Sylvatic Yellow Fever model

globals [
  forest                  ;; The patches representing the forest
  urban                   ;; The patches representing the urban area
  border                  ;; The patches representing the border between urban and forest
  angle                   ;; Heading for individuals
  vaccinated-humans       ;; The initial number of immune (vaccinated) people
]

breed [u-mosquitoes u-mosquito]      ;; To create a urban mosquito species
breed [f-mosquitoes f-mosquito]      ;; To create a forest mosquito species
breed [humans human]                 ;; To create humans
breed [monkeys monkey]               ;; To create monkeys

u-mosquitoes-own
[susceptible?             ;; If true, the urban mosquito is susceptible
 exposed?                 ;; If true, the urban mosquito is infected but in latent period
 infected?                ;; If true, the urban mosquito is infected and infectious
 min-lifespan             ;; The minimum life span before die
 virus-incubation         ;; The incubation period of the virus in mosquitoes
]
f-mosquitoes-own
[susceptible?             ;; If true, the forest mosquito is susceptible
 exposed?                 ;; If true, the forest mosquito is infected but in latent period
 infected?                ;; If true, the forest mosquito is infected and infectious
 min-lifespan             ;; The minimum life span before die
 virus-incubation         ;; The incubation period of the virus in mosquitoes
]
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
 toxic-phase?             ;; If true, the human is in toxic-phase (severe 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 mosquitoes
 toxic-phase-time         ;; The time in days that individuals will be in the toxic-phase
 walk-free?               ;; If true, the individual can walk through the forest
]
monkeys-own
[susceptible?             ;; If true, the monkey is susceptible.
 exposed?                 ;; If true, the monkey is infected but in latent period
 infected?                ;; If true, the monkey is infected and infectious
 immune?                  ;; If true, the monkey is immune
 toxic-phase?             ;; If true, the monkey is in toxic-phase
 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 mosquitoes
 toxic-phase-time         ;; The time in days that individuals will be in the toxic-phase
]

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

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

;; creating and assigning colors to patches

to setup-globals
  set border patches with [(pxcor =  0 and abs (pycor) >= 0)]
  ask border [ set pcolor pink ]
  set urban patches with [(pxcor < 0 and abs (pycor) >= 0)]
  ask urban [set pcolor gray ]
  set forest patches with [(pxcor > 0 and abs (pycor) >= 0)]
  ask forest [set pcolor green ]
end 

;; creating initial humans, monkeys, and mosquitoes

to setup-host
  create-humans initial-people
  [ask humans [move-to one-of urban]
   set shape "person"
   set size 1
   set infected? false
   set immune? false
   set susceptible? true
   set exposed? false
   set toxic-phase? false
   set walk-free? false
   if random-float 100 < vaccine-coverage [      ;;; assigning immunity to vaccinated people
    set susceptible? false
    set immune? true
    ]
   if random-float 100 < free-walkers     ;;; defining the people who can walk through the forest.
    [
      set walk-free? true
    ]
   assign-color
  ]
  set vaccinated-humans count humans with [immune?]

  create-u-mosquitoes initial-urban-mosquitoes
  [ask u-mosquitoes [move-to one-of urban]
   set shape "triangle"
   set size 0.3
   set infected? false
   set susceptible? true
   set exposed? false
   assign-color
  ]

  create-f-mosquitoes initial-forest-mosquitoes
  [ask f-mosquitoes [move-to one-of forest]
   set shape "square"
   set size 0.3
   set infected? false
   set susceptible? true
   set exposed? false
   if (random-float 100 < initial-infected-mosquitoes)  ;; defining initial number of infected forest-mosquitoes
    [
      set susceptible? false
      set infected? true
    ]
  assign-color
  ]

  create-monkeys initial-monkeys
   [ask monkeys [move-to one-of forest]
   set shape "circle"
   set size 0.5
   set infected? false
   set susceptible? true
   set immune? false
   set exposed? false
   set toxic-phase? false
   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 red ]
    if infected? [ set color black ]
    if breed = humans or breed = monkeys [
      if immune? [ set color blue ]
      if toxic-phase? [ set color yellow ] ]
end 

