facia.nlogo

;~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
; GLOBAL DEFINITIONS
;~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
globals
[
  vegetation-cover
]
patches-own
[
  state
  interaction
  ps_fac
  ps_com
  ps_buf
]

;~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
; SETUP
;~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
to setup
  ;; Reset model
  clear-all
  ;; Set random seed
  if use-seed [
    random-seed seed
  ]
  ;; Set world dimensions
  resize-world (world_max_xycor * -1) world_max_xycor (world_max_xycor * -1) world_max_xycor
  set-patch-size round ((1 / mean (list world-width world-height)) * 500)
  ;; Distribute initial patch states
  setup-vegetation
  ;; Store neighborhood patchsets in patch variables
  setup-patchsets
  ;; Reset tick counter
  reset-ticks
end

to setup-vegetation
 ;; Initialize vegetation patches:
 let n_vegetation round (count patches * (VegCoverStart / 100))
 if (n_vegetation > count patches) [set n_vegetation count patches]

 ask n-of n_vegetation patches
 [
   set state 1 + random 3
   if (paint != "none") [p_paint]
 ]
 ask patches
 [
   if (paint != "none") [p_paint]
 ]
end

to p_vegetation-noise
   let noise random-float disturbance
   set noise 2 * noise - disturbance
   set state state + noise
   if (state < 0)
     [set state 0]
   if (paint != "none") [p_paint]
end

to road-disturbance
  ;; Maintain a road
  if (road)
  [
    ask patches with [pycor = 0 or pycor = 1]
    [
      set state state - road_intensity
      if state < 0 [set state 0]
    ]
  ]
end

to setup-patchsets
  ;; Calculate coordinates for radii:
  let xy_r0 patches-in-range radius_fac geometry
  let xy_r1 patches-in-range (radius_fac + buffer) geometry
  let xy_r2 patches-in-range (radius_fac + buffer + radius_com) geometry

  ;; Calculate donut coordinates from these radii:
  let xy_d0 xy_r0  ;; All coordinates from this first radius define the first donut
  let xy_d1 filter [i -> not member? i xy_r0] xy_r1  ;; Filter the list from radius 1 to remove all coordinates that are already in the list radius 0
  let xy_d2 filter [i -> not member? i xy_r1] xy_r2  ;; Filter the list from radius 2 to remove all coordinates that are already in the list radius 1

  ;; Store donuts in patch variables (ps_fac for facilitation donut, ps_buf for buffer donut and ps_com for competition donut)
  ask patches
  [
    set ps_fac patches at-points xy_d0
    set ps_buf patches at-points xy_d1
    set ps_com patches at-points xy_d2
  ]
end

to-report patches-in-range [radius geo]
  ;; This procedure calculates general coordinate offsets based on either neumann or moore geometry within a given radius
  ;; The procedure removes the center patch in the end before reporting the list of coordinate offsets
  let result []
  if (geo = "neumann-diamond") [set result [list pxcor pycor] of patches with [abs pxcor + abs pycor <= radius]]
  if (geo = "moore-square") [set result [list pxcor pycor] of patches with [abs pxcor <= radius and abs pycor <= radius]]
  report remove [0 0] result
end


;~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
; GO
;~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
to go

  ask patches
  [
    ;; Calculate facilitation and competition values from stored neighborhoods:
    let fac sum [state * f] of ps_fac
    ifelse (fac = 0) [
      set state 0 ;; dies w/o vegetation around
    ][
      let buf sum [state * b] of ps_buf
      let com sum [state * c] of ps_com
      ;; Sum and scale interactions:
      set interaction (fac + buf - com)
      ;; Scale interaction to range -1..1 and shift this patches state after interaction
      set state state + ifelse-value (interaction > U) [U][ifelse-value (interaction < L) [L][interaction]]
    ]
    ;; add random noise
    p_vegetation-noise
    ;; Check state caps:
    set state ifelse-value (state < 0) [0][ifelse-value (state > 3) [3][state]]
    ;; Paint patches:
    if (paint != "none") [p_paint]
  ]
  road-disturbance
  ;; Increase tick counter:
  tick
end

to-report calc-vegetation-cover
  let vegetation-cells count patches with [state > 1]
  let n-cells count patches
  let veg-cover vegetation-cells / n-cells
  set vegetation-cover veg-cover
  report veg-cover
end

to p_paint  ;; patch procedure
  if (paint = "vegetation")
  [
    set pcolor ifelse-value (state < 1) [white][scale-color black (state * 10) 40 0]
  ]
  if (paint = "interaction")
  [
    set pcolor ifelse-value (interaction = 0) [white][ifelse-value (interaction > 0) [scale-color red (interaction) 200 0][scale-color blue ( -1 * interaction) 200 0]]
  ]
end


to paint_donuts
  ;; Procedure to visualize the three donuts:
  ask one-of patches
  [
    set pcolor blue
    ask ps_com [set pcolor red]
    ask ps_buf [set pcolor orange]
    ask ps_fac [set pcolor yellow]
  ]
end

to paint_patches
  ;; Procedure to repain all patches
  ask patches
  [
    p_paint
  ]
end
@#$#@#$#@
GRAPHICS-WINDOW
355
45
873
564
-1
-1
10.0
1
10
1
1
1
0
1
1
1
-25
25
-25
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1
1
1
ticks
30.0

