Covid-19 and Health System Capacity

globals [
  interaction-zone         ;; The patches representing the area of social interactions in the world
  quarantine               ;; The patches representing the humans are in quarantine
  hospital                 ;; The patches representing the hospital with severe cases of the disease
  upper-border             ;; The borders of interaction-zone
  lower-border
  crowded-patch            ;; The patch where the "CROWDED" label appears
  patients                 ;; Infected people being trated in the hospital
  count-infected           ;; Cumulative number of infected people
  count-symptomatic        ;; Cumulative number of infected and symptomatic people
  r0                       ;; The number of secondary infections that arise due to a single infective introduced in a wholly susceptible population
  s0                       ;; Initial population of susceptible people
  hospital-patch           ;; The patch where the "HOSPITAL" label appears
  quarantine-patch         ;; The patch where the "QUARANTINE" label appears
]

breed [humans human]

humans-own
[susceptible?             ;; If true, the human is susceptible.
 exposed?                 ;; If true, the human is infected but in latent period
 infected?                ;; If true, the human is infected and infectious
 immune?                  ;; If true, the human is immune
 symptomatic?             ;; If true, the infected human is symptomatic
 hospitalized?            ;; If true, the infected and symptomatic human will be hospitalized
 protect?                 ;; If true, the human is protecting himself from infection
 need-hospital?           ;; If true, an infected and symptomatic human will need a hospital
 isolated?                ;; If true, an infected human will be isolated in quarantine
 risk-population?         ;; The proportion of the population at risk of severe disease (i.e. old people, pre-existing chronic disease)
 latent-period            ;; The latent period of the virus
 viremic-time             ;; The time in days that individuals will be infectious and can transmit the virus to others
 ]


;;;;;
;;; SETUP PROCEDURES
;;;;;

to setup
  clear-all
  setup-globals
  setup-host
  reset-ticks
end 

to setup-globals
  ;; creating interaction-zone patches
  set interaction-zone patches with [(pxcor >= min-pxcor and pycor < int (max-pycor - (max-pycor / 2)) and pycor > min-pycor)]
  ask interaction-zone [ set pcolor gray ]

  ;; creating quarantine patches
  set quarantine patches with [(pxcor > (0.5 * min-pxcor) and pycor > int (max-pycor - (max-pycor / 2)) )]
  ask quarantine [set pcolor green ]

  ;; creating hospital patches
  set hospital patches with [(pxcor >= min-pxcor and pxcor <= (0.5 * min-pxcor) and pycor > int (max-pycor - (max-pycor / 2)))]
  ask hospital [set pcolor pink ]

  ;; creating border patches
  set upper-border patches with [(pycor = int (max-pycor - (max-pycor / 2)))]
  ask upper-border [ set pcolor gray ]
  set lower-border patches with [(pycor = min-pycor)]
  ask lower-border [ set pcolor gray ]

  ;; selecting patches where labels will appear
  ask patch (0.7 * min-pxcor) ( 0.8 * max-pycor) [
    set crowded-patch self
    set plabel-color black]
  ask patch (0.7 * min-pxcor) ( 0.95 * max-pycor) [
    set hospital-patch self
    set plabel "HOSPITAL"
    set plabel-color black]
  ask patch (0.3 * max-pxcor) ( 0.95 * max-pycor) [
    set quarantine-patch self
    set plabel "QUARANTINE"
    set plabel-color black]
end 

to setup-host
  ;; creating people and moving them to interaction-zone patches
  create-humans initial-people
  [ask humans [move-to one-of interaction-zone]
   set shape "person"
   set size 0.5
   set infected? false
   set immune? false
   set susceptible? true
   set exposed? false
   set risk-population? false
   set symptomatic? false
   set hospitalized? false
   set protect? false
   set need-hospital? false
   set isolated? false
   ]

   ;; selecting initial number of infected people
   ask n-of initial-infected humans [
    set susceptible? false
    set infected? true]
  ;; selecting people who will be less exposed to infection due to individual protection measures
  ask n-of (initial-people * proportion-of-population) humans [set protect? true]

  ;; selecting people who will belong to the risk group
  ask n-of (initial-people * risk-group) humans [set risk-population? true]

  ask humans [assign-color]
end 

to assign-color  ;; The colors for represent the virus circulation and individual status
    if susceptible? [ set color white ]
    if exposed? [ set color yellow ]
    if infected? [ set color red ]
    if immune? [ set color blue ]
end 

;;;;;
;;; GO PROCEDURES
;;;;;

to go
  ask crowded-patch [ set plabel "" ]
  move-humans
  if all? humans [ not exposed? and not infected? ] [stop]  ;; stopping the simulation

  ask humans with [exposed?] [become-viremic]
  ask humans with [infected?] [infect-others symptom]
  ask humans with [symptomatic?] [recovery-or-die]
  ask humans [if hospitalized? and immune? [move-to one-of interaction-zone]] ;; people who recovered at the hospital go back to interaction-zone
  ask humans with [symptomatic?] [check-for-hospital go-to-hospital]

  set patients count turtles-on hospital
  if patients > hospital-capacity [ask crowded-patch [ set plabel "CROWDED" ]] ;; If the hospital have more patients than it can handle, the label "CROWDED" will appear

  ;;Infected people who are detected will be quarantined (but only after the start of control measures).
  if isolate-infected? [ask humans with [infected? and not hospitalized?]
    [if ticks >= days-to-start-control-measures [
      if random 100 < infected-detection [
      move-to one-of quarantine
      set isolated? true]]]]

  ask humans-on quarantine [if immune? [move-to one-of interaction-zone set isolated? false]] ;; people who recovered in the quarantine go back to interaction-zone

  calculate-r0
  tick
end 

;; People move around the world randomly, but they don't move around in the quarantine and in the hospital patches.

