epiDEM Travel and Control

globals
[
  recovery-time       ;; Time (in hours) it takes to recover from the infection
  nbInfected-previous ;; Number of infected people at the previous tick
  border              ;; The patches representing the yellow border
  angle               ;; Heading for individuals
  betaN               ;; The average number of new secondary infections per infected this tick
  gamma               ;; The average number of new recoveries per infected this tick
  r0                  ;; The number of secondary infections that arise due to a single infective introduced in a wholly susceptible population
]

turtles-own
[
  infected?          ;; If true, the person is infected.
  cured?             ;; If true, the person has lived through an infection. They cannot be re-infected.
  inoculated?        ;; If true, the person has been inoculated.
  isolated?          ;; If true, the person is isolated, unable to infect anyone.
  hospitalized?      ;; If true, the person is hospitalized and will recovery in half the average-recovery-time.

  infection-length   ;; How long the person has been infected.
  isolation-tendency ;; Chance the person will self-quarantine during any hour being infected.
  hospital-going-tendency ;; Chance that an infected person will go to the hospital when infected

  continent          ;; Which continent a person lives one, people on continent 1 are squares, people on continent 2 are circles.

  ambulance?         ;; If true, the person is an ambulance and will transport infected people to the hospital.

  susceptible-0       ;; Tracks whether the person was initially susceptible
  nbInfected          ;; Number of secondary infections caused by an infected person at the end of the tick
  nbRecovered         ;; Number of recovered people at the end of the tick
]

;;;
;;; SETUP PROCEDURES
;;;

to setup
  clear-all
  setup-globals
  setup-people
  setup-ambulance
  reset-ticks
end 

to setup-globals
  ask patch (- max-pxcor / 2 ) 0 [ set pcolor white ]
  ask patch (max-pxcor / 2 ) 0 [ set pcolor white ]

  set border patches with [(pxcor =  0 and abs (pycor) >= 0)]
  ask border [ set pcolor yellow ]
end 

;; Create initial-people number of people.
;; Those that live on the left are squares; those on the right, circles.

to setup-people
  create-turtles initial-people
    [ setxy random-xcor random-ycor
      ifelse xcor <= 0
      [ set continent 1 ]
      [ set continent 2 ]

      set cured? false
      set isolated? false
      set hospitalized? false
      set ambulance? false
      set infected? false
      set susceptible-0 1

      assign-tendency

      ifelse continent = 1
        [ set shape "square" ]
        [ set shape "circle" ]

      set size 0.5

      ;; Each individual has a 5% chance of starting out infected
      if (random-float 100 < 5)
      [ set infected? true
        set susceptible-0 0
        set infection-length random recovery-time
      ]

      ifelse (not infected?) and (random-float 100 < inoculation-chance)
        [ set inoculated? true
          set susceptible-0 0 ]
        [ set inoculated? false ]

      assign-color
      ]

    if links? [ make-network ]
end 

to setup-ambulance
  create-turtles initial-ambulance
  [
    ifelse random 2 < 1
    [
      set continent 1
      setxy (- max-pxcor / 2) 0
    ]
    [
      set continent 2
      setxy (max-pxcor / 2) 0
    ]

    set cured? false
    set isolated? false
    set hospitalized? false
    set infected? false
    set inoculated? false

    set ambulance? true

    set shape "person"
    set color yellow
  ]
end 

to assign-tendency ;; Turtle procedure

  set isolation-tendency random-normal average-isolation-tendency average-isolation-tendency / 4
  set hospital-going-tendency random-normal average-hospital-going-tendency average-hospital-going-tendency / 4
  set recovery-time random-normal average-recovery-time average-recovery-time / 4

  ;; Make sure recovery-time lies between 0 and 2x average-recovery-time
  if recovery-time > average-recovery-time * 2 [ set recovery-time average-recovery-time * 2 ]
  if recovery-time < 0 [ set recovery-time 0 ]
  
