Covid 19 Contagion Dynamics

breed [humans human]
breed [statistic_agents statistic_agent]

globals [
  age_group_0_9
  age_group_10_19
  age_group_20_29
  age_group_30_39
  age_group_40_49
  age_group_50_59
  age_group_60_69
  age_group_70_79
  age_group_80
  elapsed-day-hours
  medical_care_used
  number_of_deaths
  death_list
  city_area_patches
  roads_area_patches
  change_lockdown_condition?
  cumulative_infected
  last_cumulative
  cumulative_aware_of_infection
  last_cumulative_aware_of_infection
  logged_transmitters
  R0_global
]

humans-own [
  infected?
  infection-length
  aggravated_symptoms_day
  age-group
  ontreatment?
  gotinfection?
  contagion-chance
  death-chance
  ongoing-infection-hours
  symptoms_delay
  aware_of_infection?
  infectedby
]

statistic_agents-own [
  age-group
  recovered
  deaths
]

patches-own [
  original_map_color
]

to-report calculate_R0
  let list_of_transmitters remove-duplicates logged_transmitters
  let current_case 0
  let sum_repetitions 0
  foreach list_of_transmitters [
    patient -> set current_case patient
    let transmitter_repeated length filter [ i -> i = current_case] logged_transmitters
    set sum_repetitions sum_repetitions + transmitter_repeated
  ]
  ifelse length list_of_transmitters > 0 [
    report sum_repetitions / ( length list_of_transmitters )
  ]
  [
    report 0
  ]
end 

;;;;;;;;;;;;;;;;;;;;;;;;;;;   HUMANS PROCEDURES   ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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to-report moore-neighborhood
  report humans at-points [[-1 1] [1 1] [-1 -1] [-1 0] [1 0] [0 1] [0 0] [0 -1] [1 -1]]
end 

to infection_exposure
  if (not gotinfection?) [
    let people_around moore-neighborhood
    let infected_around people_around with [infected? = true and not ontreatment? and ( ongoing-infection-hours > (average_days_for_contagion * 24)) ]
    let number_of_infected_around count infected_around
    if number_of_infected_around > 0 [
      let within_contagion_distance (random(metres_per_patch * 2 + 1)) ;; Assuming each patch represents up to metres_per_patch distance units (meters)
      set within_contagion_distance within_contagion_distance + random-float ( keep_social_distancing ) ;; Assuming the ordered social distance is not followed accurately but more randomly and proportionate to the ordered distance
      ;;;;;;;;; Chance of Contagion according to age group:
      if (contagion-chance >= (random(100) + 1) and within_contagion_distance <= maximum_contagion_distance) [
        let transmitter_person nobody
        ask one-of infected_around [ set transmitter_person who ]
        set logged_transmitters lput transmitter_person logged_transmitters
          if length ( logged_transmitters ) > 800 [ ;;Do not allow the list to grow without end, delete older elements.
            set logged_transmitters but-first logged_transmitters
          ]
        get_infected
      ]
    ]

  ]
end 

to get_infected
  set color red
  set size 3
  set infected? true
  set gotinfection? true
  set infection-length 24 * ( random-normal average_infection_length 5.0 ) ;; mean of infection length and standard-deviation multiplied by 24 hours
  set aggravated_symptoms_day round (infection-length / 2.5) ;; Aggravated infection may happen after the first week
  set symptoms_delay 24 * ( random-normal average-symptoms-show 4.0 )
  set ongoing-infection-hours 0
  set cumulative_infected cumulative_infected + 1
end 

to get-healthy
  set infected? false
  set gotinfection? true
  set infection-length 0
  set ongoing-infection-hours 0
  set aggravated_symptoms_day 0
  if ontreatment? [ free-medical-care set ontreatment? false]
  set color green
  set size 1
  set aware_of_infection? false
  update-recovered-statistics age-group
end 

