globals [  
   clock      ;; how many simulation step have passed
   grp-data
   dayhabitat
   color-min
   color-max
   clock-max 
   use-file ;; Choose whether to use a data file (1) or use simulated data (0)
   pred-killed ;; amount killed by the predator
   energy-killed ;; amount killed by running out of energy
   average-directed-movement
   total-directed-movement
   pred-killed-at-depth ;; vector describing how many are killed by predation at each depth
   energy-killed-at-depth ;; vector describing how many are killed by energy loss at each depth
  ]

patches-own [
    GRP  ;; habitat quality in patch
    prisk  ;; risk of predation in patch
  ]
   
breed [ fish fishy ]

 fish-own [ 
 PiI   ;; fear of predation (low pii = low fear)
 energy  ;; how much energy the fish has (function of resources gained versus used)
  ]

to make-movie

  ;; prompt user for movie location
  user-message "First, save your new movie file (choose a name ending with .mov)"
  let path user-new-file
  if not is-string? path [ stop ]  ;; stop if user cancelled

  ;; run the model
  setup
  movie-start path
  movie-grab-view
  while [ clock < clock-max ]
    [ go
      movie-grab-view ]

  ;; export the movie
  movie-close
  user-message (word "Exported movie to " path)
end

to setup
  clear-all
  set-default-shape fish "fish"
  create-fish 100 [
    set color orange
    setxy random-xcor (- 1) * (0 + random-float 25) ;; start fish in good GRP area
    ifelse(Pii-is-random)
      [set PiI random-float PiIMax] ;; high piimax is high predator fear
      [set PiI PiIMax]
    set energy (random-float .5) + .5  ;; start with a random amt. of energy 0.5 - 1
    set pred-killed 0
    set energy-killed 0
    set total-directed-movement 0
    set pred-killed-at-depth []
    set energy-killed-at-depth []

  ]
  
  setup-plot
  
  do-plot
   
  set clock 0
  set clock-max 259
  
  ask patches
      [set prisk  max-prisk * (((pycor + 25) / 25) ^ 7 )]
;;;;;;;;;;;;;;;;;;;;GRP FILE SECTION
  ;; load file with habitat information
  set use-file (file-exists? data-file-name)
  ifelse ( use-file)
    [ set grp-data[ ]
      file-open data-file-name ;; grpresized.txt is averaged down to 25 depth, grpresized-1to1.txt is on (-1,1), grpresized0to1.txt is on (0,1)
      while[ not file-at-end? ]
       [set grp-data sentence grp-data (list file-read)        ]
        user-message " GRP file loading complete"
           file-close
        set dayhabitat sublist grp-data 0 ( count patches ) 
    ] 
    [;user-message "There is no file of that name in current directory - using simulated data."
      update-fake-grp ]  

    
;; initially set up GRP
  if (use-file)
  [
  (foreach (sort patches) dayhabitat
  [ask ?1 [ set GRP ?2 ] ] )
  
    ask patches[
  ;; set the color scale in blue from GRP in patch
    if(data-file-name = "grpresized.txt" or data-file-name = "grpresized-2digits.txt")
      [ set pcolor 99 * GRP + 10.8222] ; for original GRP file/truncated GRP file
    if(data-file-name = "grpresized-1to1.txt" or data-file-name = "grpresized-1to1-2digits.txt")
      [ set pcolor 99 * GRP * 0.0255884 + 10.8222]  ;[ set pcolor 8 * ((GRP + 1) / 2) + 10]
    if(data-file-name = "grpresized0to1.txt" or data-file-name = "grpresized0to1-2digits.txt")
      [ set pcolor 99 * (GRP * 0.03343746 - 0.00784906) + 10.8222];[ set pcolor 8 * GRP + 10]
    ]
    ]
    end
    
