Modified Model for Phase 2.nlogo

turtles-own ;; define tutrle variable
[ sick? ;; boolean, 1 infected else 0
  immune? ;; boolean, 1 infected else 0
  symptomatic? ;; boolean, 1 symptomatic else 0
  symptomaticTested? ;; to check if the turtle did the symptomatic test
  quarantine? ;; is the turtle in quarantine
  vaccinated? ;; if the turtle has been vaccinated
  spreader? ;; super-spreader event
  quarantineDays ;; days turtle has been under quarantine
  sickDays ;; #days turtle has been infected
  immuneDays ;; #days turtle has been immune
  immune-count ;; 1 = infected / vaccinated , >1 = reinfection/booster shot. Multiplied by reinf-constant with each booster/ reinfection
  quarantine-delay
]

patches-own
[
  land-type ;; 0 for normal, 1 for "transport" nodes
]

globals ;; global variable
[
  %infected  ;; % of population infected
  %immune ;; % of population immune
  deaths ;; the total number of deaths
  population ;; the total population alive
  all-quarantine ;; all turtles on quarantine
  all-infected;; the total number of infected individuals from the start
  all-symptomatic ;; total symptomatic
  total-mild ;; total mild symptoms (hospitalised)
  total-severe ; ICU bed
  infectiousness ;; need to be separated out to prevent the "auto-reducing" bug caused by enabling mask-wearing
  transport-x  ;; xcor of transport patch
  transport-y ;; ycor of transport patch
  temp ;; temporary register
]

to setup
  clear-all
  set transport-x [-8 -4 0 4 8]
  set transport-y [-10 -5 0 5 10]

  setup-turtles ;; subroutine that setsup turtles
  setup-patches
  update-global-variables ;; subroutine that sets up global var
  set all-infected count turtles with [sick?]
  ;; if mask on we alter the infectiousness
  ifelse mask
  [set infectiousness (infectiousness-init * mask-effect)] ;; done this way so we do not change infectiousness-init
  [set infectiousness infectiousness-init]
  reset-ticks
end

to setup-patches
  ask patches [
    ifelse((member? pxcor transport-x) and (member? pycor transport-y)) ;; if it is a transport node
    [
      set land-type 1
      set pcolor orange
    ]

    [set land-type 0 ];; normal land
  ]
end

to setup-turtles
  set-default-shape turtles "person"
  crt people ;; crt refers to create random turtle
  [setxy random-xcor random-ycor ;; set turtles at random (x,y)
    set sickDays 0 ;; people are not sick initialy
    set vaccinated? false
    set immune? false
    set symptomatic? false
    set quarantine? false
    set symptomaticTested? false ;;this is also set to false upon re-infection
    set spreader? false
    set immune-count 1 ;; nvr infected (infected =1 , reinfected > 1)
    set size 1.5 ;; easier to see
    set quarantine-delay -1
    get-healthy

    if (random-float 100 > 0.8) ;; 80% vaccinated
    [become-immune
    set vaccinated? true]
  ]

  ask n-of initial-infected turtles ;; 10 can be adjusted to change the initial numbe of sick ppl
  [ifelse super-spreader
    [ set spreader? true ;; super spreaders have a 100% infectious rate and twice the mobility :)
      get-sick
      set color pink ]
    [get-sick] ;; normal spreader
  ]
end


to get-sick
  set sick? true
  set immune? false
  set symptomaticTested? false
  set color red ;; red represents sick people
end

to get-healthy
  set sick? false
  set immune? false
  set sickDays 0
  set color green ;; green represents healthy people
end

to become-immune
  set sick? false
  set sickDays 0
  set immune? true
  set immuneDays 0
  set immune-count (immune-count * reinfect-boost) ;; immune again!
  set color gray
end

to become-unimmune
  set sick? false
  set sickDays 0
  set immune? false
  set color green ;; even vaccinated ones go back to green if they lose their immunity
end

to vaccinate
  repeat vaccine-rate [
    ifelse (count turtles with [not sick? and (not immune? or not vaccinated?)]  < 1) ;; not enough turtles
    [stop]
    [ask one-of (turtles with [not sick? and (not immune? or not vaccinated?)])
      [become-immune
        set vaccinated? true];; turtle becomes vaccinated
    ]
  ]
end

