Modeling Superspreader behavior

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Default-person Alex Brown (Author)

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globals [
  max-infected
  daily-delta
  total-infected
  avg-daily-delta
  total-delta
  moving-average
  day-1
  day-2
  day-3
  day-4
  day-5
  transmissibility ; what is the chance the healthy person becomes sick if they contact a carrier
  interactions ; total dialy interactions
  pop-density
  Ro
]


turtles-own[
  infected?
  immune?
  recovered?
  mask?
  dead? ; add superspeader?
  infectionDay?
  recoveryDay?
  quarantineDay?
  death?
  mouthBreather? ;how likely is this person to ifect others if they come into contact
  secondaryinfections?
  superspreader?
  lambda?
  movement? ;how much a turtle moves - also should account for frequency
  distanced?
  quarantine-if-sick?
  quarantined?
  sub-tick-interactions?
  num-neighbors?

]

to setup
  clear-all
  set-patch-size (275 / max-pxcor) ; just resets display size
  reset-ticks
  setup-turtles
  setup-masked
  setup-mouthBreather
  setup-distancers
  setup-quarantine
  setup-infected
  set max-infected (count turtles with [infected?])
  set transmissibility (probability-of-transmission)
  set pop-density (num-people / (((max-pxcor * 2) + 1) * ((max-pycor * 2) + 1) ) )
  set Ro (0)
  update-plots
end 

to setup-turtles
  create-turtles num-people [
    set color white
    set shape "person"
    set size 2
    set infected? false
    set immune? false
    set mask? false
    set dead? false
    set death? false
    set distanced? false
    set mouthBreather? 0
    set secondaryinfections? 0
    set superspreader? false
    set lambda? random-gamma shape-r ((sociability-prob) / (1 - sociability-prob) )
    set movement? 0
    set quarantine-if-sick? false
    set quarantineDay? 0
    set quarantined? false
    set recovered? false
    set sub-tick-interactions? 0
    set num-neighbors? 0
    setxy random-pxcor random-pycor
  ]
end 

to setup-masked
  ask n-of ((percent-masked / 100) * num-people) turtles [
    set color white
    set shape "person business"
    set mask? true
  ]
end 

to setup-distancers
  ask n-of((prop-distancers / 100) * num-people) turtles [
    set distanced? true
  ]
end 

; this function makes some turtles become infected

to setup-infected
  ask n-of init-infected turtles [    ;n-of takes two inputs, an integer , and a group (turtles),
    set infected? true
    set color 26
    if mask?
      [set shape "person business"]
    recover-time
  ]
end 

to-report random-beta [ #alpha #beta ]
  let XX random-gamma #alpha 1
  let YY random-gamma #beta 1
  report XX / (XX + YY)
end 

to-report random-nbinom [ #r #p ]
  let lambda random-gamma #r ((#p) / (1 - #p) )
  report random-poisson lambda
end 

to setup-mouthBreather
  let mu (Probability-of-Transmission)
  let v (Transmission-shape-parameter)
  let alpha (mu * v)
  let beta ((1 - mu) * v)

  ask turtles [
    set mouthBreather? (random-beta alpha beta)
  ]
end 

to setup-quarantine
  ask n-of ((percent-who-quarantine / 100) * num-people) turtles [
  set quarantine-if-sick? true
  ]
end 

to change-tendencies
  setup-masked
  setup-distancers
  setup-quarantine
end 

to go
  no-display
  move-normal
  infect-susceptibles
  quarantine
  recover-infected-die
  recolor
  calculate-daily-intereactions
  if (ticks >= 1) [
      calculate-max-infected
      calculate-daily-delta
      calculate-avg-daily-delta
      calculate-total-infected
      calculate-moving-average]
  if (count turtles with [dead? or recovered?] ) >= 1 [
      set Ro (mean [secondaryinfections?] of turtles with [dead? or recovered?])
  ]
  if ( ((ticks mod 1) > 0.85) and ((ticks mod 1) < 0.95) ) [
    update-plots ]
  tick-advance 0.1
  display
end 


