turtles-own [
  sick?  ;;if true, the turtle is infected and infectious
  dead? ;;if true, turtle is dead - can't give birth or recover
  infected-count ;;turtles don't recover or die until they've been infected a few weeks
  dead-count ;;after turtle is dead for a few weeks, it'll disappear - this counts how many ticks it's been dead
  vaccinated? ;;if vaccinated, we'll say there's complete protection
]

patches-own [
  contaminated? ;;if infected snakes visit a patch, it becomes contaminated, and susceptible snakes there can get infected
]

globals [
  filename
  long-distance-dispersal ;;probability that snake moves to any patch, start at 0.007, can move to 0.005 and 5E-04
  inf-death-rate ;;probably that an infected snake dies each week.
  recovery-rate ;;probably that an infected snake recovers each week.
]

to setup
  clear-all
  ask patches with [pycor < -45 OR pycor > 52] [set pcolor 114.4] ;;this just corrects an annoying strip of black under the imperfectly sized image. 114.4 is the purple color
  set filename "ModelBackground.png"
  import-pcolors filename
  ask patches [set contaminated? false]
  set long-distance-dispersal 0.005
  set inf-death-rate 0.001
  set recovery-rate 0.001
  setup-turtles
  reset-ticks
end

to setup-turtles ;;model runs too slowly if add to many turtles, so we'll say the "real" number is X 1000
  set-default-shape turtles "circle"
  create-turtles 5000 ;;scatter 5000 across US
  [

    move-to one-of patches with [pcolor != 114.4 AND pycor > -40] ;;5000 turtles outside florida
    set color green
    set sick? false
    set dead? false
    set dead-count 0
    set infected-count 0
    set vaccinated? false
    set hidden? true
    if see-all-snakes = true [set hidden? false]
    ]
  create-turtles 1000 ;;put 1000 suceptibles in south
  [
    move-to one-of patches with [pcolor != 114.4 AND pycor < -34 AND pxcor > -15] ;;another 5000 inside florida
    set color green
    set sick? false
    set dead? false
    set dead-count 0
    set infected-count 0
    set vaccinated? false
    set hidden? true
    if see-all-snakes = true [set hidden? false]
    ]
  ask n-of 200 turtles with [pycor < -34 AND pxcor > -19] ;;start out with many dead - beginning during first observed mortality event - 100
  [
    set color black
    set dead? true
    set dead-count 1
    set vaccinated? false
    set hidden? false
  ]
  ask n-of 300 turtles with [pycor < -34 AND pxcor > -19 AND dead? = false] ;;start out with many infected, too - 100
  [
    set color magenta
    set sick? true
    set infected-count 1
    set vaccinated? false
    set hidden? false
  ]
end

;The following messy go procedure introduces seasonality into snake movement, reproduction, and observed mortality
;;snakes don't move in winter and give birth in spring and fall
;;week 0 = March 1
;;spring = ticks 0-12, 51-62, 113-125, 164-176 (March - May)
;;summer = ticks 13-25, 63-85, 126-138, 177-189   (June - Aug)
;fall = ticks 26-38, 86-100, 139-152, 190-202 (Sept - Nov)
;winter = ticks 39-50, 101-112, 153-163 (Dec - Feb)

to go
  if ticks > 200 [stop] ;;end after 200 weeks
  if ticks < 13  ;;spring 1
     [recover
      expire
      decay
      move
      infect
      get-sick
      make-babies
      tick]
    if ticks > 12 AND ticks < 26  ;;summer 1
     [recover
      expire
      decay
      move
      infect
      get-sick
      tick]
    if ticks > 25 AND ticks < 39  ;;fall 1
     [recover
      expire
      decay
      move
      infect
      get-sick
      make-babies
      tick]
    if ticks > 38 AND ticks < 51  ;;winter 1
     [recover
      expire
      decay
      tick]
    if ticks > 50 AND ticks < 63  ;;spring 2
     [recover
      expire
      decay
      move
      infect
      get-sick
      make-babies
      tick]
    if ticks > 62 AND ticks < 86  ;;summer 2
     [recover
      expire
      decay
      move
      infect
      get-sick
      tick]
    if ticks > 85 AND ticks < 101  ;;fall 2
     [recover
      expire
      decay
      move
      infect
      get-sick
      make-babies
      tick]
    if ticks > 100 AND ticks < 113  ;;winter 1
     [recover
      expire
      decay
      tick]
    if ticks > 112 AND ticks < 126  ;;spring 3
     [recover
      expire
      decay
      move
      infect
      get-sick
      make-babies
      tick]
    if ticks > 125 AND ticks < 139  ;;summer 3
     [recover
      expire
      decay
      move
      infect
      get-sick
      tick]
    if ticks > 138 AND ticks < 153  ;;fall 3
     [recover
      expire
      decay
      move
      infect
      get-sick
      make-babies
      tick]
    if ticks > 152 AND ticks < 164  ;;winter 3
     [recover
      expire
      decay
      tick]
   if ticks > 163 AND ticks < 177  ;;spring 4
     [recover
      expire
      decay
      move
      infect
      get-sick
      make-babies
      tick]
    if ticks > 176 AND ticks < 190  ;;summer 4
     [recover
      expire
      decay
      move
      infect
      get-sick
      tick]
    if ticks > 189 AND ticks < 201  ;;fall 4
     [recover
      expire
      decay
      move
      infect
      get-sick
      make-babies
      tick]
end

