Bacteria-Rust model.nlogo

globals[
  growth-rate-bacteria
  carrying-cap-bacteria
  growth-rate-rust
  carrying-cap-rust

  conversion-rate
  immigration-rate
  emmigration-rate
  death-rate

  step-size
  prop-prob
  sigma
  stepH
  stepV
  distH
  distV
  distD

 initial-conditions
]

turtles-own [
  proportion
  proportion-temp
  bacteria-size
]

to setup
  clear-all
  setup-globals
  setup-patches
  setup-turtles
  reset-ticks
end

to setup-globals
  set growth-rate-bacteria 2
  set carrying-cap-bacteria 7
    set death-rate 1.5

  set growth-rate-rust 0.15
  set carrying-cap-rust 0.284
  set immigration-rate 0.9 / 24
  set emmigration-rate 0.1 / 24
  set conversion-rate 0.9 / 24
  set prop-prob 20

  set step-size 1
  set sigma 3
  set stepH 3
  set stepV 8
  set distH 1
  set distV 2
  set distD 2.2361
end

to setup-patches
  ask patches [set pcolor green]
end

to setup-turtles
  let horizontal-spacing (world-width / column-number)
  let vertical-spacing (world-height / row-number)
  let min-xpos (min-pxcor - 0.5 + horizontal-spacing / 2)
  let min-ypos (min-pycor - 0.5 + vertical-spacing / 2)

  set-default-shape turtles "circle"

  create-turtles(column-number * row-number)[
    let row floor(who / column-number)
    let col (who mod column-number)
    setxy (min-xpos + col * horizontal-spacing) (min-ypos + row * vertical-spacing)
  ]
  ask turtles [
    set color yellow
    set bacteria-size 1
  ]
  ask n-of (floor((count turtles) * infected-proportion / 100)) turtles [set proportion random-float 0.2]
  ask turtles [
    set size proportion * 3
    set proportion-temp proportion
  ]
end

to-report report-proportion
  let S 0
  ask turtles[set S (S + ceiling(proportion - 0.00005))]
  report S
end

to go
  ask turtles [set size proportion * 3]
  grow-rust
  grow-bacteria
  tick

  if ticks = 168 [stop]
end

to grow-rust
  ask turtles[
    set proportion (proportion + proportion-temp * growth-rate-rust * (1 - proportion-temp / carrying-cap-rust) - emmigration-rate * proportion-temp - conversion-rate * bacteria-size * proportion-temp)
  ]
  disperse-rust

  ask turtles[
    set proportion max list 0 proportion
    set proportion-temp proportion
  ]
end

to disperse-rust
  let tau-1-0 0
  let tau+1-0 0
  let tau-0-1 0
  let tau-0+1 0
  let tau-1-1 0
  let tau-1+1 0
  let tau+1-1 0
  let tau+1+1 0

  let num 0
  let H-prob 0
  let V-prob 0
  let D-prob 0
  ask turtles[
    set tau-1-0 0
    set tau+1-0 0
    set tau-0-1 0
    set tau-0+1 0
    set tau-1-1 0
    set tau-1+1 0
    set tau+1-1 0
    set tau+1+1 0

    ifelse who <  column-number[
      ifelse who = 0[
        set H-prob dispProbability (1)(distH)
        set V-prob dispProbability (column-number)(distV)
        set D-prob dispProbability (column-number + 1)(distD)
        if (random-float 1) <= D-prob [set tau-1+1 1]
        if (random-float 1) <= H-prob [set tau-0+1 1]
        if (random-float 1) <= V-prob [set tau-1-0 1]

        set proportion (proportion + immigration-rate * (tau-1-0 * [proportion-temp] of turtle column-number + tau-0+1 * [proportion-temp] of turtle 1 +
          tau-1+1 * [proportion-temp] of turtle (column-number + 1)))
        ][ifelse who = (column-number - 1)[
          set H-prob dispProbability (column-number - 2)(distH)
          if (random-float 1) <= H-prob [set tau-0-1 1]
          set V-prob dispProbability (2 * column-number - 1)(distV)
          if (random-float 1) <= V-prob [set tau-1-0 1]
          set D-prob dispProbability (2 * column-number - 2)(distD)
          if (random-float 1) <= D-prob [set tau-1-1 1]

