Covid-19 virus - effects of various measures used to contain its spread

turtles-own
  [ status               ;; either: healthy, contact-infected, contact-healthy, sick or immune ;;
    infectious-time      ;; after being infetious for 14 days, become sick
    remaining-immunity   ;; how many days of immunity the turtle has left
    contact-time         ;; how long since last contact
    sick-time            ;; this determines the point in time when the agent recovers
    age                  ;; how old is the turtle
    quarantined?         ;; whether the person is quarantined
    number-of-links      ;; number of links each turtle has
  ]

patches-own
  [
  ]

globals
  [ %infected            ;; what % of the population is infectious
    %immune              ;; what % of the population is immune
    maximum-population   ;; keep it the same as the number of people who started.
    lifespan             ;; the lifespan of a turtle
    initial-ave-links    ;; initial average number of links
    immunity-duration    ;; turtle being immune in number of days
    total-died           ;; total number of people died from the virus
    total-sick           ;; total number of people who became sick
    max-sick             ;; the highest number at one time hospitalised
    number-sick          ;; number of sick people at any one moment
    number-infected      ;; number of infeccted people but not sick at any one moment, ie contact-infected status
    max-number-sick-at-one-time ;; the maximum sick at any one moemnt, hence the max in hospital
  ]

to setup
  clear-all
  resize-world 0 (size-of-world - 1) 0 (size-of-world - 1)
  set-patch-size (500 / max-pxcor)
  set maximum-population number-people  ;; this is to keep the total populace constant even though some will die
  ;; ==================================================

  set lifespan 80 * 365.25  ;; life expectancy set to 80

  set immunity-duration immunity-duration-yr * 365  ;; remain immune for number of years in days as indicated by immunity-duration-yr
  set max-number-sick-at-one-time 0
  set total-died 0
  ;; ===================================================
  create-turtles number-people
    [ set status "healthy"
      set age random lifespan
      set color green
      set sick-time 0
      set contact-time 0
      set remaining-immunity 0
      set size 1.5  ;; easier to see
      set quarantined? false
      setxy random-xcor random-ycor
    ]

;; code for number of links
  ask turtles [make-links]
  set initial-ave-links count links / count turtles
;;  =======================================================================
  ;; the next two line is to get the mean of number-of-links of turtles with high number of links
;  let max-links-turtles max-n-of 1000 turtles [number-of-links]
;  show mean [number-of-links] of max-links-turtles
;;  ========================================================================
  ask n-of initial-infectious-number turtles
    [ set status "contact-infected"
      set infectious-time 1
      set color magenta
    ]

  reset-ticks

  if hide-links? = true [ask links [hide-link]]
end 

to go
  ask turtles [
    get-older ;; everybody gets older
    if status = "healthy" [
                           reproduce ;; this is to keep population number constant when peole dies
                          ]
    if status = "contact-healthy" and quarantined? = true [set contact-time contact-time + 1
                                                           if contact-time > 14 [ set status "healthy"
                                                                                  set quarantined? false  ;; since he is healthy, can be released from quarantine
                                                                                  make-links              ;; after 14 days, and shown to be not sick, can form links agai.
                                                                                  set color green
                                                                                  set contact-time 0]
                                                          ]
    ;; if a contact has not been qurantined, depending on the efficiency in contact tracing and the delay (as measured by contact-time) in qurantine
    ;; he might be or might not be quarantine. that is determined by a raondom number.
    if status = "contact-healthy" and quarantined? = false [set contact-time contact-time + 1
                                                            if contact-time >= to-quarantine [ if random 100 < contact-tracing [getting-quarantine]]
                                                            if contact-time > 14 [ set status "healthy"
                                                                                  set color green
                                                                                  ;; no need to make links as links are still intact since it is not quarantined
                                                                                  set contact-time 0]
                                                           ]

    if status = "contact-infected" and quarantined? = true [set infectious-time infectious-time + 1
                                                            if infectious-time > random 14 [ set status "sick"             ;; if infectious-time > max incubation time of 14, but can be shorter
                                                                                             set color yellow
                                                                                             ask [my-links] of self [die]  ;; hospitalised, no longer have links to infect
                                                                                             set total-sick total-sick + 1
                                                                                             set sick-time sick-time + 1
                                                                                           ]