to go ;; command to initiate go button
  tick ;; IMPORTANT need to increment time
  get-older ;; turtle procedure to count number of days turtle has been sick
  move
  infect ;;turtle procedure to infect turtles
  recover ;; turtel procedure to ask turtles to recover
  lose-immunity ;; turtle procedure to ask turtles to lose immunity
  develop-symptoms ;; develop symptoms
  trace ;; trace symptomatic turtles and send out qo
  qo ;; serve qo and send turtles to quarantine
  quarantine;; release turtle from quarantine
  vaccinate ;; vaccinate
  update-global-variables
  if (count turtles with [sick?] = 0)
  [stop]
end

to update-global-variables
  if (count turtles > 0)
  [
    set %infected (count turtles with [sick?]) / (count turtles) * 100
    set %immune (count turtles with[immune?]) / (count turtles) * 100
    set population count turtles
  ]
end

to get-older
  ask turtles
  [ if sick?
    [ set sickDays (sickDays + 1) ]
    if immune?
    [set immuneDays (immuneDays + 1)]
    if quarantine?
    [set quarantineDays (quarantineDays + 1)]
    if quarantine-delay > -1
    [set quarantine-delay (quarantine-delay - 1)] ;;decrement quarantine delay by 1
  ]
end

to move
  ask turtles
  [
    check-patch
    ifelse sdm
    [move-sdm];; if  sdm
    [move-normal] ;; otherwise
  ]
end

to check-patch
  ask patch-here
  [ifelse land-type = 1 [set temp transport-boost][set temp 1]]  ;; set the temp register to the mobility boost. Normal road  = 1, transport node = 10
end

to move-normal
  rt random 100 ;; right turn between a random angle 0 - 100
  lt random 100 ;; left turn between 0 - 100 degrees
  ifelse spreader?
  [fd 2 * temp] ;; spreaders have twice the mobility
  [fd 1 * temp] ;; move forward in current direction by 1 step
end

to move-sdm
  rt random 100 ;; right turn between a random angle 0 - 100
  lt random 100 ;; left turn between 0 - 100 degrees
  ifelse spreader?
  [fd 2 * mobility * temp] ;; spreaders have twice the mobility
  [fd mobility * temp]
end

to infect
  ask turtles with [sick? and not quarantine?];;quarantined turtles cannot spread
    [ ask other turtles-here with [not quarantine?] ;;quarantined turtles cannot be inefected
      [ ifelse spreader? ;; super spreader event
        [get-sick] ;; 100% infectivity
        [ ifelse immune?
          ;; immune
          [  if ((random-float 100) * immunity-constant * immune-count) < infectiousness
            [ get-sick
              set all-infected (all-infected + 1) ]]
          ;; not immune
          [ if (random-float 100) * immune-count < infectiousness
            [ get-sick
              set all-infected (all-infected + 1) ]]
        ]
      ]
  ]
end

to recover
  ask turtles with [sick?]
  ;; if turtle survived pas t the vrius' duration then
  ;; it either recovers - in which case it either was asymptomatic, or symptomatic but did not visit the hospital
  ;; or hospitalised for mild symptoms or went to ICU and recovered or
  ;; or went to ICU and died
  [ if (random sickDays) > duration
    [ifelse symptomatic?
      [hospital]
      [become-immune] ;; asymptomatic recovers
    ]
  ]
end

to lose-immunity
  ask turtles with [immune?]
  ;; if the turtle has survived past the immunity's duration
  ;; immunity is lost
  [if immuneDays > immune-time
    [ become-unimmune]
  ]
end

to quarantine
  ask turtles with [quarantine?]
  [if (quarantineDays > quarantine-period)
    [set quarantine? false ;; remove the turtle from quanrantine
      set quarantineDays 0]]
end


to develop-symptoms
  ask turtles with [sick? and not symptomaticTested?]
  ;; if sickDays > incubation period, we run a probability check on being symptomatic
  [if (sickDays >= incubation-period)
    [ifelse immune?
      [if((random-float 100) * immunity-constant < chance-symptoms)
        [set symptomatic? true
          set all-symptomatic (all-symptomatic + 1)]
        set symptomaticTested? true] ;; this is so that my code will not run the probability test to make turtles symptomatic twice
                                     ;;not immune
      [if((random-float 100)  < chance-symptoms)
        [set symptomatic? true
          set all-symptomatic (all-symptomatic + 1)]
        set symptomaticTested? true]]]
end

