic, asymptomatic, symptomatic dead ;; is alive [true/false] immune ;; is immune [true / false] ;recovered or susceptible inc_p ; incubation period for presymptomatics ;at the end they bifurcates to either asymp or symp ;note:Since there's already a global variable 'incubation period', they can't be of the same name ons_p ; (onset period) symp or asymp at the end of this period, bifurcates to recovered or dead (if symp) antibody_duration ;; if not immune auto 0 else the inverse of the set antibody decay ] to setup ;; this procedure sets up the simulation for start clear-all set b2 1 - b1 set c3 1 - c2 create-turtles number_turtles [ setxy random-xcor random-ycor set infectious? false set infection_state "susceptible" set shape "person" set dead false set immune false set inc_p 0 set ons_p 0 set antibody_duration 0 ] ask one-of turtles [ set infectious? true set infection_state "presymptomatic" set inc_p incubation_period ;set infection_state "asymptomatic" ;set ons_p onset_period ] ;;one gets infected ask turtles [recolor] reset-ticks end to go ;; each tick of simulation turtle do this if all? turtles [infectious?] [stop] if all? turtles [infectious? = false] [stop] ask turtles [move] ask turtles [spread] ask turtles [transform] ask turtles [recover] ask turtles [recolor] tick end to move if dead = false and infection_state != "symptomatic" ;at the simplest form, symptomatics won't move since they're assumed to be quarantined [ ;ig better if there are specific patches that is either their home or the hospital to be quarantined in (future endeavor) right random 150 left random 150 fd 1 ] end to spread ifelse infection_state != "susceptible" [] [ if any? other turtles-here in-radius 1 with [infectious?] [ if immune = false [ if random-float 1.0 < infection_rate [ set infectious? true set infection_state "presymptomatic" set inc_p incubation_period if connection [ ask self [create-links-from other turtles-here with [infectious?]] ] ] ] ] ;; checking if there is virus near this agent ] end to transform ;change states ;presymptomatic bifurcation ;presymptomatic to symptomatic - b1 ;presymptomatic to asymptomatic - b2 if infection_state = "presymptomatic" and infectious? = true [ ifelse inc_p = 0 [ if b1 > b2 [ ifelse random-float 1 < b1 [ set infection_state "symptomatic" set infectious? false set ons_p onset_period] [ set infection_state "asymptomatic" set ons_p onset_period] ] if b2 > b1 [ ifelse random-float 1 < b2 [ set infection_state "asymptomatic" set ons_p onset_period] [ set infection_state "symptomatic" set infectious? false set ons_p onset_period] ] if b2 = b1 [ ifelse random-float 1.0 < 0.5 [ set infection_state "symptomatic" set infectious? false set ons_p onset_period] [ set infection_state "asymptomatic" set ons_p onset_period] ] ] [ set inc_p inc_p - 1 ] ] ;recovered goes back to susceptible after some time if infection_state = "recovered" and infectious? = false and immune = true [ ifelse antibody_duration = 0 [ set infection_state "susceptible" set immune false ] [ set antibody_duration antibody_duration - 1] ] end to recover ;symptomatic to recover or death? ;asymptomatic to recover? if infection_state = "asymptomatic" and infectious? = true [ ifelse ons_p = 0 [ set infection_state "recovered" set infectious? false set immune true set antibody_duration 1 / antibody_decay ][ set ons_p ons_p - 1] ] if infection_state = "symptomatic" and infectious? = false [ ;either death or recovery ifelse ons_p = 0 [ if c2 > c3 [ ifelse random-float 1 < c2 [ set infection_state "recovered" set infectious? false set immune true set antibody_duration 1 / antibody_decay] [ set infection_state "dead" set dead true ] ] if c3 > c2 [ ifelse random-float 1 < c3 [ set infection_state "dead" set dead true] [ set infection_state "recovered" set infectious? false set immune true set antibody_duration 1 / antibody_decay] ] if c2 = c3 [ ifelse random-float 1.0 < 0.5 [ set infection_state "recovered" set infectious? false set immune true set antibody_duration 1 / antibody_decay] [ set infection_state "dead" set dead true] ] ][ set ons_p ons_p - 1] ] end to recolor ;green-susceptible ;yellow-presymptomatic ;red-asymptomatic ;violet-symptomatic ;blue-recovered ;black-dead if infectious? = false and infection_state = "susceptible" [set color gray + 1] if infectious? and infection_state = "presymptomatic" [set color yellow] if infectious? and infection_state = "asymptomatic" [set color red] if infectious? = false and infection_state = "symptomatic" [set color violet] if immune [set color blue] if dead [set color black] end ;;;;;;;;;;;;; to-report b2-value report 1 - b1 end to-report c3-value report 1 - c2 end to-report antibody-duration report 1 / antibody_decay end ;;;;;;;;;;;;; to-report susceptible report count turtles with [infection_state = "susceptible"] end to-report presymptomatic report count turtles with [infection_state = "presymptomatic"] end to-report asymptomatic report count turtles with [infection_state = "asymptomatic"] end to-report symptomatic report count turtles with [infection_state = "symptomatic"] end to-report recovered report count turtles with [immune = true] end to-report deceased report count turtles with [dead = true] end
There is only one version of this model, created 6 months ago by Neal Clarin.
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SIIR Agent-Based Model.png | preview | Preview for 'SIIR Agent-Based Model' | 6 months ago, by Neal Clarin | Download |
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