Bats

extensions [bitmap]        ; allows for import of png map (later in code - during setup)

globals 
     [habitats]
                           ; some globals seen in other models - seemed applicable, these 
                          ; represent things that all agents interact with so apply to all in model
breed [bats bat]
breed [peoples people]
breed [specialists specialist]
breed [caves cave]        ; names the different agentsets in the model
breed [lands land]


bats-own
  [age 
  days
  eat-bugs
  fly-around
  check-death
  bat-energy
  hibernate         ; defines specific bat behavior attributes
  max-lifespan
  gets-sick
  average-offspring
  ]
  
peoples-own 
   [visit-caves
   carries-disease 
]
                            ; some of visitors will carry disease into cave
patches-own 
    [habitat-cave         ; differentiates between area that is cave,
    caves-with-disease         ;; whether cave has G. destructans growing
    habitat-land          ; and whether area is open land for bats to fly around
]

specialists-own
   [inspect-caves
   find-cave-has-disease
   ]                                          ; defines what wildlife specialists do
                                              ; label caves that have WNS (color is white, 9.9)  

to setup                                           
  __clear-all-and-reset-ticks             ; (for this model to work with NetLogo's new plotting features
  
  import-pcolors-rgb "Bat-caves.png"      ; the map used that shows W.Va and Va.cave areas in karst topo
  create-bats number-bats [
  setup-habitats
  setup-agents
  ]
  do-plots
end 

to setup-habitats
  ask patches [
         if pcolor > 1 and pcolor < 6 [
           set pcolor 47
           set habitats habitat-cave
         ]
         if pcolor > 31 and pcolor < 38 [
           set pcolor 47
           set habitats habitat-cave
         ]
         if pcolor > 51 and pcolor < 68 [          ; this section of the code changes the perception of the
           set pcolor 47                                       ; bitmap for agents so that some areas (near kartst, where there a                                      ; be green for bat habitat in which they fly, eat and then hiberna                           ; (and in some cases get sick) in the caves
           set habitats habitat-cave
           ]
  ask patches [ 
           if pcolor > 47 and pcolor < 47 [
            set pcolor 67 
            set habitats habitat-land
  ]]]
end   

to setup-agents 
  ask bats [set shape "bats"
           set size .5 
           set color 35]
  
  ask specialists [set shape "person"
                  set size 2 
                  set color green
             set inspect-caves 12] 
                                                ; distinguishes shapes sizes and colors 
  ask peoples [set shape "person"
              set size 2 
              set color black]                  ; of 3 diff. agents: bats, people & specialists         
end 

to setup-bats
  ask patches[
    hatch n-of 100 [number-bats]
      set bat-energy random 30 
      set age random 25               ; starts bats with shape, energy, color and lifespan of 25 max
      show count gets-sick                  ; average offspring is set to 5 (in nature is 5 or 6)
      set max-lifespan 25
      set average-offspring 5
      if bat-energy = 0 [die]
  ]
end 

to go 
      move-bats  
     if not any? bats [stop]
     if count bats > 1200 [stop]           ; these are the basics to start up the model with moving bats
      set hibernate ticks                   ; people and wildlife specialists, but to first check that
      move-people                           ; there are in fact bats, (when there are none model will stop or if
                                            ; there are so many, like  1200                           
      set carries-disease random 3         ; this only allows for up to 3 people to carry the disease to caves
      inspect habitat-cave                                ; for this size model
      do-plots
      tick
end 

to move-bats  
    ask bats [set age age + 1]
    if age > 25 [die]
      if average-offspring < 5 [                  ; the most challenging part of the code was to get
        hatch 1]                                  ; bats to move, eat, gain and lose energy, hibernate
      set bat-energy bat-energy - 25              ; graze, reproduce and get sick if in contact with
      ask bats [                                  ; cave patches carrying G. destructans
        set bat-energy bat-energy + 25
   ]                                               ; to identify their two parts of habitat (caves and land)
   ask bats [
     set hibernate habitat-cave
     let c one-of (habitat-cave in-radius 1)
      move-to habitat-cave
      if days = 75 [ 
         move-to habitat-cave 
         set hibernate habitat-cave = 25 
         set bat-energy bat-energy - 10
      if patch-here ? pcolor white 
           set gets-sick]
    [if (bats-on or if bat 0 bat 2 bat 9 gets-sick)
       self gets-sick] [
    set bat-energy bat-energy - 20
      ]]
     
  ]]]
end   

to move-people
  ask people [ 
    let p n-of 5 people                                   ; should move people (6 per year?) into caves randomly, 
    move-to visit-caves                                   ; and this would leave disease if person is a carrier
    let k min-one-of habitat-cave [distance myself]
    face k
    move-to k  fd 2 rt 30 fd 1 lt 30 fd 2 lt 180 fd 5]
    let d n-of 1 carries-disease
    if carries-disease [
      ask one-of patches [set pcolor white]             ; the cave patch turns white to show it has disease now
    ]
end 

to check-for-disease
  ask specialist [
    let s n-of 3 specialist 
    move-to habitat-cave 
    let t min-one-of habitat-cave [distance myself]       ; specialists inspect and label the caves that have disease
    face t 
    move-to t [range-of-view 60 radius 2]
     fd 2 rt 30 fd 1 rt 30 fd 2 lt 45 fd 1 lt 60]
     if patch [self] pcolor white
        [set cave-with-disease
          add count + 1
]
end 

to do-plots
    ; update plots with new values
  
  set-current-plot "Bat Population" 
  set-current-plot-pen "healthy/" 
  plot count bats                                ; plot Total number of bats
  set-current-plot-pen "sick bats"                ; plot number of bats sick
  plot count becomes-sick  
  set-current-plot "Human visits to caves"
  set-current-plot-pen "people visit caves"
  plot count visit-caves
end 

to ruler    
                                                               ; set up the white ruler lines around the edge of the model window
                                                               ; to give an approximate linear scale to the 'map'
  ask patches with [pxcor = max-pxcor ][set pcolor 78]         ; a nice touch taken from Orangatango model
  ask patches with [pycor = max-pycor ][set pcolor 78]
  ask patches with [pxcor = min-pxcor ][set pcolor 78]
  ask patches with [pycor = min-pycor ][set pcolor 78]

    ask patches with [pxcor mod 10 = 0 and
                    pycor < (min-pycor + 2)]
    [ set pcolor black ]     
    ask patches with [pxcor mod 100 = 0 and
                    pycor < (min-pycor + 8)]
    [ set pcolor black ]     
    ask patches with [pxcor < (min-pxcor + 2) and
                    pycor mod 10 = 0]
    [ set pcolor black ]
    ask patches with [pxcor < (min-pxcor + 8) and
                    pycor mod 100 = 0]
    [ set pcolor black ]
end