;;;
;;; GO PROCEDURES
;;;

to go
  move-f-mosquitoes
  move-u-mosquitoes
  move-monkeys
  move-humans
  if all? turtles [ not exposed? and not infected? ] and all? humans [ not toxic-phase? ] and all? monkeys [ not toxic-phase? ] [stop]  ;; stopping the simulation
  ask f-mosquitoes with [infected?] [infect-primates]
  ask u-mosquitoes with [infected?] [infect-primates]
  ask monkeys with [infected?] [infect-mosquitoes stop-infect]
  ask humans with [infected?] [infect-mosquitoes stop-infect]
  ask f-mosquitoes with [exposed?] [extrinsic-incubation-period]
  ask u-mosquitoes with [exposed?] [extrinsic-incubation-period]
  ask monkeys with [exposed?] [become-viremic]
  ask humans with [exposed?] [become-viremic]
  ask f-mosquitoes [maybe-die]
  ask u-mosquitoes [maybe-die]
  ask monkeys with [toxic-phase?] [recovery-or-die]
  ask humans with [toxic-phase?] [recovery-or-die]
  tick
end 

to move-monkeys   ;; turtle procedure
  ask monkeys [
    rt random-float 360.0
    forward random-float monkey-mobility
    if xcor < 0 ;; outside forest
    [
      set angle random-float 180
      let new-patch patch-at-heading-and-distance angle (1)
      if new-patch != nobody
      [
        move-to new-patch
      ] ]
    if xcor > (max-pxcor - 0.1)  ;; at the edge of world
      [
        set angle random-float 180
        let new-patch2 patch-at-heading-and-distance angle (-1)
        if new-patch2 != nobody
      [
        move-to new-patch2
      ] ]
    assign-color
  ]
end 

to move-humans  ;; turtle procedure
  ask humans [
    rt random-float 360.0
    forward random-float human-mobility
    if xcor > 0 and not walk-free? ;; outside urban area
    [
      set angle random-float 180
      let new-patch patch-at-heading-and-distance angle (-1)
      if new-patch != nobody
      [
        move-to new-patch
      ] ]
     if xcor > (max-pxcor / 2) and walk-free?  ;; Don't go too far in the woods
    [
      set angle random-float 180
      let new-patch patch-at-heading-and-distance angle (-1)
      if new-patch != nobody
      [
        move-to new-patch
      ] ]
    if xcor < (min-pxcor + 0.1)  ;; at the edge of world
      [
      set angle random-float 180
      let new-patch patch-at-heading-and-distance angle (1)
      if new-patch != nobody
      [
        move-to new-patch
      ] ]
    assign-color
  ]
end 

to move-u-mosquitoes  ;; turtle procedure
 ask u-mosquitoes [
    rt random-float 360.0
    forward random-float 0.2
    if xcor > 0  ;; outside urban area
    [
      set angle random-float 180
      let new-patch patch-at-heading-and-distance angle (-1)
      if new-patch != nobody
      [
        move-to new-patch
      ] ]
    if xcor < (min-pxcor + 0.1)  ;; at the edge of world
      [
        set angle random-float 180
        let new-patch2 patch-at-heading-and-distance angle (1)
      if new-patch2 != nobody
      [
        move-to new-patch2
      ] ]
    assign-color
  ]
end 

to move-f-mosquitoes  ;; turtle procedure
 ask f-mosquitoes [
    rt random-float 360.0
    forward random-float 0.2
    if xcor < 0  ;; outside forest
    [
      set angle random-float 180
      let new-patch patch-at-heading-and-distance angle (1)
      if new-patch != nobody
      [
        move-to new-patch
      ] ]
    if xcor > (max-pxcor - 0.1)  ;; at the edge of world
      [
        set angle random-float 180
        let new-patch2 patch-at-heading-and-distance angle (-1)
        if new-patch2 != nobody
      [
        move-to new-patch2
      ] ]
    assign-color
  ]
end 