          set proportion (proportion + immigration-rate * (tau-1-0 * [proportion-temp] of turtle (2 * column-number - 1) +
            tau-0-1 * [proportion-temp] of turtle (column-number - 2) + tau-1-1 * [proportion-temp] of turtle (2 * column-number - 2)))
        ][
          set H-prob dispProbability (who - 1)(distH)
          if (random-float 1) <= H-prob [set tau-0-1 1]
          set H-prob dispProbability (who + 1)(distH)
          if (random-float 1) <= H-prob [set tau-0+1 1]
          set V-prob dispProbability (who + column-number)(distV)
          if (random-float 1) <= V-prob [set tau-1-0 1]
          set D-prob dispProbability (column-number + 1)(distD)
          if (random-float 1) <= D-prob [set tau-1+1 1]
          set D-prob dispProbability (column-number - 1)(distD)
          if (random-float 1) <= D-prob [set tau-1-1 1]

          set proportion (proportion + immigration-rate * (tau-0-1 * [proportion-temp] of turtle (who - 1) + tau-0+1 * [proportion-temp] of turtle (who + 1) +
            tau-1-0 * [proportion-temp] of turtle (who + column-number) + tau-1-1 * [proportion-temp] of turtle (who + column-number - 1) +
            tau-1+1 * [proportion-temp] of turtle (who + column-number + 1)))
        ]
      ]
      ][ifelse who >= (column-number * (row-number - 1))[
        ifelse who = (column-number * (row-number - 1))[
          set H-prob dispProbability (who + 1)(distH)
          if (random-float 1) <= H-prob [set tau-0+1 1]
          set V-prob dispProbability (who - column-number)(distV)
          if (random-float 1) <= V-prob [set tau+1-0 1]
          set D-prob dispProbability (who - column-number + 1)(distD)
          if (random-float 1) <= D-prob [set tau+1+1 1]

          set proportion (proportion + immigration-rate * (tau-0+1 * [proportion-temp] of turtle (who + 1) + tau+1-0 * [proportion-temp] of turtle (who - column-number) +
            tau+1+1 * [proportion-temp] of turtle (who - column-number + 1)))
          ][ifelse who = (column-number * row-number - 1)[
            set H-prob dispProbability (who - 1)(distH)
            if (random-float 1) <= H-prob [set tau-0-1 1]
            set V-prob dispProbability (who - column-number)(distV)
            if (random-float 1) <= V-prob [set tau+1-0 1]
            set D-prob dispProbability (who - column-number - 1)(distD)
            if (random-float 1) <= D-prob [set tau+1-1 1]

            set proportion (proportion + immigration-rate * (tau-0-1 * [proportion-temp] of turtle (who - 1) + tau+1-0 * [proportion-temp] of turtle (who - column-number) +
              tau+1-1 * [proportion-temp] of turtle (who - column-number - 1)))
          ][
            set H-prob dispProbability (who - 1)(distH)
            if (random-float 1) <= H-prob [set tau-0-1 1]
            set H-prob dispProbability (who + 1)(distH)
            if (random-float 1) <= H-prob [set tau-0+1 1]
            set V-prob dispProbability (who - column-number)(distV)
            if (random-float 1) <= V-prob [set tau+1-0 1]
            set D-prob dispProbability (who - column-number + 1)(distD)
            if (random-float 1) <= D-prob [set tau+1+1 1]
            set D-prob dispProbability (who - column-number - 1)(distD)
            if (random-float 1) <= D-prob [set tau+1-1 1]

