Honey Bee Colony Collapse Disorder Model

breed [bees bee]  
breed [hives hive]
breed [flowers flower]
turtles-own [
  energy
  age
  visible-neighbors
  closest-neighbor
  ]       
bees-own [
  pollen 
  infected
  ]
hives-own [
  nectar
  growth-num
  ]
flowers-own [
  pollen-count
  pollinated?
  ]
patches-own [
  countdown
  ]

to setup
  clear-all
  ask patches [ set pcolor 55.5 ]
  
   set-default-shape hives "hex"
  create-hives initial-number-hives  ;; create the hives, then initialize their variables
  [
    set color yellow
    set size 1  ;; easier to see
    set energy 200
    set age random 1000
    setxy random-xcor random-ycor
  ]
  
  set-default-shape bees "bee"
  create-bees initial-number-bees  ;; create the bees, then initialize their variables
  [
    
    set size 0.5 
    set energy random (2 * bees-gain-from-food)
    set age random 1000
    setxy 
     [xcor] of hive 0 [ycor] of hive 0
    if random-float 100 < mite-infection-rate [ 
      set infected 1
    ]
  ]

  set-default-shape flowers "flower"
  create-flowers initial-number-flowers ;; create the flowers, then initialize their variables
  [
    set pollen-count random 20
    set age (random 1000 - count flowers) ;; Set random age, the more flowers there are the smaller lifespan new flowers have
    set size 3  ;; easier to see
    setxy random-xcor random-ycor
  ]
  reset-ticks
end 

to go
  if not any? turtles [ stop ]
  if mouse-interaction = "pesticide" [ ;; If the mouse-interaction is set to pesticide, mouse clicking will spray pesticides
    pesticides
  ]
  if mouse-interaction = "roads" [ ;; If the mouse-interaction is set to roads, mouse clicking will build roads
    deforestation
  ]
  if mouse-interaction = "grass" [ ;; If the mouse-interaction is set to grass, mouse clicking will make grass
    grass
  ]
  ask patches [
    pesticide-countdown ;; count down pesticide fading
  ]
  ask bees [
    ifelse pollen > 5[                        ;; If bees have more than 5 pollen, return to hive and deposit
      deposit-to-hive                         ;; Call deposit-to-hive procedure
    ]
    [
      set visible-neighbors (other flowers in-cone 10 120)  ;; Else, go find flowers in cone of vision
      ifelse any? visible-neighbors [
        set closest-neighbor min-one-of visible-neighbors [distance myself]   ;; If flower found, go towards it
        face closest-neighbor
        fd 0.5
        collect-pollen                                ;; Call collect-pollen procedure
      ]
      [
        move                                          ;; If flwoer not found, move randomly
      ]
    ]
    if energy < bees-gain-from-food [                 ;; If energy is lover than bees-gain-from-food, eat pollen if any and gain energy
      if pollen > 0 [
        set pollen (pollen - 1)
        set energy (energy + bees-gain-from-food)
      ]
    ]
    corn-syrup                                        ;; Call corn-syrup procedure
    if (ticks + random 5) mod 10 = 0 [                ;; Every 10 ticks or so, reproduce bees from hive
      reproduce-bees
    ]
    set energy (energy - 1)                           ;; Bees lose energy every tick
    if member? ([pcolor] of patch-here) (list 17 19 59) [
      set energy (energy - pesticide-strength)        ;; If flying on pesticides, lose energy based on pesticide-strength
      if corn-syrup? [
        set energy (energy - pesticide-strength)      ;; If corn syrup is on, lose twice as much energy
      ]
    ]
    if mites? [                                       ;; If mites are on,lose energy based on mite-damage every 5 ticks or so
      mite-effects                                    ;; Call mite-effects procedure
    ]
    set age (age - 1)                                ;; Age bees every tick
    death                                            ;; Die if no energy or too old
  ]

  ask hives [
    if count bees = 0 [                              ;; If no more bees, start hive collapse
        set energy energy - 1                        ;; hives lose energy per tick in collapse
    ]
    if hive 0 != nobody [
      reproduce-hives                                ;; Make adjacent hives when growing
    ]
    death                                            ;; Die in collapse
  ]
  ask flowers [
    if [pcolor] of patch-here = 2 or [pcolor] of neighbors = 2 [ ;; Die on roads/Never spawn
      die
    ]
    if any? hives-here or any? hives-on neighbors[               ;; Can't spawn on hives
      die
    ]                     
    if random-float 100 < flower-pollen-rate [                   ;; Produce pollen per tick based on flower-pollen-rate
      set pollen-count (pollen-count + 1)
    ]
    if age < 600 [
      if (ticks + random 5) mod 10 = 0[                          ;; Every 10 ticks or so when a flower has under 600 ticks of age left, a flower has the chance of reproducing if pollinated already
        if pollinated? = 1 [
          reproduce-flowers
        ]
      ]
    ]
    if test-pesticides? [
      ask patch-here [                                             ;; For testing purposes only, spray all flowers
        set pcolor 17
      ]
    ]
    set age (age - 1)
    death                                                        ;; Age and die if too old
  ]
  tick
end 

to move  ;; turtle procedure, moves turtle randomly
  rt random 50
  lt random 50
  fd 0.25
end 

