SIIR

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