to recover ;; turtle procedure - some sick individuals clear their infections and go back to being susceptible
  ask turtles with [sick? = true AND dead? = false] [set infected-count infected-count + 1]
  ask turtles with [sick? = true AND dead? = false AND infected-count > 2] [
      if random-float 100 <= recovery-rate ;;small chance that infected individuals recover
        [set sick? false
        set dead? false
        set vaccinated? true ;;we'll say recovered snakes are fully immune to future infection, for simplicity (students won't know this)
        set infected-count 0
        if see-all-snakes = true [set hidden? false]
         set color green]
  ]
end

to expire ;; turtle procedure - susceptible and infected turtles have different mortality rates
  ask turtles with [sick? = false AND dead? = false] [
      if random-float 100 <= 1 ;;;;background mortality for susceptible turtles is 1% per tick
      [die]
  ask turtles with [sick? = true AND dead? = false AND infected-count > 2] [
      if random-float 100 <= inf-death-rate ;;disease-induced mortality rate - is 1% or 5% too high?
        [set dead? true
          set sick? false
          set vaccinated? false
          set hidden? false
         set color black]
       ]
  ]
end

to decay ;; turtle procedure - dead snakes eventually decay/disappear
  ask turtles with [dead? = true and sick? = false] [
      set dead-count dead-count + 1
      if dead-count > 3
        [die]
       ]
end

to move
  ask turtles with [dead? = false] [
    if random-float 100 <= long-distance-dispersal [ ;;very rarely get transported to any patch
      move-to one-of patches with [pcolor != 114.4]]
    if random-float 100 <= 20 [   ;;change to a nearby patch 20% of the time - moving one patch in a week is pretty far for a snake
      move-to one-of neighbors with [pcolor != 114.4] ;;don't move into ocean
  ]
 ]
end

to make-babies
  ask turtles with [dead? = false AND sick? = false] [
    if random-float 100 <= 0.5 [ ;;1% chance of female snakes (half of snakes, so 0.5% of snakes) reproducing each tick
      hatch 5 [
        set color green
        set sick? false
        set dead? false
        set vaccinated? false
        set dead-count 0
        ifelse see-all-snakes = true [set hidden? false][set hidden? true]
      ]
    ]
  ]
end

to infect
  ask turtles with [sick?]
    [ ask patch-here [
      set contaminated? true]]
end

to get-sick ;; patch procedure
  ask patches with [contaminated? = true] [
    ask turtles-here with [sick? = false AND dead? = false AND vaccinated? = false] [
      if random-float 100 <= 50 [ ;chance of getting infected per tick on an infected patch
          set sick? true
          set color magenta
        set hidden? false
        set infected-count 1
      ]
  ]
  ]
end

;;to treat-infected-snakes
  ;;ask n-of ((count turtles with [sick? = true]) * 0.30) turtles with [sick? = true] [recover]
;;end
@#$#@#$#@
GRAPHICS-WINDOW
270
10
683
594
-1
-1
5.0
1
10
1
1
1
0
0
0
1
-40
40
-57
57
0
0
1
ticks
30.0

BUTTON
26
48
92
81
Setup
setup
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
25
119
156
152
Advance 1 Week
Go
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

PLOT
696
10
1177
287
Epidemic Tracking - Eastern United States
Time (weeks)
Number of snakes
0.0
210.0
0.0
60000.0
true
true
"" ""
PENS
"Infected" 1.0 0 -5825686 true "" "plot (count turtles with [sick? = true]) * 1000"
"Dead" 1.0 0 -7500403 true "" "plot (count turtles with [dead? = true]) * 1000"

BUTTON
25
554
172
587
Run Full Simulation
go
T
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

PLOT
696
294
1175
588
Epidemic Tracking - Florida
Time (weeks)
Number of snakes
0.0
210.0
0.0
10.0
true
true
"" ""
PENS
"Infected" 1.0 0 -7858858 true "" "plot (count turtles with [sick? = true AND dead? = false AND pycor < -35 AND pxcor > -15]) * 1000"
"Dead" 1.0 0 -7500403 true "" "plot (count turtles with [dead? = true AND pycor < -35 AND pxcor > -15]) * 1000"

SWITCH
24
514
172
547
see-all-snakes
see-all-snakes
1
1
-1000

TEXTBOX
24
479
227
518
Don't click these until you're ready to explore the model in Part II
11
0.0
1