    
;;;;;;;;;;;;;;;;;;;; END GRP FILE SECTION
 
;;______________________________________________________________________________________________________________
to go
  ifelse (clock < clock-max)
    [
    ifelse (use-file)
      [update-grp]
      [update-fake-grp]
    set average-directed-movement 0
    let numfish count turtles
    move
    ifelse (numfish != 0)
      [set average-directed-movement average-directed-movement / numfish]
      [set average-directed-movement 0]
    set total-directed-movement total-directed-movement + average-directed-movement / 260
    set clock clock + 1
    if not any? turtles
      [ stop ]               
      ]
   [stop]
   do-plot
 end 
to update-grp
  set dayhabitat sublist grp-data (clock * 26 * 7) ((clock + 1) * 26 * 7)
 ( foreach sort patches dayhabitat  [ask ?1 [ set GRP ?2 ] ] )
    ask patches[
  ;; set the color scale in blue from GRP in patch
    if(data-file-name = "grpresized.txt" or data-file-name = "grpresized-2digits.txt")
      [ set pcolor 99 * GRP + 10.8222] ; for original GRP file/truncated GRP file
    if(data-file-name = "grpresized-1to1.txt" or data-file-name = "grpresized-1to1-2digits.txt")
      [ set pcolor 99 * GRP * 0.0255884 + 10.8222] ;[ set pcolor 8 * ((GRP + 1) / 2) + 10]
    if(data-file-name = "grpresized0to1.txt" or data-file-name = "grpresized0to1-2digits.txt") 
      [ set pcolor 99 * (GRP * 0.03343746 - 0.00784906) + 10.8222];[ set pcolor 8 * GRP + 10]
    ]
     
end

to update-fake-grp
  ask patches
  [
  if( sim-function-choice = "original") [
    let py pycor * (8 / 25)
    let time-coord clock * (100 / 100)
    ;; Function approximating GRP data shape (from suitability.m)
    set GRP (exp(-((py -(4 * sin((pi / 4.5) * time-coord) - 5.25)) ^ 6) /(2 *(0.4 + 0.00025 *(time-coord - 50) ) ^ 2))) 
    ]
  if ( sim-function-choice = "happy constant day" )
   [ set GRP 0.7 ]
  if ( sim-function-choice = "bad constant day")
   [ set GRP 0.2 ]
  if ( sim-function-choice = "middle bad" )
    [set GRP .4 * (abs((pycor + 12.5) / 12.5) )]
  if ( sim-function-choice = "middle good" )
    [set GRP (1 - .4 * (abs((pycor + 12.5) / 12.5) ))]
  if ( sim-function-choice = "hypoxic day" )
    [set GRP .4 * (((pycor + 25) / 25) ^ 2 )]
  if ( sim-function-choice = "hypoxic day - extreme" )
    [set GRP .4 * (((pycor + 25) / 25) ^ 5 )]
  ]

  ask patches
   ;;set the color scale in red from GRP in patch
    [ set pcolor (GRP * 8 + 10)]
end

to move
  ask fish
  [ step  ;; random motion
    set energy (1 - 0.1) * energy ;; maybe make daily energy loss dynamic
    if (Pii-is-energy)
      [set PiI energy]
    follow-best
    if ((random-float 100) < prisk ) ;; check if fish survives area predation
    [
    set color red
    set shape "x"
    stamp
    set pred-killed pred-killed + 1  ;; fish dies due to predation
    set pred-killed-at-depth lput ycor pred-killed-at-depth

    die 
    ]
    if(energy < death-threshold)  ;; check if fish has enough energy to live
      [
      set color grey
      set shape "face sad"
      stamp
      set energy-killed energy-killed + 1 ;; fish dies due to lack of energy
      set energy-killed-at-depth lput ycor energy-killed-at-depth

      die
      ]
      
    set energy (energy + (1 - energy) * (GRP * GRP-mult)) ;; how much energy is gained
   ]
end

to follow-best
  ;move-to patch-here  ;; go to patch center
  let mypi PiI
  let my-ycor ycor
  let my-energy energy
  let p max-one-of patches [((1 - mypi) * GRP) - (mypi * prisk)] 
  if [((1 - mypi) * GRP) - (mypi * prisk)] of p > (((1 - mypi) * GRP) - (mypi * prisk)) [  ;; if p is better than current location
      face p
      let vert-displacement abs(([pycor] of p) - ycor)  ;; energy loss depends on vertical displacement alone
      set energy energy * (1 - energy-loss) ^ vert-displacement ;; lose a percentage of energy based on displacement
      set average-directed-movement (average-directed-movement + distance p) ;; for adm plot - uses total distance
      move-to p ] 
      
