Ecology of Lyme 1

;;----- Agent types
breed [blticks bltick]
breed [mice mouse]
breed [squirrels squirrel]
breed [possums possum]
breed [chipmunks chipmunk]

blticks-own [infected? fed?]                                     ;; larval ticks feed once and may become carriers of Lyme as a result
mice-own [body-burden reservoir-competence host-quality]         ;; each species can carry Lyme and have a probability of transmitting Lyme
squirrels-own [body-burden reservoir-competence host-quality]
possums-own [body-burden reservoir-competence host-quality]
chipmunks-own [body-burden reservoir-competence host-quality]

to setup

  ca

  ;; color the patches
  ask patches [set pcolor 63]

  ;; intialize breeds and randomly distribute them in the world
  create-blticks larval-ticks [
    set shape "spider"
    set color black
    set size 0.5
    set infected? FALSE
    set fed? FALSE
    setxy random-xcor random-ycor
  ]

  create-mice mouse-density [
    set shape "mouse side"
    set color gray
    set size 2.5
    set body-burden 28
    set reservoir-competence 0.91
    set host-quality 0.493
    setxy random-xcor random-ycor
  ]

    create-squirrels squirrel-density [
    set shape "squirrel"
    set color gray
    set size 3
    set body-burden 142
    set reservoir-competence 0.02
    set host-quality 0.172
    setxy random-xcor random-ycor
  ]

    create-chipmunks chipmunk-density [
    set shape "chipmunk"
    set color brown
    set size 2.5
    set body-burden 36
    set reservoir-competence 0.57
    set host-quality 0.243
    setxy random-xcor random-ycor
  ]

    create-possums possum-density [
    set shape "possum"
    set color gray + 3
    set size 3
    set body-burden 254
    set reservoir-competence 0.03
    set host-quality 0.035
    setxy random-xcor random-ycor
  ]


  reset-ticks
end 

to go

  ;; stop when all ticks have fed
  ;if all? blticks [ fed? ] [ stop ]
  if ticks = 1000 [stop]
  ;; have each breed move at a different speed
  move

  ;; ticks will feed on a host if one is on the same patch
  ask blticks [feed]

  tick
end 

to move

  ;; all hosts move randomly around the world
  ask squirrels [
    left random 50
    right random 50
    repeat 8 [fd 0.1]
  ]

  ask mice [
    left random 50
    right random 50
    repeat 1 [fd 0.1]
  ]

   ask possums [
    left random 50
    right random 50
    repeat 6 [fd 0.1]
  ]

   ask chipmunks [
    left random 50
    right random 50
    repeat 2 [fd 0.1]
  ]
end 

to feed

    ;; define local variables
    let pInfected  0
    let pFed 0
    let burden 0

    ;;find a host, exclude other ticks
    let host one-of other turtles-here with [member? self blticks = FALSE ]

    ;; set local variables to the host's properties
    ;; for each feeding event if larva has not aready fed
    if host != nobody and not fed?[
      ask host [
        set pFed host-quality
        set pInfected reservoir-competence
        set burden body-burden
      ]

    ;; ticks feed once, molt, and become larger
    ;; survival is determined based on the host quality
    ;; infection status is determined based on the host's reservoir competence
      if random 254 <= burden [                       ;; is host below its body burden?
        ifelse random-float 1.0 <= pFed               ;; does host feed larva?
        [
          set fed? TRUE                               ;; feed
          set size size * 2                           ;; molt
            if random-float 1.0 <= pInfected          ;; did B.burgdorferi transfer?
            [
              set infected? TRUE                      ;; if so change infection status
              set color red                           ;; and color
            ]
        ]
        [ die ]                                       ;; else larva dies
      ]
    ]
end 

to-report DON

  report count blticks with [fed?]
end 

to-report DIN

  report count blticks with [infected?]
end 

to-report NIP

  report 100 * DIN / DON
end 

to reset

  ;;  resets model parameters to intial satate

  set larval-ticks 1000
  set mouse-density 40
  set squirrel-density 8
  set possum-density 1
  set chipmunk-density 20
end