BUTTON
5
30
170
63
NIL
setup
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
5
100
85
133
go once
go
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

INPUTBOX
108
567
158
627
c
1.0
1
0
Number

INPUTBOX
59
567
109
627
b
0.0
1
0
Number

INPUTBOX
10
630
60
690
L
-1.0
1
0
Number

INPUTBOX
60
630
110
690
U
1.0
1
0
Number

BUTTON
5
65
170
98
go loop
go
T
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

CHOOSER
5
155
170
200
paint
paint
"none" "vegetation" "interaction"
1

CHOOSER
5
385
175
430
geometry
geometry
"neumann-diamond" "moore-square"
1

SLIDER
5
510
175
543
radius_com
radius_com
0
5
2.0
1
1
NIL
HORIZONTAL

SLIDER
5
440
175
473
radius_fac
radius_fac
0
5
2.0
1
1
NIL
HORIZONTAL

BUTTON
85
100
170
133
paint_donuts
paint_donuts
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

SLIDER
5
290
175
323
world_max_xycor
world_max_xycor
10
500
25.0
1
1
NIL
HORIZONTAL

SLIDER
5
325
175
358
VegCoverStart
VegCoverStart
0
100
0.0
1
1
NIL
HORIZONTAL

TEXTBOX
10
10
160
28
Control Model
11
0.0
1

TEXTBOX
10
210
160
228
Setup Parameter
11
0.0
1

TEXTBOX
10
140
160
158
Output
11
0.0
1

TEXTBOX
5
365
155
383
Radius Parameter
11
0.0
1

TEXTBOX
10
550
160
568
Interaction Parameter
11
0.0
1

SLIDER
5
475
175
508
buffer
buffer
0
5
1.0
1
1
NIL
HORIZONTAL

BUTTON
355
10
410
43
zoom
set-patch-size patch-size + 1
NIL
1
T
OBSERVER
NIL
+
NIL
NIL
1

BUTTON
410
10
465
43
zoom
set-patch-size patch-size - 1
NIL
1
T
OBSERVER
NIL
-
NIL
NIL
1

TEXTBOX
190
465
305
561
INTERACTION MATRIX \n       -a -a -a -a -a \n       -a  b  b  b -a \n       -a  b  *  b -a \n       -a  b  b  b -a \n       -a -a -a -a -a 
10
14.0
1

TEXTBOX
180
155
330
200
Choose paint procedure:\n- vegetation/non-vegetation map\n- facilitation/competition map
10
0.0
1

TEXTBOX
180
245
330
281
Choose random number generator seed (switch-off for random seed)\n
10
0.0
1

TEXTBOX
180
300
310
318
Set world size
10
0.0
1

TEXTBOX
180
335
330
353
Set initial vegetation cover
10
0.0
1

TEXTBOX
180
380
330
431
Set type of neighborhood geometry:\n- moore -> square shaped\n- neumann -> diamond shaped
10
0.0
1

TEXTBOX
180
450
330
468
Define radii for interactions:
10
0.0
1

TEXTBOX
170
570
330
664
Define interaction parameter:\nf = facilitation factor\nb = buffer factor\nc = competition factor\nL = lower limit of state changes\nU = upper limit of state changes
10
0.0
1

SLIDER
175
65
347
98
disturbance
disturbance
0
3
1.0

.1
1
NIL
HORIZONTAL

INPUTBOX
5
225
55
285
seed
9.0
1
0
Number

SWITCH
55
250
172
283
use-seed
use-seed
1
1
-1000

SWITCH
10
705
113
738
road
road
1
1
-1000

SLIDER
10
745
182
778
road_intensity
road_intensity
0
3
1.0
.1
1
NIL
HORIZONTAL

INPUTBOX
10
567
60
627
f
4.5

1
0
Number

@#$#@#$#@
## 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)
@#$#@#$#@
default
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airplane
true
0
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arrow
true
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box
false
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bug
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butterfly
true
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car
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circle
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Circle -7500403 true true 0 0 300

circle 2
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cow
false
0
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cylinder
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dot
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face happy
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face neutral
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Circle -16777216 true false 60 75 60
Circle -16777216 true false 180 75 60
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face sad
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Circle -16777216 true false 180 75 60
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fish
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Circle -16777216 true false 215 106 30

flag
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Polygon -7500403 true true 90 150 270 90 90 30
Line -7500403 true 75 135 90 135
Line -7500403 true 75 45 90 45

flower
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Circle -7500403 true true 130 147 38
Circle -7500403 true true 192 85 38
Circle -7500403 true true 85 40 38
Circle -7500403 true true 177 40 38
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Circle -16777216 true false 113 68 74
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house
false
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leaf
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line
true
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line half
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pentagon
false
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person
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Polygon -7500403 true true 195 90 240 150 225 180 165 105
Polygon -7500403 true true 105 90 60 150 75 180 135 105