to check_health_state
  if infected? [
    if ongoing-infection-hours >= ( symptoms_delay + random(diagnosis_delay) ) and not ontreatment? [
      if not aware_of_infection? [
        set aware_of_infection? true
        set cumulative_aware_of_infection cumulative_aware_of_infection + 1
      ]
      ifelse prioritise_elderly? [
        ifelse age-group >= age_group_60_69 [
          if get-medical-care = true [
            set ontreatment? true
          ]
        ]
        [
          if %medical-care-availability >= 25 [ ;;If not an elderly person then only take medical care if availability >= 25%
            if get-medical-care = true [
              set ontreatment? true
            ]
          ]
        ]
      ]
      [
        if get-medical-care = true [
          set ontreatment? true
        ]
      ]
    ]
    if (ongoing-infection-hours = aggravated_symptoms_day) ;;Check if patient is going to die
    [
      ;;;;;;;;;; Decide if patient survived or not the infection:
      let chance_to_die 0
      let severity_factor 1
      if ( ( chance_of_severe_infection * 1000 ) >= random(100000) ) [ ;;Patient got a severe infection increasing the death chance by a severity factor
        set severity_factor severity_death_chance_multiplier
      ]
      ifelse (ontreatment?) [
        set chance_to_die ((death-chance * 1000) * severity_factor) * 0.5 ;; Death chance is reduced to 50%, Survival chance is increased by 50%
      ]
      [
        set chance_to_die (death-chance * 1000) * severity_factor
      ]

      if (chance_to_die >= (random(100000) + 1)) [
        update-death-statistics age-group
        set number_of_deaths number_of_deaths + 1
        delete-person
      ]
    ]

    ifelse (ongoing-infection-hours >= infection-length)
    [
      set ongoing-infection-hours 0
      get-healthy
    ]
    [
      set ongoing-infection-hours ongoing-infection-hours + 1
    ]
  ]
end 

to move [ #speed ]
  if not ontreatment?
  [
    rt random-float 360
    let next_patch_color white
    ask patch-ahead 1 [ set next_patch_color original_map_color ]
    if (next_patch_color = white ) [ fd #speed ]
  ]
end 

to delete-person
  if ontreatment? [ free-medical-care ]
  die
end 

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;   SETUP PROCEDURES   ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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to draw_road_lines
  let rows 1
  repeat 8 [
    ask patches with [pxcor > -260 and pxcor < 260 and pycor = -250 + (rows * 60) and pcolor = white ][set pcolor yellow]
    let roads 1
    repeat 3 [
      ask patches with [pxcor = -260 + (rows * 60) + roads and pycor > -250 and pycor < 260 and pcolor = white ][set pcolor yellow]
      set roads roads + 1
    ]
    set rows rows + 1
  ]
end 

to create_city_map
  ask patches with [pxcor > -270 and pxcor < 270 and pycor > -270 and pycor < 260 ] [ set pcolor white ]
  let rows 1
  repeat 8 [
    ask patches with [pxcor > -260 and pxcor < 260 and pycor = -250 + (rows * 60) ][set pcolor yellow]
    let roads 1
    repeat 3 [
      ask patches with [pxcor = -260 + (rows * 60) + roads and pycor > -250 and pycor < 260 ][set pcolor yellow]
      set roads roads + 1
    ]
    set rows rows + 1
  ]
end 

to setup-globals
  ifelse load_city_map? [
    import-pcolors "Argentina_outline.png"
    draw_road_lines
  ]
  [
    create_city_map
  ]
  ask patches [ set original_map_color pcolor ]
  set age_group_0_9 9
  set age_group_10_19 19
  set age_group_20_29 29
  set age_group_30_39 39
  set age_group_40_49 49
  set age_group_50_59 59
  set age_group_60_69 69
  set age_group_70_79 79
  set age_group_80  80
  set elapsed-day-hours 0
  set medical_care_used 0
  set number_of_deaths 0
  set cumulative_infected 0
  set last_cumulative 0
  set city_area_patches patches with [ pcolor != black ]
  set roads_area_patches patches with [ pcolor = yellow ]
  set complete_lockdown? false
  set change_lockdown_condition? false
  set prioritise_elderly? false
  set partial_lockdown? false
  set cumulative_aware_of_infection 0
  set last_cumulative_aware_of_infection 0
  set logged_transmitters[]
  set R0_global 0
end 

