Covid-19 variation on the theme

turtles-own
  [ sick?                ;; if true, the turtle is infectious
    remaining-immunity   ;; how many weeks of immunity the turtle has left
    sick-time            ;; how long, in days, the turtle has been infectious
    age ]                ;; how many weeks old the turtle is

globals
  [ %infected            ;; what % of the population is infectious
    %immune              ;; what % of the population is immune
    max-%infected        ;; maximun % infected population reached (at the peak)
    peak                 ;; day of the peak
    alive                ;; total population alive that tick
    now-infected         ;; number of people infected at the current day
    immune               ;; number of people immune at the present day
    total-infected       ;; total infected from the beginning
    lifespan             ;; the lifespan of a turtle
    chance-reproduce     ;; the probability of a turtle generating an offspring each tick
    chance-recover       ;; the probability of recovery at each tick
    carrying-capacity    ;; the number of turtles that can be in the world at one time
    immunity-duration ]  ;; how many weeks immunity lasts

;; The setup is divided into four procedures

to setup
  clear-all
  reset-ticks
  setup-constants
  setup-turtles
  update-global-variables
  update-display

  reset-ticks
end 

;; We create a variable number of turtles of which 1 are infectious,
;; and distribute them randomly

to setup-turtles
  create-turtles number-people
    [ setxy random-xcor random-ycor
      set age random lifespan
      set sick-time 0
      set remaining-immunity 0
      if age < 10 * 52 * 7 [set color blue]
      if age > 60 * 52 * 7 [set color yellow]
      set size .7 ;; easier to see
      get-healthy ]
  ask n-of init-infected turtles
    [ get-sick ]
  set total-infected (count turtles with [sick?])
end 

to get-sick ;; turtle procedure
  set sick? true
  set remaining-immunity 0
  set total-infected (total-infected + 1)
end 

to get-healthy ;; turtle procedure
  set sick? false
  set remaining-immunity 0
  set sick-time 0
end 

to become-immune ;; turtle procedure
  set sick? false
  set sick-time 0
  set remaining-immunity immunity-duration
  ask my-links [ die ] ;; remove link to turtle who infected us, if there was one
end 

;; This sets up basic constants of the model.

to setup-constants
  set lifespan 80 * 52 * 7     ;; 80 times 52 weeks times 7 days = 50 years = 2600 weeks old = 18200 days
  set carrying-capacity 1000
  set chance-reproduce 0.005 ;; birth rate per 1000 people per day
  set immunity-duration 52 * 7
  if Weather = "Hot-Humid" [set chance-recover .98]
  if Weather = "Hot-Dry" [set chance-recover .96]
  if Weather = "Cold-Dry" [set chance-recover .95]
  if Weather = "Cold-Humid" [set chance-recover .94]
end 

to go
  if all? turtles [not sick?]
  [stop]
  ask turtles [
    get-older
    move
    if sick? [ recover-or-die ]
    ifelse sick? [ infect ] [ reproduce ]
  ]
  update-global-variables
  update-display
  tick
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 alive (count turtles)
      set now-infected (count turtles with [sick?])
      set immune (count turtles with [immune?])
      if %infected > max-%infected [set peak ticks + 1]
      if %infected > max-%infected [set max-%infected %infected]
      ;;set peak ticks + 1]
      ]
end 

to update-display
  ask turtles
    [ if shape != turtle-shape [ set shape turtle-shape ]
      set label ifelse-value show-age? [ floor (age / 364) ] [ "" ]
      set color ifelse-value sick? [ red ] [ ifelse-value immune? [ grey ] [ green ] ] ]
  stop-inspecting-dead-agents
  if watch-a-person? and subject = nobody
    [ watch one-of turtles with [ not hidden? ]
      clear-drawing
      ask subject [ pen-down ]
      inspect subject ]
  if not watch-a-person? and subject != nobody
    [ stop-inspecting subject
      ask subject
        [ pen-up
          ask my-links [ die ] ]
      clear-drawing
      reset-perspective ]
  ask patches [
  if Weather = "Hot-Humid" [set pcolor 68]
  if Weather = "Hot-Dry" [set pcolor 48]
  if Weather = "Cold-Dry" [set pcolor 38]
  if Weather = "Cold-Humid" [set pcolor 108]
  ]
end 

;;Turtle counting variables are advanced.

to get-older ;; turtle procedure
  ;; Turtles die of old age once their age exceeds the
  ;; lifespan (set at 80 years in this model).
  set age age + 1
  if age > lifespan [ die ]
  if age > 60 * 52 * 7 [ set chance-recover .93]
  if age < 60 * 52 * 7 [ set chance-recover .97]
  if immune? [ set remaining-immunity remaining-immunity - 1 ]
  if sick? [ set sick-time sick-time + 1 ]
end 

;; Turtles move about at random.

to move ;; turtle procedure
  rt random 100
  lt random 100
  fd mobility
end 

;; If a turtle is sick, it infects other turtles on the same patch.
;; Immune turtles don't get sick.

to infect ;; turtle procedure
  ask other turtles-here with [ not sick? and not immune? ]
    [ if random-float 100 < infectiousness
      [ get-sick
        if self = subject             ;; if its the watched turtle getting sick
          [ create-link-with myself   ;; create a link with the one that infected it
            [ set color red
              set thickness .3 ] ] ] ]
end 

;; Once the turtle has been sick long enough, it
;; either recovers (and becomes immune) or it dies.

to recover-or-die ;; turtle procedure
  if sick-time > duration * 7                       ;; If the turtle has survived past the virus' duration, then
    [ ifelse random-float 100 < chance-recover * 100   ;; either recover or die
      [ become-immune ]
      [ die ] ]
end 

;; If there are less turtles than the carrying-capacity
;; then turtles can reproduce.

to reproduce
  if count turtles < carrying-capacity and random-float 100 < chance-reproduce
    [ hatch 1
      [ set age 1
        lt 45 fd 1
        pen-up ;; in case we're hatched from the watched turtle
        get-healthy ] ]
end 

to-report immune?
  report remaining-immunity > 0
end 

to startup
  setup-constants ;; so that carrying-capacity can be used as upper bound of number-people slider
end 


; Copyright 1998 Uri Wilensky.
; See Info tab for full copyright and license.