      ;; prevents all integral coordinates
      set xcor xcor + (random-float 1 - .5)
      let y-rand random-float 1
      ifelse (ycor - y-rand) > -25
      [set ycor ycor - y-rand]
      [set ycor -25]

end

to step   ;random motion
  rt random-float 359 ;; turn in a random direction
  fd random-steps-per-day  ;; go forward a few steps
  if ycor < -25
    [set ycor -25]
end

to do-plot
    set-current-plot "Fish Depth"
    set-current-plot-pen "Average"
    plot ((sum [ycor] of fish)/ (count fish) )
    set-current-plot-pen "Median"
    plot ((median [ycor] of fish) )
;    set-current-plot-pen "Average + SD"
;    plot ((sum [ycor] of fish)/ (count fish) + (standard-deviation[ycor] of fish))
;    set-current-plot-pen "Average - SD"
;    plot ((sum [ycor] of fish)/ (count fish) - (standard-deviation[ycor] of fish))
    
    set-current-plot "Average Daily Movement"
    set-current-plot-pen "Directed"
    plot (average-directed-movement)
    set-current-plot-pen "Random"
    plot (random-steps-per-day)
    
    set-current-plot "Depth"
    set-current-plot-pen "# fish"
    histogram [ycor] of fish    

    set-current-plot "Death vs Depth Predation"
    set-current-plot-pen "Predation"
    histogram pred-killed-at-depth

    set-current-plot "Death vs Depth Energy"
    set-current-plot-pen "Energy"
    histogram energy-killed-at-depth
    
    set-current-plot "Fish Distribution in Water Column"
    set-current-plot-pen "% Deep"
    plot (count fish with [ycor < -17]/ (count fish) )
    set-current-plot-pen "% Middle"
    plot (count fish with [ycor >= -17 AND ycor < -7]/ (count fish) )
    set-current-plot-pen "% Top"
    plot (count fish with [ycor >= -7]/ (count fish) )

end


to setup-plot
  set-current-plot "Fish Depth"
  set-plot-y-range -25 0
  
  set-current-plot "Average Daily Movement"
  
  set-current-plot "Depth"
  set-plot-y-range 0 50
  set-plot-x-range -25 0

  set-current-plot "Death vs Depth Predation"
  set-plot-y-range 0 10
  set-plot-x-range -25 0
  
  set-current-plot "Death vs Depth Energy"
  set-plot-y-range 0 50
  set-plot-x-range -25 0
  
  set-current-plot "Fish Distribution in Water Column"
  set-plot-y-range 0 1

end
@#$#@#$#@
GRAPHICS-WINDOW
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CC-WINDOW
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Command Center
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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
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OBSERVER
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MONITOR
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clock
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BUTTON
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NIL
make-movie
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OBSERVER
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PLOT
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Fish Depth
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Depth
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PENS
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TEXTBOX
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A lighter shade of red correspondes to a higher GRP (growth rate potential), i.e. better habitat quality\n\nRED (X) died due to predation.\nGREY (Skull) ran out of energy.
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SLIDER
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SLIDER
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PiIMax
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MONITOR
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Count Fish
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PLOT
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Average Daily Movement
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PENS
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Depth
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PENS
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PLOT
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Death vs Depth Predation
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Death vs Depth Energy
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PENS
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MONITOR
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GRP Loaded %
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CHOOSER
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data-file-name
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PLOT
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Fish Distribution in Water Column
Time
%
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249.0
0.0
1.0
true
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PENS
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"% Middle" 1.0 0 -13345367 true
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SWITCH
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Pii-is-random
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SWITCH
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SLIDER
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CHOOSER
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sim-function-choice
sim-function-choice
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3

@#$#@#$#@
WHAT IS IT?
-----------
This project explores a simple ecosystem made up of rabbits, grass, and weeds. The rabbits wander around randomly, and the grass and weeds grow randomly.   When a rabbit bumps into some grass or weeds, it eats the grass and gains energy. If the rabbit gains enough energy, it reproduces. If it doesn't gain enough energy, it dies.

The grass and weeds can be adjusted to grow at different rates and give the rabbits differing amounts of energy.  The model can be used to explore the competitive advantages of these variables.


HOW TO USE IT
-------------
Click the SETUP button to setup the rabbits (red), grass (green), and weeds (violet). Click the GO button to start the simulation.

The NUMBER slider controls the initial number of rabbits. The BIRTH-THRESHOLD slider sets the energy level at which the rabbits reproduce.  The GRASS-GROWTH-RATE slider controls the rate at which the grass grows.  The WEEDS-GROWTH-RATE slider controls the rate at which the weeds grow.

The model's default settings are such that at first the weeds are not present (weeds-grow-rate = 0, weeds-energy = 0).  This is so that you can look at the interaction of just rabbits and grass.  Once you have done this, you can start to add in the effect of weeds.