to setup_statistic_agent [ #age-group ]
  create-statistic_agents 1
  [
    set age-group #age-group
    set recovered 0
    set deaths 0
    ht
  ]
end 

to setup-people [#number #age-group]
  create-humans #number
    [
      let random_x 0
      let random_y 0
      ask one-of city_area_patches [ set random_x pxcor set random_y pycor ]
      setxy random_x random_y
      set shape "circle"
      set infected? false
      set aggravated_symptoms_day 0
      set ongoing-infection-hours 0
      set color green
      set age-group #age-group
      set ontreatment? false
      set gotinfection? false
      set symptoms_delay 0
      set aware_of_infection? false
      set infectedby nobody

      ifelse age-group <= age_group_0_9 [
        set contagion-chance chance_of_infection_0-9
        set death-chance chance_of_death_0-9
      ]
      [
        ifelse age-group <= age_group_10_19 [
          set contagion-chance chance_of_infection_10-19
          set death-chance chance_of_death_10-19
        ]
        [
          ifelse age-group <= age_group_20_29 [
            set contagion-chance chance_of_infection_20-29
            set death-chance chance_of_death_20-29
          ]
          [
            ifelse age-group <= age_group_30_39 [
              set contagion-chance chance_of_infection_30-39
              set death-chance chance_of_death_30-39
            ]
            [
              ifelse age-group <= age_group_40_49 [
                set contagion-chance chance_of_infection_40-49
                set death-chance chance_of_death_40-49
              ]
              [
                ifelse age-group <= age_group_50_59 [
                  set contagion-chance chance_of_infection_50-59
                  set death-chance chance_of_death_50-59
                ]
                [
                  ifelse age-group <= age_group_60_69 [
                    set contagion-chance chance_of_infection_60-69
                    set death-chance chance_of_death_60-69
                  ]
                  [
                    ifelse age-group <= age_group_70_79 [
                      set contagion-chance chance_of_infection_70-79
                      set death-chance chance_of_death_70-79
                    ]
                    [
                        set contagion-chance chance_of_infection_80
                        set death-chance chance_of_death_80
                    ]
                  ]
                ]
              ]
            ]
          ]

        ]
      ]
     ]
end 

to setup
  clear-all
  ;random-seed 25000000
  setup-globals
  setup-people population_0-9 age_group_0_9
  setup-people population_10-19 age_group_10_19
  setup-people population_20-29 age_group_20_29
  setup-people population_30-39 age_group_30_39
  setup-people population_40-49 age_group_40_49
  setup-people population_50-59 age_group_50_59
  setup-people population_60-69 age_group_60_69
  setup-people population_70-79 age_group_70_79
  setup-people population_80 age_group_80
  let affected_number round (count humans * (initial_infected_population / 100))
  infect_people affected_number

  setup_statistic_agent age_group_0_9
  setup_statistic_agent age_group_10_19
  setup_statistic_agent age_group_20_29
  setup_statistic_agent age_group_30_39
  setup_statistic_agent age_group_40_49
  setup_statistic_agent age_group_50_59
  setup_statistic_agent age_group_60_69
  setup_statistic_agent age_group_70_79
  setup_statistic_agent age_group_80
  reset-ticks
end 

;;;;;;;;;;;;;;;;;;;;;;;;;   ENVIRONMENT - STATISTIC_AGENTS PROCEDURES   ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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to update-recovered-statistics [ #age-group ]

  ask statistic_agents with [ age-group = #age-group ] [ set recovered recovered + 1 ]
end 

to update-death-statistics [ #age-group ]

  ask statistic_agents with [ age-group = #age-group ] [ set deaths deaths + 1 ]
end 