; see social distancing model for implementing social distancing w/r turtles

to move-normal

  ask turtles with [not dead? and not distanced? and not quarantined?] [
    right random 360 ;;get a new random heading
    set movement? (random-poisson lambda?)
    forward movement? ;default socialbility is 3 integer becasue finite number of patches maybe change to long tail distribution,
    ; add quarrentine metric, see social distance model - sociability distanced: how much do people who are social distances move- typically set at zero
  ]
end 

to recover-time

  set infectionDay? (floor ticks) ; maybe remove this floor? but also dont if add incubation period
  let rv (random-poisson 14)
  set recoveryDay? (infectionDay? + rv)
   ifelse random-float 1 < 0.01
    [set death? true]
    [set death? false]
  set quarantineDay? (infectionDay? + 5) ; this should eventually be changed
end 

to infect-susceptibles ;; S -> I version of Susceptible Infected Recover model
  ask turtles with [infected? and not dead? and not quarantined?][
    let x 0
    let infectivity ifelse-value (mask? = true)
    [(mouthBreather? * masked-transmissibility)]
    [mouthBreather?]
    ask turtles-on neighbors  [
      if (not infected? and not immune?)[
        if (random-float 1 < infectivity)[
          set secondaryinfections? 0
          set infected? true
          recover-time
          set x (x + 1)
        ]
      ]
    ]
    set secondaryinfections? (secondaryinfections? + x)
    if (secondaryinfections? >= Super-Spreader-Threshold)[
      set superspreader? true
    ]


  ]
end 

to quarantine ;
  ask turtles with [infected? and not dead? and quarantine-if-sick?]
  [
    if (ticks >= quarantineDay?)
    [set quarantined? true
    ]
  ]
end 

to recover-infected-die ;;I -> R

  ;;avg case length is 2 weeks.
  ;;should have 50% chance of becoming immune at 2 weeks
  ;;if we are saying each tick equals 1 day,
  ;;daily odds of recovering should be (1-x)^14=.5, x= 0.0483 ;eventually change this to a Normal? distribution look into this


  ask turtles with [infected? and not dead?]
  [
    if (ticks >= recoveryDay?)
    [
      ifelse (death? = false)
      [
        set infected? false
        set recovered? true ;added
        ifelse (are-survivors-immune? = true)
        [
          set immune? true
          ;set color gray
        ]
        [
          ;set color white
        ]
      ]
      [ set dead? true
        ;set color green
        set infected? false

      ]
      set quarantined? false
    ]
  ]
end 

to recolor

  ask turtles with [infected? and not dead? and (secondaryinfections? < Super-Spreader-Threshold)]
  [ set color 26]
  ask turtles with [infected? and not dead? and (secondaryinfections? >= Super-Spreader-Threshold)]
  [ set color red]
  ask turtles with [not infected?]
  [set color white]
  ask turtles with [immune?]
  [set color gray]
  ask turtles with [dead?]
  [ set color green]
  ask turtles with [quarantined?]
  [ set color pink]
end 

to calculate-max-infected
  let x (count turtles with [infected? and not dead?])
  if x > max-infected
  [set max-infected x]
end 

to calculate-total-infected
  set total-infected ((count turtles with [infected? and not dead?])) ;double parenthesis not necessary
end 

to calculate-daily-delta
  set daily-delta (count turtles with [infected? and not dead?] - total-infected)
end 

to calculate-avg-daily-delta
  let y (daily-delta)
  set total-delta (total-delta + y)
  set avg-daily-delta (total-delta / ticks)
end 

to calculate-moving-average

  set day-1 (day-2)
  set day-2 (day-3)
  set day-3 (day-4)
  set day-4 (day-5)
  set day-5 (daily-delta)
 if (ticks >= 5) [
  set moving-average ((day-1 + day-2 + day-3 + day-4 + day-5) / 5)
  ]
end 

to calculate-daily-intereactions
  if (((ticks + 0.00000000001) mod 1) < 0.05) [
    ask turtles [
      set sub-tick-interactions? (0)
    ]
  ]
  ask turtles [
    set sub-tick-interactions? (sub-tick-interactions? + (count turtles-on neighbors) )
    set num-neighbors? sub-tick-interactions? ; this is pretty dumb and can be cleaned up - but it works rn
  ]
end 

to-report max-infected-prop
  report max-infected / num-people
end 

to-report prop-dead
  let y (count turtles with [dead?])
  report y / num-people
end 

to-report prop-uninfected
  report (count turtles with [not infected? and not immune?]) / num-people
end 

There is only one version of this model, created 2 months ago by Alex Brown.

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