  ;; Similarly for isolation and hospital going tendencies
  if isolation-tendency > average-isolation-tendency * 2 [ set isolation-tendency average-isolation-tendency * 2 ]
  if isolation-tendency < 0 [ set isolation-tendency 0 ]
  
  if hospital-going-tendency > average-hospital-going-tendency * 2 [ set hospital-going-tendency average-hospital-going-tendency * 2 ]
  if hospital-going-tendency < 0 [ set hospital-going-tendency 0 ]
end 


;; Different people are displayed in 5 different colors depending on health
;; green is a survivor of the infection
;; blue is a successful innoculation
;; red is an infected person
;; white is neither infected, innoculated, nor cured
;; yellow is an ambulance

to assign-color ;; turtle procedure

  ifelse cured?
    [ set color green ]
    [ ifelse inoculated?
      [ set color blue ]
      [ ifelse infected?
        [set color red ]
        [set color white]]]
  if ambulance?
    [ set color yellow ]
end 

to make-network
  ask turtles
  [
    create-links-with turtles-on neighbors
  ]
end 


;;;
;;; GO PROCEDURES
;;;

to go
  if all? turtles [ not infected? ]
    [ stop ]
  ask turtles
    [ clear-count ]

  ask turtles
    [ if not isolated? and not hospitalized? and not ambulance?
        [ move ] ]

  ask turtles
    [ if infected? and not isolated? and not hospitalized?
         [ infect ] ]

  ask turtles
    [ if not isolated? and not hospitalized? and infected? and (random 100 < isolation-tendency)
        [ isolate ] ]

  ask turtles
    [ if not isolated? and not hospitalized? and infected? and (random 100 < hospital-going-tendency)
        [ hospitalize ] ]

  ask turtles
  [
    if ambulance?
    [
      move
      ask turtles-on neighbors
      [
        if (ambulance? = false) and (infected? = true)
        [ hospitalize ]
      ]
    ]
  ]

  ask turtles
    [ if infected?
       [ maybe-recover ]
    ]

  ask turtles
    [ if (isolated? or hospitalized?) and cured?
        [ unisolate ] ]

  ask turtles
    [ assign-color
      calculate-r0 ]

  tick
end 

to move  ;; turtle procedure
  if travel?
  [
    if random 100 < (travel-tendency) and not ambulance?  ;; up to 1% chance of travel
    [ set xcor (- xcor) ]
  ]

  ifelse continent = 1
  [
    ifelse xcor > (- 0.5)  ;; and on border patch
    [
      set angle random-float 180
      let new-patch patch-at-heading-and-distance angle (-1)
      if new-patch != nobody
      [
        move-to new-patch
      ]
    ]
    [ ;; if in continent 1 and not on border
      ifelse xcor < (min-pxcor + 0.5)  ;; at the edge of world
      [
        set angle random-float 180
      ]
      [
        set angle random-float 360  ;; inside world
      ]
      rt angle

      ifelse ambulance?
      [
        fd intra-mobility * 5  ;; ambulances move 5 times as fast than the ppl
      ]
      [
        fd intra-mobility
      ]
    ]

  ]
  [ ;; in continent 2
    ifelse xcor < 1  ;; and on border patch
    [
      set angle random-float 180
      let new-patch patch-at-heading-and-distance angle (1)
      if new-patch != nobody
      [
        move-to new-patch
      ]
    ]
    [ ;; if in continent 2 and not on border
      ifelse xcor > (max-pxcor - 1) ;; at the edge of world
      [
        set angle random-float 180
      ]
      [
        set angle random-float 360
      ]
      lt angle

      ifelse ambulance?
      [
        fd intra-mobility * 5
      ]
      [
        fd intra-mobility
      ]
    ]

  ]
end 

to clear-count
  set nbInfected 0
  set nbRecovered 0
end 

to maybe-recover
  set infection-length infection-length + 1

      ;; If people have been infected for more than the recovery-time
      ;; then there is a chance for recovery
      ifelse not hospitalized?
      [
        if infection-length > recovery-time
        [
          if random-float 100 < recovery-chance
          [
            set infected? false
            set cured? true
            set nbRecovered (nbRecovered + 1)
          ]
        ]
      ]
      [ ;; If hospitalized, recover in a fifth of the recovery time
        if infection-length > (recovery-time / 5)
        [
          set infected? false
          set cured? true
          set nbRecovered (nbRecovered + 1 )
        ]
      ]
end 

