Ecology of Lyme 2

;;----- Breed types

breed [blticks bltick]
breed [mice mouse]
breed [chipmunks chipmunk]
breed [deers deer]
breed [racoons racoon]
breed [possums possum]
breed [skunks skunk]
breed [st-shrews st-shrew]
breed [birds bird]
breed [sx-shrews sx-shrew]
breed [squirrels squirrel]

;;----- Breed properties

blticks-own [infected? molt?]                                        ;; larval ticks molt once and may become carriers of Lyme as a result
mice-own [body-burden reservoir-competence molting-percentage]       ;; each species can carry Lyme and have a probability of transmitting Lyme
chipmunks-own [body-burden molting-percentage reservoir-competence]
deers-own [body-burden molting-percentage reservoir-competence]
racoons-own [body-burden molting-percentage reservoir-competence]
possums-own [body-burden molting-percentage reservoir-competence]
skunks-own [body-burden molting-percentage reservoir-competence]
st-shrews-own [body-burden molting-percentage reservoir-competence]
birds-own [body-burden molting-percentage reservoir-competence]
sx-shrews-own [body-burden molting-percentage reservoir-competence]
squirrels-own [body-burden molting-percentage reservoir-competence]

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 molt? FALSE
  ]

  create-mice mouse-density [
    set shape "mouse side"
    set color gray
    set size 2.5
    set body-burden 28
    set reservoir-competence 0.921
    set molting-percentage 0.415
  ]

  create-chipmunks chipmunk-density [
    set shape "chipmunk"
    set color brown
    set size 2.5
    set body-burden 36
    set reservoir-competence 0.55
    set molting-percentage 0.412
  ]

  create-deers deer-density [
    set shape "moose"
    set color brown + 2
    set size 4
    set body-burden 239
    set reservoir-competence 0.046
    set molting-percentage 0.563
  ]

  create-racoons racoon-density [
    set shape "racoon"
    set color brown
    set size 3
    set body-burden 127
    set reservoir-competence 0.013
    set molting-percentage 0.365
  ]

  create-possums possum-density [
    set shape "possum"
    set color gray + 3
    set size 3
    set body-burden 254
    set reservoir-competence 0.026
    set molting-percentage 0.441
  ]

  create-skunks skunk-density [
    set shape "skunk"
    set color black
    set size 3
    set body-burden 67
    set reservoir-competence 0.097
    set molting-percentage 0.639
  ]

  create-st-shrews st-shrew-density [
    set shape "mouse side"
    set color brown
    set size 1.5
    set body-burden 63
    set reservoir-competence 0.418
    set molting-percentage 0.468
  ]

  create-birds bird-density [
    set shape "bird"
    set color blue + 1
    set size 3
    set body-burden 2
    set reservoir-competence 0.117
    set molting-percentage 0.339
  ]

  create-sx-shrews sx-shrew-density [
    set shape "mouse side"
    set color black
    set size 1.5
    set body-burden 56
    set reservoir-competence 0.512
    set molting-percentage 0.496
  ]

  create-squirrels squirrel-density [
    set shape "squirrel"
    set color gray
    set size 3
    set body-burden 142
    set reservoir-competence 0.147
    set molting-percentage 0.593
  ]

  ask turtles [setxy random-xcor random-ycor]

  reset-ticks
end 

to go

  ;; stop when all ticks have fed
  ;if all? blticks [ molt? ] [ 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 mice [
    left random 50
    right random 50
    repeat 1 [fd 0.1]
  ]

  ask chipmunks [
    left random 50
    right random 50
    repeat 3 [fd 0.1]
  ]

  ask deers [
    left random 50
    right random 50
    repeat 10 [fd 0.1]
  ]

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

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

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

  ask st-shrews [
    left random 50
    right random 50
    repeat 1 [fd 0.1]
  ]

  ask birds [
    left random 50
    right random 50
    repeat 10 [fd 0.1]
  ]

  ask sx-shrews [
    left random 50
    right random 50
    repeat 1 [fd 0.1]
  ]

  ask squirrels [
    left random 50
    right random 50
    repeat 6 [fd 0.1]
  ]
end 

to feed

    ;; define local variables
    let pInfected  0
    let pMolt 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 already fed
    if host != nobody and not molt?[
      ask host [
        set pMolt molting-percentage
        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 <= pMolt              ;; does larva survive to molt?
        [
          set molt? 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 [molt?]
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
  ;; multiply parameters from literature by 20 to normalize all as integers? HUGE numbers!

  set larval-ticks 1000
  set mouse-density 40
  set chipmunk-density 20
  set deer-density 1
  set racoon-density 1
  set possum-density 1
  set skunk-density 1
  set st-shrew-density 25
  set bird-density 32
  set sx-shrew-density 25
  set squirrel-density 8
end