;; REPRODUCTION

to reproduce-bees  ;; bees procedure, reproduces the bees
  if random-float 100 < bees-reproduce [  ;; throw "dice" to see if you will reproduce
    ask hive 0 [
      hatch-bees 1 [ 
        set size 0.5  
        set age random 1000
        set energy random (2 * bees-gain-from-food)
        rt random-float 360 fd 0.5
        if random-float 100 < mite-infection-rate [  ;; Set infection by mite (no effect unless mite? switch turned on)
          set infected 1
        ]
      ] 
    ]
  ]
end 

to reproduce-hives  ;; hive procedure to reproduce hives
  if [growth-num] of hive 0 > 100 [  ;; If growth number reaches 100 (100 nectar put into hive), reproduce another yellow rectangle onto it
    hatch 1 [ 
      set energy random 100          ;; Energy within 100
      rt random-float 360 fd 0.5
      ]  ;; hatch an offspring and move it forward 0.5 step next to first hive
    ask hive 0 [
      set growth-num 0               ;; Reset growth number     
    ]
  ]
end 

to reproduce-flowers  ;; Flower procedure, reproduces flowers
  if random-float 100 < flower-reproduce [                          ;; throw "dice" to see if you will reproduce
    hatch 1 [ 
      set pollen-count 0
      set color (color + (random 2) - (random 2))                   ;; Spawn color is a variant of parent color
      set age (random 1000 - count flowers)
      set size 3  ;; easier to see
      rt random-float 360 fd random 15                              ;; Set spawn placement at most 15 patches away
      while [any? other flowers-here or any? flowers-on neighbors][ ;; If flower already here, randomly move 2 to find different patch
        rt random-float 360 fd 2
      ]
      if any? hives-here or any? hives-on neighbors[                ;; Can't spawn on hives
        die
      ]
      set pollinated? 0
      if [pcolor] of patch-here = 2 or [pcolor] of neighbors = 2 [ ;; Can't spawn on roads
        die
      ]
    ]
    set pollinated? 0                                               ;; Flower not pollinated anymore
  ]
end 

;; POLLEN PROCEDURES

to collect-pollen  ;; bee procedure to collect pollen from flowers
  let buddy one-of flowers-here                    ;; grab flower present
  if buddy != nobody[
    if [pollen-count] of buddy > 0                 ;; did we get one?  if so,
    [ 
      ask buddy [                                  ;; collect pollen from flower, and pollinate it
        set pollen-count (pollen-count - 1)
        set pollinated? 1
 
      ]
      set pollen (pollen + 1)

    ] 
  ]
end 

to deposit-to-hive                        ;; Procedure to deposit pollen into hive which is converted to nectar
  face hive 0
  fd 0.5
  let home-hive one-of hives-here         
  if home-hive = hive 0 [
    set pollen (pollen - 5)               ;; Deposit pollen
    ask hive 0 [
      set nectar (nectar + 1)
      set growth-num (growth-num + 1)     ;; increase nectar and growth number
    ]
  ]
end 

;; PESTICIDES 

to pesticides ;; CCD Factor procedure, mouse click to set pesticides
  if mouse-down?[ 
    ask patch mouse-xcor mouse-ycor [ 
      if pcolor = 55.5 [
        set pcolor 17
        set countdown 1000
      ]
        ask neighbors [                         ;; Also set it on neighbors
          if pcolor = 55.5 [
            set pcolor 17
            set countdown 1000
          ]
        ]
    ] 
   ]
end 

to pesticide-countdown          ;; Patch procedure to cause pesticide fading
  if pcolor = 17 [              ;; This block of code will make pesticide sprayed grass turn light pink after 100 ticks, then light green, then back to green (grass).
    if countdown = 0 [          ;; When the grass is green again, the pesticides have faded away. This entire procedure is done through the use of a countdown variable.
      set pcolor 19
      set countdown 1000
    ]
  ]
  if pcolor = 19 [
    if countdown = 0 [
      set pcolor 59
      set countdown 1000
    ]
  ]
  if pcolor = 59 [
    if countdown = 0 [
      set pcolor 55.5           
    ]
  ]
  if countdown > 0 [
    set countdown (countdown - 1) ;; End block of fading pesticides
  ]
end 

;; VARROA MITES

to mite-effects
  if infected = 1 [
    if (ticks + random 5) mod 5 = 0 [
      set energy (energy - mite-damage)
      if corn-syrup? [                            ;; If corn syrup is on, lose twice as much energy
        set energy (energy - mite-damage)
      ]
    ]
  ]
end 

;; HIGH FRUCTOSE CORN SYRUP

to corn-syrup                              ;; Turn on corn syrup and feed bees every 10 ticks or so
  if (ticks + random 5) mod 10 = 0 [
    set energy (energy + corn-syrup-value)
  ]
end 

;; DEFORESTATION

to deforestation ;; CCD Factor procedure, mouse click to set roads
  if mouse-down?[ 
    ask patch mouse-xcor mouse-ycor [ 
      set pcolor 2
      ask neighbors [                      ;; Also set on neighbors
        set pcolor 2
        ]
      ] 
    ]
end 

;; SET GRASS

to grass ;; Patch procedure, change patches back to grass
  if mouse-down?[ 
    ask patch mouse-xcor mouse-ycor [ 
      set pcolor 55.5
      ask neighbors [                      ;; Also set on neighbors
        set pcolor 55.5
        ]
      ] 
    ]
end 

to death  ;; turtle procedure, cause death
  ;; when energy or age dips below zero, die
  if energy < 0 [ die ]
  if age < 1 [die]
end