disease propagatiion model

globals [          ;; definition of global variables
  day_counter      ;; counter
  bodycount        ;; counter for agents dying from disease
  new_infections   ;; counter for daily new infections
  new_sick         ;; counter for daily new sick agents
  new_recovered        ;; counter for daily new recovered agents
  new_h2h
  new_e2h
  new_bodycount
  total_h2h
  total_e2h
]

patches-own [       ;; definition of patch-related variables
  contamination?    ;; patch contaminated w/ virus: true/false
  cont_timer        ;; counter for duration of patch contamination
]

turtles-own [      ;; definition of agent-related variables
  age              ;; age of agent; random 0...90
  status           ;; health status of agent: healthy...infected...sick...recovered
  mortality        ;; mortality rate by age in case of infection
  daily_mortality  ;; daily mortality over duration of acute stadium
  inc_timer        ;; counter for duration of infection
  sick_timer       ;; counter for duration of acute stadium
  infectuous_timer ;; counter for duration if infectivity before acute stadium
  immune_timer     ;; counter for duration of immunity after sickness
  infectuous?      ;; agent infectuous?? true/false
  quarantine?      ;; sick agent under quarantine? true/false
]


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;; Setup of playing field ;;
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to setup
  clear-all
  crt population [                      ;; creation of agents
    set shape "circle"
    set color white
    set size 1
    set xcor random-xcor
    set ycor random-ycor
    set age random 90
    ifelse age >= 65 [                 ;; agents' mortality in case of infection, depending on agents' age
      set mortality 0.1
    ][
      ifelse age < 65 and age >= 35 [
        set mortality 0.01
      ][
        set mortality 0.005
      ]
    ]
    set inc_timer 0
    set status "healthy"
    set immune_timer 0
    set infectuous? false
    set quarantine? false
  ]

  ask patches [                         ;; preparation of patches on playing field
    set pcolor black
    set contamination? false
    set cont_timer 0
  ]

  set new_infections 0                 ;; global variables set to 0
  set new_sick 0
  set new_recovered 0
  set new_h2h 0
  set new_e2h 0
  set total_h2h 0
  set total_e2h 0
  set new_bodycount 0
  set bodycount 0

  ask n-of initial_infections turtles [                ;; infection of tuned in number of "patients zero"
    set status "infected"
    set color yellow
    set inc_timer round (abs (random-normal incubation_time (incubation_time * 0.5)))                  ;; incubation- sick- and infectivity-counter set to values according to sliders in GUI
    set sick_timer round (abs (random-normal sick_time (sick_time * 0.5)))
    set infectuous_timer (min (list (inc_timer) (random i_b_s)))
    set new_infections new_infections + 1
  ]
end 

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;; the procedure "go" is the actual framework of the simulation, within which different procedures of agents and patches are organized ;;
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to go

  contain                                   ;; procedure "contain" is called (see further down)
  repeat (steps_per_round) [                ;; via the repetition according to slider "steps per round", the number of potentitial social contacts is simulated
    move                                  ;; non-quarantined agents start moving around...
    infect                                ;; ... and once in place, each of them calls the procedure "infect"
    if env_contamination? [               ;; in case "contamination" in the GUI is on, procedure "contaminate is called to carry out human-2-environment contamination events
      contaminate
    ]
  ]
  evolve                                                     ;; procedure "evolve" are called... (see further down)
  set day_counter day_counter + 1                            ;; "day" counter is increased by one
  update-plots                                               ;; plots are being updated
  set new_infections 0                                       ;; counters for daily infection data are reset
  set new_sick 0
  set new_recovered 0
  set new_h2h 0
  set new_e2h 0
  set new_bodycount 0
  if ( count turtles with [status = "infected"] = 0 ) and ( count turtles with [status = "sick"] = 0 ) [     ;; simulation is interrupted, if there are no more infected or sick agents on the playing field
    stop
  ]
  ;;contain
end 

to move
  ask turtles with [quarantine? = false] [                   ;; non-quarantined Agents move around on the playing field
    let reach random-normal mobility mobility / 3            ;; mobility range for each step via slider "mobility
    rt random 360
    while [ [pcolor] of patch-ahead reach = blue] [          ;; blue patches (cordon sanitaire around sick agents) shall be avoided
      set reach reach + 5]
    fd reach
  ]
end 