BUTTON
22
193
164
226
treat-infected-snakes
let %t 0.30\nlet n count turtles with [sick? = true]\nask (n-of (%t * n)  turtles with [sick? = true]) [ \n        set sick? false\n        set dead? false\n        set infected-count 0\n        if see-all-snakes = true [set hidden? false] \n         set color green \n]
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
22
231
231
264
spray-contaminated-environment
let %t 0.20\nlet n count patches with [contaminated? = true]\nask (n-of (%t * n)  patches with [contaminated? = true]) [ \n        set contaminated? false\n        ask turtles-here with [sick? = true] [\n        set sick? false\n        set dead? false\n        set infected-count 0\n        if see-all-snakes = true [set hidden? false] \n         set color green \n        ]\n]
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
23
270
163
303
cull-infected-snakes
let %t 0.30\nlet n count turtles with [sick? = true]\nask (n-of (%t * n)  turtles with [sick? = true]) [ \n        set sick? false\n        set dead? true\n         set color black\n       set dead-count 1\n]\n
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
23
308
126
341
cull-snakes
let %t 0.20\nlet max-lat max [ycor] of turtles with [sick? = true]\nlet min-lat min [ycor] of turtles with [sick? = true]\nlet n count turtles with [ycor < max-lat AND ycor > min-lat]\n\nask (n-of (%t * n) turtles with [dead? = false AND ycor < max-lat AND ycor > min-lat]) [\n         set sick? false\n        set dead? true\n         set color black\n         set dead-count 1\n]\n
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
23
346
141
379
vaccinate-snakes
let %t 0.30\nlet max-lat max [ycor] of turtles with [sick? = true]\nlet min-lat min [ycor] of turtles with [sick? = true]\nlet n count turtles with [ycor < max-lat AND ycor > min-lat AND dead? = false AND sick? = false AND vaccinated? = false]\n\nask (n-of (%t * n) turtles with [dead? = false AND sick? = false AND vaccinated? = false AND ycor < max-lat AND ycor > min-lat]) [\n         set vaccinated? true \n         set color blue\n         set hidden? false\n]
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

PLOT
23
672
542
991
United States Epidemic Tracker with Susceptibles
Time (weeks)
Number of snakes
0.0
210.0
0.0
10.0
true
false
"" ""
PENS
"Susceptible" 1.0 0 -13840069 true "" "if see-all-snakes = true [plot (count turtles with [sick? = false AND dead? = false]) * 1000]"
"Infected" 1.0 0 -7858858 true "" "plot (count turtles with [sick? = true]) * 1000"
"Dead" 1.0 0 -12895429 true "" "plot (count turtles with [dead? = true]) * 1000"

PLOT
563
671
1130
991
Florida Epidemic Tracker with Susceptibles
Time (Weeks)
Number of Snakes
0.0
10.0
0.0
210.0
true
false
"" ""
PENS
"Susceptible" 1.0 0 -14439633 true "" "if see-all-snakes = true [plot (count turtles with [sick? = false AND dead? = false AND pycor < -35 AND pxcor > -15]) * 1000]"
"Infected" 1.0 0 -7858858 true "" "plot (count turtles with [sick? = true AND dead? = false AND pycor < -35 AND pxcor > -15]) * 1000"
"Dead" 1.0 0 -12895429 true "" "plot (count turtles with [dead? = true AND pycor < -35 AND pxcor > -15]) * 1000"

BUTTON
23
384
215
417
public-service-announcement
  set long-distance-dispersal 0.003\n  set inf-death-rate 0.0008
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
23
421
122
454
ban-pet-trade
set long-distance-dispersal 5E-04
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

TEXTBOX
24
173
220
201
These buttons do interventions
11
0.0
1

TEXTBOX
27
13
265
55
Click once to initiate simulation and never click again
11
0.0
1

TEXTBOX
27
97
242
125
Click once to advance one week/tick
11
0.0
1

@#$#@#$#@
## WHAT IS IT?

(a general understanding of what the model is trying to show or explain)

## HOW IT WORKS

(what rules the agents use to create the overall behavior of the model)

## HOW TO USE IT

(how to use the model, including a description of each of the items in the Interface tab)

## THINGS TO NOTICE

(suggested things for the user to notice while running the model)

## THINGS TO TRY

(suggested things for the user to try to do (move sliders, switches, etc.) with the model)

## EXTENDING THE MODEL

(suggested things to add or change in the Code tab to make the model more complicated, detailed, accurate, etc.)

## NETLOGO FEATURES

(interesting or unusual features of NetLogo that the model uses, particularly in the Code tab; or where workarounds were needed for missing features)

## RELATED MODELS

(models in the NetLogo Models Library and elsewhere which are of related interest)

## CREDITS AND REFERENCES

(a reference to the model's URL on the web if it has one, as well as any other necessary credits, citations, and links)
@#$#@#$#@
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