                                                           ]

    if status = "contact-infected" and quarantined? = false [infect              ;; these are the agents who were not quarantined, though infectious.
                                                             set infectious-time infectious-time + 1
                                                             set contact-time contact-time + 1
                                                             if contact-time >= to-quarantine [if random 100 < contact-tracing [getting-quarantine]]
                                                             if infectious-time > random 14 [ set status "sick"             ;; if infectious-time > max incubation time of 14, but can be shorter
                                                                                             set color yellow
                                                                                             ask [my-links] of self [die]  ;; hospitalised, no longer have links to infect
                                                                                             set total-sick total-sick + 1
                                                                                             set sick-time sick-time + 1
                                                                                            ]

                                                           ]


    if status = "sick" [ infect  ;; this line of code comes before severing links, as he might infect other first before identified and go to hospital
                                 ;; if links are cut already in the previous round, he won't be able to infect others. (See procedure on "to infect"
                         set sick-time sick-time + 1
                         ask [my-links] of self [die]  ;; with links severed, it cannot infect anyone - equivalent of going to hospital
                         if sick-time > random-exponential 14 [recover-or-die]  ;; average sick time is 14 days, beween 6 to  42 days.
                       ]

    if status = "immune" [set color grey
                          ask [my-links] of self [die]
                          set remaining-immunity remaining-immunity - 1
                          if remaining-immunity <= 0 [get-healthy] ;; no longer immune, and becomes like normal
                         ]
  ]
  set number-sick count turtles with [status = "sick"] ;; this show the number sick at any ONE time
  set %infected (count turtles with [status = "sick"] + count turtles with [status = "contact-infected"]) / count turtles * 100
  set %immune  count turtles with [status = "immune"] / count turtles * 100
    if number-sick > max-number-sick-at-one-time [set max-number-sick-at-one-time number-sick]
  if count turtles with [status = "sick"] + count turtles with [status = "contact-infected"] = 0 [stop]
  tick
end 

to get-older
  set age age + 1
end 

to make-links
  ifelse max-number-of-links = 0
      [let K exp(ln(random-float 1) / (- gamma))
                  if K > count turtles with [quarantined? = false] [ set K count turtles with [quarantined? = false] - 1] ;; only those not with quarantined? = true can form links
                  set K round K
                  create-links-with n-of K other turtles
                  set number-of-links K]
       [let K exp(ln(random-float 1) / (- gamma))
                  if K > max-number-of-links [ set K max-number-of-links] ;; this will set the upper limit of links
                  set K round K
                  create-links-with n-of K other turtles
                  set number-of-links K]
end 

to reproduce
  if count turtles < number-people [hatch (number-people - count turtles) [set status "healthy"
                                                                           set age random lifespan
                                                                           set sick-time 0
                                                                           set remaining-immunity 0
                                                                           set size 1.5  ;; easier to see
                                                                           set quarantined? false
                                                                           make-links
                                                                           setxy random-xcor random-ycor]
                                    ]
end 

to infect
  ask link-neighbors [ifelse random 100 <= chance-infected [set status "contact-infected"
                                                           set color magenta
                                                           set contact-time 1]  ;; contact time is set as marker for when he is detected to be a contact
                                                          [set status "contact-healthy"
                                                           set color pink - 3
                                                           set contact-time 1 ]  ;; contact time is set as market for when he is detected to be a contact
                     ]
end 

to getting-quarantine
  set quarantined? true
  ask [my-links] of self [die] ;; once the agentis quarantined, he is not linked to anyone
end 

to recover-or-die
  ifelse random 100 > chance-recover [set total-died total-died + 1
                                      die
  print total-died]
                                     [set status "immune"
                                      set color grey
                                      set sick-time 0
                                      set contact-time 0
                                      set quarantined? false
                                      set remaining-immunity immunity-duration-yr * 365.25
                                     ]
end 

to get-healthy
  set status "healthy"
  set color green
  set sick-time 0
  set contact-time 0
  set remaining-immunity 0
  set quarantined? false
  make-links
end