            set proportion (proportion + immigration-rate * (tau-0-1 * [proportion-temp] of turtle (who - 1) + tau-0+1 * [proportion-temp] of turtle (who + 1) +
              tau+1-0 * [proportion-temp] of turtle (who - column-number) + tau+1+1 * [proportion-temp] of turtle (who - column-number + 1) +
              tau+1-1 * [proportion-temp] of turtle (who - column-number - 1)))
          ]
        ]
        ][ifelse (who mod column-number) = 0[
          set H-prob dispProbability (who + 1)(distH)
          if (random-float 1) <= H-prob [set tau-0+1 1]
          set V-prob dispProbability (who + column-number)(distV)
          if (random-float 1) <= V-prob [set tau-1-0 1]
          set V-prob dispProbability (who - column-number)(distV)
          if (random-float 1) <= V-prob [set tau+1-0 1]
          set D-prob dispProbability (who - column-number + 1)(distD)
          if (random-float 1) <= D-prob [set tau+1+1 1]
          set D-prob dispProbability (who + column-number - 1)(distD)
          if (random-float 1) <= D-prob [set tau-1+1 1]

          set proportion (proportion + immigration-rate * (tau-0+1 * [proportion-temp] of turtle (who + 1) + tau-1-0 * [proportion-temp] of turtle (who + column-number) +
            tau+1-0 * [proportion-temp] of turtle (who - column-number) + tau+1+1 * [proportion-temp] of turtle (who - column-number + 1) +
            tau-1+1 * [proportion-temp] of turtle (who + column-number + 1)))
          ][ifelse (who mod column-number) = (column-number - 1)[
            set H-prob dispProbability (who - 1)(distH)
            if (random-float 1) <= H-prob [set tau-0-1 1]
            set V-prob dispProbability (who + column-number)(distV)
            if (random-float 1) <= V-prob [set tau-1-0 1]
            set V-prob dispProbability (who - column-number)(distV)
            if (random-float 1) <= V-prob [set tau+1-0 1]
            set D-prob dispProbability (who - column-number - 1)(distD)
            if (random-float 1) <= D-prob [set tau+1-1 1]
            set D-prob dispProbability (who + column-number - 1)(distD)
            if (random-float 1) <= D-prob [set tau-1-1 1]

            set proportion (proportion + immigration-rate * (tau-0-1 * [proportion-temp] of turtle (who - 1) + tau-1-0 * [proportion-temp] of turtle (who + column-number) +
              tau+1-0 * [proportion-temp] of turtle (who - column-number) + tau+1-1 * [proportion-temp] of turtle (who - column-number - 1) +
              tau-1-1 * [proportion-temp] of turtle (who + column-number - 1)))
          ][
            set H-prob dispProbability (who + 1)(distH)
            if (random-float 1) <= H-prob [set tau-0+1 1]
            set H-prob dispProbability (who - 1)(distH)
            if (random-float 1) <= H-prob [set tau-0-1 1]
            set V-prob dispProbability (who + column-number)(distV)
            if (random-float 1) <= V-prob [set tau-1-0 1]
            set V-prob dispProbability (who - column-number)(distV)
            if (random-float 1) <= V-prob [set tau+1-0 1]
            set D-prob dispProbability (who - column-number - 1)(distD)
            if (random-float 1) <= D-prob [set tau+1-1 1]
            set D-prob dispProbability (who - column-number + 1)(distD)
            if (random-float 1) <= D-prob [set tau+1+1 1]
            set D-prob dispProbability (who + column-number - 1)(distD)
            if (random-float 1) <= D-prob [set tau-1-1 1]
            set D-prob dispProbability (who + column-number + 1)(distD)
            if (random-float 1) <= D-prob [set tau-1+1 1]

            set proportion (proportion + immigration-rate * (tau-0-1 * [proportion-temp] of turtle (who - 1) + tau-0+1 * [proportion-temp] of turtle (who + 1) +
              tau-1-0 * [proportion-temp] of turtle (who + column-number) + tau+1-0 *[proportion-temp] of turtle (who - column-number) +
              tau+1-1 * [proportion-temp] of turtle (who - column-number - 1) + tau+1+1 * [proportion-temp] of turtle (who - column-number + 1) +
              tau-1-1 * [proportion-temp] of turtle (who + column-number - 1) + tau-1+1 * [proportion-temp] of turtle (who + column-number + 1)))
          ]
        ]
      ]
    ]
  ]
end

to-report dispProbability [num d]
  report prop-prob * ([proportion-temp] of turtle num) * exp(-1 * d ^ 2 /(2 * sigma ^ 2)) / (2 * pi * sigma ^ 2)
end