to move-humans
    ask humans-on interaction-zone
    [rt random-float 360.0
    forward random-float 1
    assign-color]
    ask humans-on upper-border [
    move-to patch-at-heading-and-distance 180 1
    assign-color]
    ask humans-on lower-border [
    move-to patch-at-heading-and-distance 180 -1
    assign-color]
    ask humans-on hospital[
     assign-color ]
    ask humans-on quarantine [
      assign-color]
end 

;; Infected people can infect susceptible ones

to infect-others
 ;; selecting a susceptible target in neighbor patches
 let target-h (humans-on neighbors)
 let hosth one-of (target-h with [susceptible?])

  ;; The chance of a susceptible person becoming infected will depend on the transmission rate and whether or not he is protecting himself from the transmission.
  if hosth != nobody [
  ifelse not protect? [
   if random-float 1 < transmission-rate [
    ask hosth [
      set susceptible? false
      set exposed? true
      set count-infected count-infected + 1
    ] ] ]
      [ if ticks < days-to-start-control-measures [
      if random-float 1 < transmission-rate [
      ask hosth [
      set susceptible? false
      set exposed? true
      set count-infected count-infected + 1
      ] ] ]
      if ticks >= days-to-start-control-measures [
      if random-float 1 < (transmission-rate * (1 - protection-level)) [
      ask hosth [
      set susceptible? false
      set exposed? true
      set count-infected count-infected + 1
      ] ] ]
  ] ]
end 

;; A human who has been infected with the virus will become infectious after the latency period

to become-viremic
  set latent-period latent-period + 1
  if latent-period > random-poisson 3 [  ;; An average latency period of 3 days was considered here
     set infected? true
     set exposed? false
     ]
end 

;; A given proportion of infected people will become symptomatic

to symptom
  set viremic-time viremic-time + 1

  ;;It was considered that the first symptoms may appear in 2 days after the virus latency period, which means an incubation period of 5 days on average.
  if viremic-time = 2 [
  if random 100 < symptomatic-proportion [
    set symptomatic? true
    set count-symptomatic  count-symptomatic + 1
  ]]

  ;; asymptomatic people become immune after recovery time
    if viremic-time = recovery-time and not symptomatic? [
      set infected? false
      set immune? true
      ]
end 

;; Check if infected-symptomatic people need a hospital

to check-for-hospital
 ifelse risk-population? [
    if random 100 < 20 [  ;; For the people of the risk group, a 20% chance of needing a hospital was considered
      set need-hospital? true]]
   [if random 100 < 5 [   ;; For people who are not of risk group, a 5% chance of needing a hospital was considered
    set need-hospital? true ]]
end 

;; If the Hospital is not crowded, go to it.

to go-to-hospital
  set patients count turtles-on hospital
  if need-hospital? [
   if patients < hospital-capacity + 1 [
      move-to one-of hospital
      set hospitalized? true]]
end 

;; After a few days, infected symptomatic people may recover from illness or die
;; This will depend on the severity of the case (need-hospital?), whether or not the person is hospitalized, and whether or not he belongs to the risk group.

to recovery-or-die
  if need-hospital?
  [
  ifelse not hospitalized?
    [
   if viremic-time >= random-poisson recovery-time * 1.5  ;; severe cases will take 50% more time to recover
      [
     if risk-population?
        [
       ifelse random 100 < random-poisson 20 [    ;;people in the risk group who need a hospital and are not hospitalized have an average 20% chance of surviving
        set infected? false
        set symptomatic? false
        set immune? true
        set need-hospital? false]
       [ die ]]
     if not risk-population?
        [
       ifelse random 100 < random-poisson 60      ;;people who are not in the risk group who need a hospital and are not hospitalized have an average 60% chance of surviving
          [
        set infected? false
        set symptomatic? false
        set immune? true
        set need-hospital? false]
        [ die ]]]]

  [if viremic-time >= random-poisson recovery-time * 1.5
      [
    if risk-population?
        [
       ifelse random 100 < (100 - random-poisson 7)  ;; people who are the risk group and who are hospitalized have an average 93% chance of surviving
          [
       set infected? false
       set symptomatic? false
       set immune? true
       set need-hospital? false]
       [ die ]]
    if not risk-population?
        [
       ifelse random 100 < (100 - random-poisson 1)    ;; people who are not in the risk group and who are hospitalized have an average 99% chance of surviving
          [
       set infected? false
       set symptomatic? false
       set immune? true
       set need-hospital? false]
       [ die ]]]]]

  if not need-hospital?  ;; Infected-symptomatic people who do not need a hospital will always recover from infection
  [
    if viremic-time >= random-poisson recovery-time
    [
      set infected? false
      set symptomatic? false
      set immune? true
       ]]
end 


;; This R0 is a numerical estimate of the basic reproduction number, as proposed by Uri Wilensky.
;; For more information on how this R0 equation was obtained, see the models 'epiDEM basic' and 'epiDEM travel and control'.

to calculate-r0
  set s0 initial-people - initial-infected

  if ((initial-people - count turtles with [ susceptible? ]) != 0 and (count turtles with [ susceptible? ] != 0))   ;; Prevent from dividing by 0
  [
    set r0 (ln (s0 / count turtles with [ susceptible? ]) / (initial-people - count turtles with [ susceptible? ]))
    set r0 r0 * s0 ]
end