plant
false
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Polygon -7500403 true true 135 255 90 210 45 195 75 255 135 285
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Polygon -7500403 true true 135 105 90 60 45 45 75 105 135 135
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sheep
false
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Circle -7500403 true false 214 72 67
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square
false
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square 2
false
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star
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target
false
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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
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truck
false
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Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194
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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
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0
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wheel
false
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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
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x
false
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Polygon -7500403 true true 30 75 75 30 270 225 225 270
@#$#@#$#@
NetLogo 6.1.1
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
<experiments>
  <experiment name="ParameterScan" repetitions="1" runMetricsEveryStep="false">
    <setup>setup</setup>
    <go>go</go>
    <final>export-view (word "parasweep_"paint "-" a "-" b "-" radius_com "-" radius_fac "-" buffer "-" geometry "-" VegCoverStart "-" L "-" seed "-" U "-" radius_fac "-" c".png")
set paint "interaction"
paint_patches
export-view (word "parasweep_"paint "-" a "-" b "-" radius_com "-" radius_fac "-" buffer "-" geometry "-" VegCoverStart "-" L "-" seed "-" U "-" radius_fac "-" c".png")</final>
    <timeLimit steps="50"/>
    <enumeratedValueSet variable="c">
      <value value="0.4"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="geometry">
      <value value="&quot;moore-square&quot;"/>
      <value value="&quot;neumann-diamond&quot;"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="world_max_xycor">
      <value value="50"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="VegCoverStart">
      <value value="15"/>
    </enumeratedValueSet>
    <steppedValueSet variable="buffer" first="0" step="1" last="3"/>
    <enumeratedValueSet variable="U">
      <value value="1"/>
    </enumeratedValueSet>
    <steppedValueSet variable="radius_com" first="0" step="1" last="3"/>
    <enumeratedValueSet variable="seed">
      <value value="1"/>
    </enumeratedValueSet>
    <steppedValueSet variable="radius_fac" first="0" step="1" last="3"/>
    <enumeratedValueSet variable="paint">
      <value value="&quot;vegetation&quot;"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="a">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="L">
      <value value="-1"/>
    </enumeratedValueSet>
    <steppedValueSet variable="b" first="0.3" step="0.3" last="10.8"/>
  </experiment>
  <experiment name="FCR" repetitions="1" runMetricsEveryStep="false">
    <setup>setup</setup>
    <go>go</go>
    <final>export-view (word vegetation-cover "-parasweep_"paint "-"  a "-" b "-" radius_com "-" radius_fac "-" buffer "-" geometry "-" VegCoverStart "-" L "-" seed "-" U "-" radius_fac".png")
set paint "interaction"
paint_patches
export-view (word "parasweep_"paint "-"  vegetation-cover "-" a "-" b "-" radius_com "-" radius_fac "-" buffer "-" geometry "-" VegCoverStart "-" L "-" seed "-" U "-" radius_fac".png")</final>
    <timeLimit steps="350"/>
    <metric>calc-vegetation-cover</metric>
    <enumeratedValueSet variable="geometry">
      <value value="&quot;moore-square&quot;"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="world_max_xycor">
      <value value="50"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="VegCoverStart">
      <value value="0"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="buffer">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="radius_com">
      <value value="2"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="radius_fac">
      <value value="2"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="U">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="L">
      <value value="-1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="seed">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="paint">
      <value value="&quot;vegetation&quot;"/>
    </enumeratedValueSet>
    <steppedValueSet variable="facilitation-competition-ratio" first="1" step="0.01" last="5"/>
  </experiment>
  <experiment name="FCR-detailed" repetitions="1" runMetricsEveryStep="false">
    <setup>setup</setup>
    <go>go</go>
    <final>export-view (word vegetation-cover "-parasweep_"paint "-"  a "-" b "-" radius_com "-" radius_fac "-" buffer "-" geometry "-" VegCoverStart "-" L "-" seed "-" U "-" radius_fac".png")
set paint "interaction"
paint_patches
export-view (word "parasweep_"paint "-"  vegetation-cover "-" a "-" b "-" radius_com "-" radius_fac "-" buffer "-" geometry "-" VegCoverStart "-" L "-" seed "-" U "-" radius_fac".png")</final>
    <timeLimit steps="350"/>
    <metric>calc-vegetation-cover</metric>
    <enumeratedValueSet variable="geometry">
      <value value="&quot;moore-square&quot;"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="world_max_xycor">
      <value value="50"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="VegCoverStart">
      <value value="0"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="buffer">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="radius_com">
      <value value="2"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="radius_fac">
      <value value="2"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="U">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="L">
      <value value="-1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="seed">
      <value value="5"/>
      <value value="6"/>
      <value value="7"/>
      <value value="8"/>
      <value value="9"/>
      <value value="10"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="paint">
      <value value="&quot;vegetation&quot;"/>
    </enumeratedValueSet>
    <steppedValueSet variable="facilitation-competition-ratio" first="4.68" step="0.01" last="4.72"/>
  </experiment>
</experiments>
@#$#@#$#@
@#$#@#$#@
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
@#$#@#$#@
1
@#$#@#$#@