to grow-bacteria
  ask turtles[
    set bacteria-size (bacteria-size + bacteria-size * (growth-rate-bacteria * (1 - bacteria-size / carrying-cap-bacteria) - death-rate))
  ]
  ask turtles[control-strategy]
end

to control-strategy
  ifelse global-control
  ;;Global control
  [set bacteria-size (bacteria-size + main-irrigation)]
  ;;Local control
  [ifelse who <  column-number[
    ifelse who = 0[
      set bacteria-size (bacteria-size + main-irrigation * proportion + secondary-irrigation * ([proportion-temp] of turtle column-number + [proportion-temp] of turtle 1))
      ][ifelse who = (column-number - 1)[
        set bacteria-size (bacteria-size + main-irrigation * proportion + secondary-irrigation * ([proportion-temp] of turtle (2 * column-number - 1) + [proportion-temp] of turtle (column-number - 2)))
      ][
        set bacteria-size (bacteria-size + main-irrigation * proportion + secondary-irrigation * ([proportion-temp] of turtle (who - 1) + [proportion-temp] of turtle (who + 1) + [proportion-temp] of turtle (who + column-number)))
      ]
    ]
    ][ifelse who >= (column-number * (row-number - 1))[
      ifelse who = (column-number * (row-number - 1))[
        set bacteria-size (bacteria-size + main-irrigation * proportion + secondary-irrigation * ([proportion-temp] of turtle (who + 1) + [proportion-temp] of turtle (who - column-number)))
        ][ifelse who = (column-number * row-number - 1)[
          set bacteria-size (bacteria-size + main-irrigation * proportion + secondary-irrigation * ([proportion-temp] of turtle (who - 1) + [proportion-temp] of turtle (who - column-number)))
        ][
          set bacteria-size (bacteria-size + main-irrigation * proportion + secondary-irrigation * ([proportion-temp] of turtle (who - 1) + [proportion-temp] of turtle (who + 1) + [proportion-temp] of turtle (who - column-number)))
        ]
      ]
      ][ifelse (who mod column-number) = 0[
        set bacteria-size (bacteria-size + main-irrigation * proportion + secondary-irrigation * ([proportion-temp] of turtle (who + 1) + [proportion-temp] of turtle (who + column-number) + [proportion-temp] of turtle (who - column-number)))
        ][ifelse (who mod column-number) = (column-number - 1)[
          set bacteria-size (bacteria-size + main-irrigation * proportion + secondary-irrigation * ([proportion-temp] of turtle (who - 1) + [proportion-temp] of turtle (who + column-number) + [proportion-temp] of turtle (who - column-number)))
        ][
          set bacteria-size (bacteria-size + main-irrigation * proportion + secondary-irrigation * ([proportion-temp] of turtle (who - 1) + [proportion-temp] of turtle (who + 1) + [proportion-temp] of turtle (who + column-number) + [proportion-temp] of turtle (who - column-number)))
        ]
      ]
    ]
    ]
  ]
end

to set-initial-conditions
  foreach initial-conditions[
    x -> run (word "ask turtle " (item 0 x) " [set proportion " (item 1 x) "]")
  ]
end
@#$#@#$#@
GRAPHICS-WINDOW
234
12
671
450
-1
-1
13.0
1
10
1
1
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ticks
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BUTTON
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Setup
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T
OBSERVER
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BUTTON
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Go
go
T
1
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OBSERVER
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1

SLIDER
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column-number
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row-number
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SLIDER
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SWITCH
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global-control
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PLOT
709
427
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778
Proportion of Infected Plants
Time
Proportion
0.0
4392.0
0.0
100.0
false
false
"" ""
PENS
"default" 1.0 0 -16777216 true "" "plot 100 * report-proportion / (count turtles)"

PLOT
1240
10
1792
401
Proportion of rust
Time
Proportion
0.0
4392.0
0.0
100.0
false
false
"" ""
PENS
"default" 1.0 0 -16777216 true "" "plot sum([proportion] of turtles)"