;; To better show that isolation has occurred, the patch below the person turns gray

to isolate ;; turtle procedure
  set isolated? true
  move-to patch-here ;; move to center of patch
  ask (patch-at 0 0) [ set pcolor gray - 3 ]
end 

;; After unisolating, patch turns back to normal color

to unisolate  ;; turtle procedure
  set isolated? false
  set hospitalized? false

  ask (patch-at 0 0) [ set pcolor black ]

  ask border [ set pcolor yellow ]                      ;; patches on the border stay yellow
  ask (patch (- max-pxcor / 2) 0) [ set pcolor white ]  ;; hospital patch on the left stays white
  ask (patch (max-pxcor / 2) 0) [ set pcolor white ]    ;; hospital patch on the right stays white
end 

;; To hospitalize, move to hospital patch in the continent of current residence

to hospitalize ;; turtle procedure
  set hospitalized? true
  set pcolor black
  ifelse continent = 1
  [
    move-to patch (- max-pxcor / 2) 0
  ]
  [
    move-to patch (max-pxcor / 2) 0
  ]
  set pcolor white
end 

;; Infected individuals who are not isolated or hospitalized have a chance of transmitting their disease to their susceptible neighbors.
;; If the neighbor is linked, then the chance of disease transmission doubles.

to infect  ;; turtle procedure

    let caller self

    let nearby-uninfected (turtles-on neighbors)
    with [ not infected? and not cured? and not inoculated? ]
    if nearby-uninfected != nobody
    [
       ask nearby-uninfected
       [
           ifelse link-neighbor? caller
           [
             if random 100 < infection-chance * 2 ;; twice as likely to infect a linked person
             [
               set infected? true
               set nbInfected (nbInfected + 1)
             ]
           ]
           [
             if random 100 < infection-chance
             [
               set infected? true
               set nbInfected (nbInfected + 1)
             ]
           ]
       ]

    ]
end 

to calculate-r0

  let new-infected sum [ nbInfected ] of turtles
  let new-recovered sum [ nbRecovered ] of turtles
  set nbInfected-previous (count turtles with [ infected? ] + new-recovered - new-infected)  ;; Number of infected people at the previous tick
  let susceptible-t (initial-people - (count turtles with [ infected? ]) - (count turtles with [ cured? ]))  ;; Number of susceptibles now
  let s0 sum [ susceptible-0 ] of turtles  ;; Initial number of susceptibles

  ifelse nbInfected-previous < 10
  [ set betaN 0 ]
  [
    set betaN (new-infected / nbInfected-previous)       ;; This is the average number of new secondary infections per infected this tick
  ]

  ifelse nbInfected-previous < 5
  [ set gamma 0 ]
  [
    set gamma (new-recovered / nbInfected-previous)     ;; This is the average number of new recoveries per infected this tick
  ]

  if ((initial-people - susceptible-t) != 0 and (susceptible-t != 0))   ;; Prevent from dividing by 0
  [ set r0 (ln (s0 / susceptible-t) / (initial-people - susceptible-t)) ;; This is derived from integrating dI / dS = (beta*SI - gamma*I) / (-beta*SI)
    set r0 r0 * s0 ]                                                    ;; Assuming one infected individual introduced in the beginning, and hence counting I(0) as negligible,
end                                                                      ;; we get the relation
                                                                        ;; N - gamma*ln(S(0)) / beta = S(t) - gamma*ln(S(t)) / beta, where N is the initial 'susceptible' population.
                                                                        ;; Since N >> 1
                                                                        ;; Using this, we have R_0 = beta*N / gamma = N*ln(S(0)/S(t)) / (K-S(t))


; Copyright 2011 Uri Wilensky.
; See Info tab for full copyright and license.