to trace
  ask turtles with [symptomatic? and not quarantine?]
  ;; if the turtle is sick, we trace every other turtle within the x-step radius and test them
  [ask turtles in-radius trace-radius ;; in-radius is inclusive of agent
    [if (sick? and ((random-float 100) < test-rate)) ;; quarantine those tested sick
      [ set quarantine-delay trace-delay]]] ;;preparing to send QO
end

to qo ;quarantine order
  ask turtles with [quarantine-delay > 0] ;; delay is up
  [
    set quarantine? true ;; sent the turtle to quarantine
    set color yellow
    set quarantineDays 0
    set all-quarantine (all-quarantine + 1)
    set quarantine-delay -1 ;; reset delay
  ]
end

to hospital
  ifelse immune?
  [ifelse ((random-float 100) * immunity-constant < chance-mild)
    [ set total-mild (total-mild + 1) ;; increment total mild by 1
      icu] ;; check if turtle will go to ICU
    [become-immune]]  ;; else recovers
                      ;; not immune
  [ifelse ((random-float 100) < chance-mild)
    [ set total-mild (total-mild + 1) ;; increment total mild by 1
      icu]
    [become-immune]]  ;; else recovers
end

to icu
  ifelse immune?
  [ifelse ((random-float 100) * immunity-constant < chance-severe)
    [ set total-severe (total-severe + 1) ;; increment total severe by 1
      death] ;; check if turtle will die
    [become-immune]]  ;; else recovers ;; check if turtle will die
                      ;; not immune
  [ifelse ((random-float 100) < chance-severe)
    [ set total-severe (total-severe + 1) ;; increment total severe by 1
      death]
    [become-immune]]  ;; else recovers
end

to death ;; need aggregated death rate for immune and non-immune since i do not plan on stratifying by age grp
  ifelse immune?
  [ifelse ((random-float 100) * immunity-constant < chance-death)
    [ set deaths (deaths + 1) ;; increment total death by 1
      die]
    [become-immune]]  ;; else recovers
                      ;; not immune
  [ifelse ((random-float 100) < chance-death)
    [ set deaths (deaths + 1) ;; increment total death by 1
      die]
    [become-immune]]  ;; else recovers
end
@#$#@#$#@
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"" ""
PENS
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"immune" 1.0 0 -7500403 true "" "plot count turtles with [immune?]"
"susceptible " 1.0 0 -13840069 true "" "plot count turtles with [not sick? and not immune?]"
"total" 1.0 0 -14454117 true "" "plot count turtles"
"Quarantine" 1.0 0 -1184463 true "" "plot count turtles with [quarantine?]"
"Symptomatic" 1.0 0 -955883 true "" "plot count turtles with [symptomatic?]"
"vaccinated" 1.0 0 -5825686 true "" "plot count turtles with [vaccinated?]"

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@#$#@#$#@
## WHAT IS IT?

(a general understanding of what the model is trying to show or explain)

## HOW IT WORKS

(what rules the agents use to create the overall behavior of the model)

## HOW TO USE IT

(how to use the model, including a description of each of the items in the Interface tab)

## THINGS TO NOTICE

(suggested things for the user to notice while running the model)

## THINGS TO TRY

(suggested things for the user to try to do (move sliders, switches, etc.) with the model)

## EXTENDING THE MODEL

(suggested things to add or change in the Code tab to make the model more complicated, detailed, accurate, etc.)

## NETLOGO FEATURES

(interesting or unusual features of NetLogo that the model uses, particularly in the Code tab; or where workarounds were needed for missing features)

## RELATED MODELS

(models in the NetLogo Models Library and elsewhere which are of related interest)

## CREDITS AND REFERENCES

(a reference to the model's URL on the web if it has one, as well as any other necessary credits, citations, and links)
@#$#@#$#@
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@#$#@#$#@
NetLogo 6.2.0
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@#$#@#$#@
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<experiments>
  <experiment name="experiment" repetitions="30" sequentialRunOrder="false" runMetricsEveryStep="true">
    <setup>setup</setup>
    <go>go</go>
    <metric>count turtles with [sick?]</metric>
    <metric>count turtles</metric>
  </experiment>
</experiments>
@#$#@#$#@
@#$#@#$#@
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Line -7500403 true 150 150 210 180
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0
@#$#@#$#@