to infect-mosquitoes  ;; turtle procedure
 let target-p (u-mosquitoes-on neighbors)
 let hostm one-of (target-p with [susceptible?])
 let target-p2 (f-mosquitoes-on neighbors)
 let hostm2 one-of (target-p2 with [susceptible?])
 if hostm != nobody [
  if  random-float 1 < mosquito-daily-biting-rate [
   if random-float 1 < u-mosq-transmission-competence [
    ask hostm [
      set susceptible? false
      set exposed? true
  ] ] ] ]
 if hostm2 != nobody [
  if  random-float 1 < mosquito-daily-biting-rate [
   if random-float 1 < f-mosq-transmission-competence [
    ask hostm2 [
      set susceptible? false
      set exposed? true
  ] ] ] ]
end 

to infect-primates  ;; turtle procedure
let target-m (humans-on neighbors)
 let hostp one-of (target-m with [susceptible?])
 let target-m2 (monkeys-on neighbors)
 let hostp2 one-of (target-m2 with [susceptible?])
 if breed = u-mosquitoes [
  if hostp != nobody [
    if  random-float 1 < mosquito-daily-biting-rate [
     if random-float 1 < u-mosq-infection-competence [
     ask hostp [
      set susceptible? false
      set exposed? true
    ] ] ] ]
 if hostp2 != nobody [
   if  random-float 1 < mosquito-daily-biting-rate [
    if random-float 1 < u-mosq-infection-competence [
    ask hostp2 [
      set susceptible? false
      set exposed? true
    ] ] ] ] ]
 if breed = f-mosquitoes [
  if hostp != nobody [
    if  random-float 1 < mosquito-daily-biting-rate [
     if random-float 1 < f-mosq-infection-competence [
     ask hostp [
      set susceptible? false
      set exposed? true
    ] ] ] ]
 if hostp2 != nobody [
   if  random-float 1 < mosquito-daily-biting-rate [
    if random-float 1 < f-mosq-infection-competence [
    ask hostp2 [
      set susceptible? false
      set exposed? true
    ] ] ] ] ]
end 

;; the incubation period in mosquitoes

to extrinsic-incubation-period  ;; turtle procedure
  set virus-incubation virus-incubation + 1
  if virus-incubation > 14 [
    if breed = u-mosquitoes [
      set exposed? false
      set infected? true
      ]
    if breed = f-mosquitoes [
      set exposed? false
      set infected? true
      ] ]
end 

;; the start of infectious period

to become-viremic  ;; turtle procedure
  set latent-period latent-period + 1
  if latent-period > 4 [
     set infected? true
     set exposed? false
     ]
end 

;; The end of infectious period

to stop-infect  ;; turtle procedure
  set viremic-time viremic-time + 1
  if breed = humans [
  if viremic-time > 6 [
    ifelse random 100 < 85 [
     set infected? false
     set immune? true
     ] [
      set infected? false
      set toxic-phase? true
      ] ] ]
  if breed = monkeys [
    if viremic-time > 6 [
      set infected? false
      set toxic-phase? true
      ] ]
end 

;; defining the individuals who will survive or die

to recovery-or-die  ;; turtle procedure
  set toxic-phase-time toxic-phase-time + 1
  if breed = humans [
  if toxic-phase-time > 7 [
    ifelse random 100 < 50 [
    set toxic-phase? false
    set immune? true
     ] [
        die ] ] ]
  if breed = monkeys [
  if toxic-phase-time > 10 [
    ifelse random 100 < 20 [
    set toxic-phase? false
    set immune? true
     ] [
        die ] ] ]
end 

;; defining a lifespan to mosquitoes

to maybe-die  ;; turtle procedure
  set min-lifespan min-lifespan + 1
  if min-lifespan > 15 [
  if random-float 1 < mosquito-mortality-rate [
   if breed = u-mosquitoes [
     hatch-u-mosquitoes 1 [
     set infected? false
     set susceptible? true
     set exposed? false
     move-to one-of urban
    ] ]
   if breed = f-mosquitoes [
     hatch-f-mosquitoes 1 [
     set infected? false
     set susceptible? true
     set exposed? false
     move-to one-of forest
    ] ]
    die ] ]
end