Wolbachia

;; Model for simulate mosquitoes infected with bacterial symbiont Wolbachia

turtles-own
  [ wolb?        ;; if true, the turtle has Wolbachia
    wolb-carrying-count   ;; how long the turtle has Wolbachia
    age          ;; how many weeks old the turtle is
    recover-prob ;; not really used (set to zero)
    x-pos
    y-pos
    ]

globals
[
  %infected            ;; percentage of the population has Wolbachia
  carrying-capacity    ;; the number of turtles that can be in the world at one time
  initialInfected
  avgWolb
  avgNorm
  lifespan-with-Wolbachia
;;  ndays-week
]

to setup
  clear-all
  setup-constants
  setup-turtles
  update-global-variables
  reset-ticks
end 

;; Create a variable number of mosquitoes (nMosquitoes) of which initialWolbachia is
;; the number of mosquitoes that start with Wolbachia

to setup-turtles
  set-default-shape turtles "dot"
  crt nMosquitoes
    [ 
      set x-pos random-xcor 
      set y-pos random-xcor
      setxy x-pos y-pos
      set age random normal-lifespan
      set wolb-carrying-count 0
      set recover-prob  0
      set size 0.5  ;; easier to see
      get-free ]
  ask n-of initialInfected turtles
    [ set age random lifespan-with-Wolbachia
;;      setxy ((random world-height/4)- world-height/8) ((random world-width/4)- world-width/8)
      setxy (x-pos / 4.0) (y-pos / 4.0)
      get-wolb ]
end 

to get-wolb ;; turtle procedure
  set wolb? true
  set color red
end 

to get-free ;; turtle procedure
  set wolb? false
  set wolb-carrying-count 0
  set color blue
end 

to setup-constants
  set carrying-capacity 4000
  set initialInfected freqInitWolbachia * nMosquitoes
;;  set ndays-week 7
  set avgNorm rateOffspring * normal-lifespan
  set lifespan-with-Wolbachia fracLifespanWolbachia * normal-lifespan
  set avgWolb (fracRateOffspWolbachia * rateOffspring) * lifespan-with-Wolbachia
end 

to go
  get-older
  move
  reproduce-wolbachia
  update-global-variables
  tick
end 

to update-global-variables
  if count turtles > 0
  [
    set %infected (count turtles with [wolb?]) / (count turtles) * 100
  ]
end 

;;Turtle counting variables are advanced.

to get-older
  ask turtles
  [
    set age age + 1
    if wolb?
      [ set wolb-carrying-count (wolb-carrying-count + 1) ]
    ;; Turtles die of old age once their age equals the
    ;; lifespan (set at 1500 in this model).
    ifelse wolb?
    [ if age > lifespan-with-Wolbachia
      [ die ]
    ]
    [
     if age > normal-lifespan
     [ die ]
    ]
  ]
end 

;;Turtles move about at random.

to move
  ask turtles
  [ rt random 100
    lt random 100
    fd 1 ]
end 

to reproduce-wolbachia
;;  ask turtles with [not sick?]
ask turtles
    [ if (count turtles) < carrying-capacity
       [ ifelse wolb? 
         ;; for sick the average offspring is set for a normal lifespan
         ;;          change to hatch a vqariable number b
         [ if (random lifespan-with-Wolbachia) < avgWolb
           [ hatch 1
             [ set age 1
               lt 45 fd 1
               get-wolb ] ] 
         ]
         [ if (random normal-lifespan) < avgNorm and (random 100) > %infected 
           [ hatch 1
             [set age 1
               lt 45 fd 1
               get-free]
             ]           
           
         ]
       ]
     ]    
end 


; Copyright 2013 Daniel Villela.
; See Info tab for full copyright and license.