SLIDER
26
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main-irrigation
main-irrigation
0
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0.1
0.1
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NIL
HORIZONTAL

SLIDER
26
369
198
402
secondary-irrigation
secondary-irrigation
0
1
0.7
0.1
1
NIL
HORIZONTAL

PLOT
707
10
1212
409
Bacteria Population
Time
bacteria-size
0.0
10.0
0.0
20.0
true
false
"" ""
PENS
"default" 1.0 0 -16777216 true "" "plot ([bacteria-size] of turtle 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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Polygon -1 true true 195 285 210 285 210 240 240 210 195 210
Polygon -7500403 true false 276 85 285 105 302 99 294 83
Polygon -7500403 true false 219 85 210 105 193 99 201 83

square
false
0
Rectangle -7500403 true true 30 30 270 270

square 2
false
0
Rectangle -7500403 true true 30 30 270 270
Rectangle -16777216 true false 60 60 240 240

star
false
0
Polygon -7500403 true true 151 1 185 108 298 108 207 175 242 282 151 216 59 282 94 175 3 108 116 108

target
false
0
Circle -7500403 true true 0 0 300
Circle -16777216 true false 30 30 240
Circle -7500403 true true 60 60 180
Circle -16777216 true false 90 90 120
Circle -7500403 true true 120 120 60

tree
false
0
Circle -7500403 true true 118 3 94
Rectangle -6459832 true false 120 195 180 300
Circle -7500403 true true 65 21 108
Circle -7500403 true true 116 41 127
Circle -7500403 true true 45 90 120
Circle -7500403 true true 104 74 152

triangle
false
0
Polygon -7500403 true true 150 30 15 255 285 255

triangle 2
false
0
Polygon -7500403 true true 150 30 15 255 285 255
Polygon -16777216 true false 151 99 225 223 75 224

truck
false
0
Rectangle -7500403 true true 4 45 195 187
Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194
Rectangle -1 true false 195 60 195 105
Polygon -16777216 true false 238 112 252 141 219 141 218 112
Circle -16777216 true false 234 174 42
Rectangle -7500403 true true 181 185 214 194
Circle -16777216 true false 144 174 42
Circle -16777216 true false 24 174 42
Circle -7500403 false true 24 174 42
Circle -7500403 false true 144 174 42
Circle -7500403 false true 234 174 42

turtle
true
0
Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210
Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105
Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105
Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87
Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210
Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99

wheel
false
0
Circle -7500403 true true 3 3 294
Circle -16777216 true false 30 30 240
Line -7500403 true 150 285 150 15
Line -7500403 true 15 150 285 150
Circle -7500403 true true 120 120 60
Line -7500403 true 216 40 79 269
Line -7500403 true 40 84 269 221
Line -7500403 true 40 216 269 79
Line -7500403 true 84 40 221 269

wolf
false
0
Polygon -16777216 true false 253 133 245 131 245 133
Polygon -7500403 true true 2 194 13 197 30 191 38 193 38 205 20 226 20 257 27 265 38 266 40 260 31 253 31 230 60 206 68 198 75 209 66 228 65 243 82 261 84 268 100 267 103 261 77 239 79 231 100 207 98 196 119 201 143 202 160 195 166 210 172 213 173 238 167 251 160 248 154 265 169 264 178 247 186 240 198 260 200 271 217 271 219 262 207 258 195 230 192 198 210 184 227 164 242 144 259 145 284 151 277 141 293 140 299 134 297 127 273 119 270 105
Polygon -7500403 true true -1 195 14 180 36 166 40 153 53 140 82 131 134 133 159 126 188 115 227 108 236 102 238 98 268 86 269 92 281 87 269 103 269 113

x
false
0
Polygon -7500403 true true 270 75 225 30 30 225 75 270
Polygon -7500403 true true 30 75 75 30 270 225 225 270
@#$#@#$#@
NetLogo 6.0.1
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default
0.0
-0.2 0 0.0 1.0
0.0 1 1.0 0.0
0.2 0 0.0 1.0
link direction
true
0
Line -7500403 true 150 150 90 180
Line -7500403 true 150 150 210 180
@#$#@#$#@
0
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