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;; agents check for human-2-human (and environment-2-human) infection events ;;
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to infect
  ask turtles with [status = "healthy"] [                                       ;; "healthy" agents check for infectuous agents within the infection radius...
    let a count turtles in-radius infection_radius with [infectuous?]
    if random-float 1 <= (H2H_infection * a) [                                    ;; ...and check for human-to-human infection events according to infection probability and number of infected agents within infection radius
      set status "infected"
      set color yellow
      set inc_timer round (abs (random-normal incubation_time (incubation_time * 0.3)))             ;; individual incubation time...
      set sick_timer round (abs (random-normal sick_time (sick_time * 0.3)))                         ;; ... as well as individual duration of acute phase...
      set infectuous_timer (min (list (inc_timer) ceiling (1.2 * random i_b_s)))  ;; ... and the individual infectivity before outbreak of sickness are set
      set new_infections new_infections + 1
      set new_h2h new_h2h + 1
      set total_h2h total_h2h + 1
    ]
    if [contamination?] of patch-here = true and random-float 1 <= E2H_infection [                     ;; if their patch is contaminated, they check for environment-to-human infection according to the respective infection probability
      set status "infected"
      set color yellow
      set inc_timer round (abs (random-normal incubation_time (incubation_time * 0.3)))                  ;; incubation- sick- and infectivity-counter set to values according to sliders in GUI
      set sick_timer round (abs (random-normal sick_time (sick_time * 0.3)))
      set infectuous_timer (min (list (inc_timer) ceiling (1.2 * random i_b_s)))
      set new_infections new_infections + 1
      set new_e2h new_e2h + 1
      set total_e2h total_e2h + 1
    ]
  ]
end 

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;; patches check for human-2-environment contamination events ;;
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to contaminate
  ask patches [
    if any? turtles-here with [status = "infected"] and random-float 1 <= E_contamination [      ;; contamination event according to contamination probability
      set contamination? true
      set cont_timer 1
      set pcolor grey                                                                            ;; contaminated patches are marked grey
    ]
  ]
end 


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;; agents individually check for necessity of quarantine measures ;;
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to contain
  if containment? = true[
    ask turtles with [quarantine? = true] [    ;; in case the quarantine-marker is active, agents draw a cordon sanitaire of blue patches around themselves...
      ask patches in-radius (1.1 * infection_radius) [
        set pcolor blue
      ]
    ]
    ask turtles with [quarantine? = false] [   ;; ... and non-quarantined agents move off the blue patches
      while [ [pcolor] of patch-here = blue] [
        fd 5
      ]
    ]
  ]
end 

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;; the procedure "evolve" prepares the agents and patches for the upcoming simulation round ;;
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to evolve
  if immunity? = false [                                           ;; time for immunity after acute phase is limited, if switch is inactive.
    ask turtles with [status = "recovered"] [
      ifelse immune_timer > 0 [
        set immune_timer immune_timer - 1
      ][
        set status "healthy"
        set color white
        set mortality mortality / 3
        set inc_timer 0
        set immune_timer 0
        set infectuous? false
        set quarantine? false
      ]
    ]
  ]
  ask turtles with [status = "sick"] [                          ;; sick agents ceck, if they die from the disease within the acute stadium (sick timer > 0)...
    ifelse sick_timer = 0 [                                  ;; if the sick timer reaches zero, the agent can switch off the cordon sanitaire (set patches back to black)...
      set_back_patches
      set status "recovered"                ;; and set their status to "recovered", which also makes them immune to new infections
      set new_recovered new_recovered + 1
      set color green
      if immunity? = false [
        set immune_timer round (abs (random-normal immunity_duration (immunity_duration * 0.2)))
      ]
      set infectuous? false
      set quarantine? false

    ][
      set sick_timer max (list (0) (sick_timer - 1))                             ;; ... but first, the sich timer counts down by one...
      if random-float 1 <= daily_mortality [                    ;; ... and in case of bad luck, switch off their cordon sanitaire...
        set_back_patches
        set bodycount bodycount + 1                            ;; ...update the body count, and die
        set new_bodycount new_bodycount + 1
        die
      ]
    ]
  ]


  ask turtles with [status = "infected"] [                      ;; first, infected agents update their infectivity status and update counters related to their course of infection
    if inc_timer <= infectuous_timer [
      set infectuous? true
      set infectuous? true
      set color orange
    ]
    if inc_timer = 0 [                                          ;; then, they check for a status update from "infected" to "sick" (the acute stadium)
      set status "sick"
      set new_sick new_sick + 1
      set color red
      set daily_mortality mortality / max (list (1) (sick_timer))
      if containment? = true [                                  ;; quarantine marker is only set "true", if "containment" switch in GUI is activated
        set quarantine? true
      ]
    ]
    if inc_timer > 0 [
      set inc_timer max (list (inc_timer - 1) (0))                  ;; counter for course of infection is updated
    ]
  ]
  ask patches with [contamination? = true] [               ;; contamination timers of each contaminated patch count down by 1...
    ifelse cont_timer > 0 [
      set cont_timer max (list (0) (cont_timer - 1))
    ][                                                     ;; in case the timer is zero, contamination is switched off and tach color is set back to black
      set contamination? false
      set pcolor black
    ]
  ]
end 

to set_back_patches
  ask patches in-radius (1.1 * infection_radius) [
    set pcolor black
  ]
end