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;   ENVIRONMENT - HUMAN PROCEDURES   ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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to infect_people [#affected_number]
  ask n-of #affected_number humans with [ not gotinfection? ] [ get_infected ]
end 

to-report get-medical-care
  if medical_care_used < medical_care_capacity [
    set medical_care_used medical_care_used + 1
    report true
  ]
  report false
end 

to-report %medical-care-availability
  report ( (medical_care_capacity - medical_care_used) / medical_care_capacity ) * 100
end 

to free-medical-care
  set medical_care_used medical_care_used - 1
end 

to people-enter-city [#people_entering #percentage_entering_infected_population]
  let entering_per_age_group #people_entering / 9
  setup-people entering_per_age_group age_group_0_9
  setup-people entering_per_age_group age_group_10_19
  setup-people entering_per_age_group age_group_20_29
  setup-people entering_per_age_group age_group_30_39
  setup-people entering_per_age_group age_group_40_49
  setup-people entering_per_age_group age_group_50_59
  setup-people entering_per_age_group age_group_60_69
  setup-people entering_per_age_group age_group_70_79
  setup-people entering_per_age_group age_group_80
  infect_people #people_entering * #percentage_entering_infected_population / 100
end 

to people-leave-city [#people_leaving]
  ask n-of #people_leaving humans with [not ontreatment?] [ delete-person ]
end 

;;;;;;;;;;;;;;;;;;;;;;;;;;;   SOCIAL INTERACTIONS - HUMANS PROCEDURES   ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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to gather_in_schools
  if partial_lockdown? [ stop ]
  let gatherings_size 200 ;Students per school 200
  repeat active_schools [
    let place_x 0
    let place_y 0
    ask one-of city_area_patches [ set place_x pxcor set place_y pycor]
    ask up-to-n-of gatherings_size humans with [ ( age-group = age_group_0_9 or age-group = age_group_10_19 ) and not aware_of_infection? ][set xcor place_x - 4 + random(8) set ycor place_y - 4 + random(8) ]
  ]
end 

to gather_in_colleges
  if partial_lockdown? [ stop ]
  let gatherings_size 300 ;Students per college
  repeat active_colleges [
    let place_x 0
    let place_y 0
    ask one-of city_area_patches [ set place_x pxcor set place_y pycor]
    ask up-to-n-of gatherings_size humans with [ age-group = age_group_20_29 and not aware_of_infection? ][set xcor place_x - 4 + random(8) set ycor place_y - 4 + random(8) ]
  ]
end 

to gather_in_hosp_venues
  if partial_lockdown? [ stop ]
  let gatherings_size 40 ;40 people per venue
  repeat active_hosp_venues [
    let place_x 0
    let place_y 0
    ask one-of city_area_patches [ set place_x pxcor set place_y pycor]
    ask up-to-n-of gatherings_size humans with [ not aware_of_infection? ][set xcor place_x - 2 + random(3) set ycor place_y - 2 + random(3) ]
  ]
end 

to gather_in_public_transport_lines
  if partial_lockdown? [ stop ]
  let gatherings_size 60 ;60 people per bus/tram line
  repeat active_public_transport_lines [
    let place_x 0
    let place_y 0
    ask one-of roads_area_patches [ set place_x pxcor set place_y pycor]
    ask up-to-n-of gatherings_size humans with [ not aware_of_infection? ][set xcor place_x - 2 + random(3) set ycor place_y - 4 + random(10) ]
  ]
end 

to gather_in_adult_venues
  if partial_lockdown? [ stop ]
  let gatherings_size 40 ; 40 people per venue
  repeat active_adult_venues [
    let place_x 0
    let place_y 0
    ask one-of city_area_patches [ set place_x pxcor set place_y pycor]
    ask up-to-n-of gatherings_size humans with [ ( age-group != age_group_0_9 and age-group != age_group_10_19 ) and not aware_of_infection? ][set xcor place_x - 2 + random(3) set ycor place_y - 2 + random(3) ]
  ]
end 