THINGS TO NOTICE
----------------
Watch the COUNT-RABBITS monitor and the POPULATIONS plot window to see how the rabbit population changes over time. At first, there is not enough grass for the rabbits, and many rabbits die. But that allows the grass to grow more freely, providing an abundance of food for the remaining rabbits. The rabbits gain energy and reproduce. The abundance of rabbits leads to a shortage of grass, and the cycle begins again.

The rabbit population goes through a damped oscillation, eventually stabilizing in a narrow range. The total amount of grass also oscillates, out of phase with the rabbit population.

These dual oscillations are characteristic of predator-prey systems. Such systems are usually described by a set of differential equations known as the Lotka-Volterra equations. NetLogo provides a new way of studying predatory-prey systems and other ecosystems.


THINGS TO TRY
-------------
Leaving other parameters alone, change the grass-grow-rate and let the system stabilize again.  Would you expect that there would now be more grass?  More rabbits?

Change only the birth-threshold of the rabbits.  How does this affect the steady-state levels of rabbits and grass?

With the current settings, the rabbit population goes through a damped oscillation. By changing the parameters, can you create an undamped oscillation? Or an unstable oscillation?

In the current version, each rabbit has the same birth-threshold. What would happen if each rabbit had a different birth-threshold? What if the birth-threshold of each new rabbit was slightly different from the birth-threshold of its parent? How would the values for birth-threshold evolve over time?

Now add weeds by making the sliders WEEDS-GROW-RATE the same as GRASS-GROW-RATE and WEEDS-ENERGY the same as GRASS-ENERGY.  Notice that the amount of grass and weeds is about the same.

Now make grass and weeds grow at different rates.  What happens?

What if the weeds grow at the same rate as grass, but they give less energy to the rabbits when eaten (WEEDS-ENERGY is less than GRASS-ENERGY)?

Think of other ways that two plant species might differ and try them out to see what happens to their relative populations.  For example, what if a weed could grow where there was already grass, but grass couldn't grow where there was a weed?  What if the rabbits preferred the plant that gave them the most energy?

Run the model for a bit, then suddenly change the birth-threshold to zero.  What happens?


NETLOGO FEATURES
----------------
Notice that every black patch has a random chance of growing grass or
weeds each turn, using the rule:

|    if (random-float 1000) < weeds-grow-rate and pcolor = black
|      [ set pcolor violet ]
|    if (random-float 1000) < grass-grow-rate and pcolor = black
|      [ set pcolor green ]


RELATED MODELS
--------------
Look at Wolf Sheep Predation for another interacting ecosystem with different rules.


CREDITS AND REFERENCES
----------------------
To refer to this model in academic publications, please use:  Wilensky, U. (2001).  NetLogo Rabbits Grass Weeds model.  http://ccl.northwestern.edu/netlogo/models/RabbitsGrassWeeds.  Center for Connected Learning and Computer-Based Modeling, Northwestern University, Evanston, IL.

In other publications, please use:  Copyright 2001 Uri Wilensky.  All rights reserved.  See http://ccl.northwestern.edu/netlogo/models/RabbitsGrassWeeds for terms of use.
@#$#@#$#@
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Rectangle -7500403 true true 135 165 165 270

pentagon
false
0
Polygon -7500403 true true 150 15 15 120 60 285 240 285 285 120

person
false
0
Circle -7500403 true true 110 5 80
Polygon -7500403 true true 105 90 120 195 90 285 105 300 135 300 150 225 165 300 195 300 210 285 180 195 195 90
Rectangle -7500403 true true 127 79 172 94
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
0
Rectangle -7500403 true true 135 90 165 300
Polygon -7500403 true true 135 255 90 210 45 195 75 255 135 285
Polygon -7500403 true true 165 255 210 210 255 195 225 255 165 285
Polygon -7500403 true true 135 180 90 135 45 120 75 180 135 210
Polygon -7500403 true true 165 180 165 210 225 180 255 120 210 135
Polygon -7500403 true true 135 105 90 60 45 45 75 105 135 135
Polygon -7500403 true true 165 105 165 135 225 105 255 45 210 60
Polygon -7500403 true true 135 90 120 45 150 15 180 45 165 90

rabbit
false
0
Circle -7500403 true true 76 150 148
Polygon -7500403 true true 176 164 222 113 238 56 230 0 193 38 176 91
Polygon -7500403 true true 124 164 78 113 62 56 70 0 107 38 124 91

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

@#$#@#$#@
NetLogo 4.0.4
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
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

@#$#@#$#@