to gather_in_senior_venues
  if partial_lockdown? [ stop ]
  let gatherings_size 40 ; 40 people per venue
  repeat active_adult_venues [
    let place_x 0
    let place_y 0
    ask one-of city_area_patches [ set place_x pxcor set place_y pycor]
    ask up-to-n-of gatherings_size humans with [ ( age-group = age_group_60_69 or age-group = age_group_70_79 or age-group = age_group_80 ) and not aware_of_infection? ][set xcor place_x - 2 + random(3) set ycor place_y - 2 + random(3) ]
  ]
end 

to gather_in_food_shops
  if partial_lockdown? [ stop ]
  let gatherings_size 50 ; 50 people in a supermarket, bakery, small shop
  repeat active_adult_venues [
    let place_x 0
    let place_y 0
    ask one-of city_area_patches [ set place_x pxcor set place_y pycor]
    ask up-to-n-of gatherings_size humans with [ age-group != age_group_0_9 and not aware_of_infection? ][set xcor place_x - 2 + random(4) set ycor place_y - 2 + random(4) ]
  ]
end 

to go_back_home
  ask humans with [ not aware_of_infection? ]
  [
    let random_x 0
    let random_y 0
    ask one-of city_area_patches [ set random_x pxcor set random_y pycor ]
    setxy random_x random_y
  ]
end 

;;;;;;;;;;;;;;;;;;;;;;;;;;;   GO PROCEDURE   ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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to go

  ifelse prioritise_elderly? [
    foreach sort-on [(- age-group)] humans
    [ patient -> ask patient [ check_health_state ] ]
  ]
  [
      ask humans [ check_health_state ]
  ]
  ask humans [
    ;check_health_state
    if elapsed-day-hours > 6  [ infection_exposure ]
    ifelse not complete_lockdown? [ move 1.5 ][ move 0.1 ]
  ]
  ifelse elapsed-day-hours >= 24
  [
    set R0_global calculate_R0
    print cumulative_aware_of_infection
    if log_infection_data? [
      ;let delta_cumulative cumulative_infected / (last_cumulative + 1)
      ;print ( word ceiling (ticks / 24) "," cumulative_infected "," number_of_deaths "," delta_cumulative )
      let delta_cumulative cumulative_aware_of_infection / (last_cumulative_aware_of_infection + 1)
      print ( word ceiling (ticks / 24) "," cumulative_infected "," number_of_deaths "," delta_cumulative )
      set last_cumulative_aware_of_infection cumulative_aware_of_infection
      set last_cumulative cumulative_infected
    ]
    set elapsed-day-hours 1
  ]
  [
    if not complete_lockdown? [
      if elapsed-day-hours mod 7 = 0 [ gather_in_hosp_venues ] ;;3 times a day
      if elapsed-day-hours mod 10 = 0 [ gather_in_food_shops ] ;;2 times a day
      if elapsed-day-hours > 6 and elapsed-day-hours mod 2 = 0 [ gather_in_public_transport_lines ] ;; 8 times a day
      ifelse elapsed-day-hours = 7 [ ;;Rush Hour
         ;;;;; People enter and leave the city once a day:
        people-leave-city people_entering_city_per_day; people_leaving_city_per_day
        people-enter-city people_entering_city_per_day infected_visitors;[#people_entering #percentage_entering_infected_population]
        ;;;;; Gatherings once a day
        gather_in_schools
        gather_in_colleges
        gather_in_senior_venues
      ]
      [
        if elapsed-day-hours = 22 [
          gather_in_adult_venues
        ]
      ]

    ]
    set elapsed-day-hours elapsed-day-hours + 1
  ]
  if change_lockdown_condition? != complete_lockdown? [
    set change_lockdown_condition? complete_lockdown?
    go_back_home
  ]

  tick
end 

to-report %infected
  ifelse any? humans
    [ report (count humans with [infected?] / count humans) * 100 ]
    [ report 0 ]
end