PROJET_JPK_FINAL.nlogo

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;PROJET VIRUS : Justine, Praveen et Kilian;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

;; cost is a global variable
globals [ cost 
  treatment-level]

;; lifetime-patch is a patch variable
patches-own [ lifetime-patch ]

;; 2 different breeds: viruses and houses. Viruses can move and houses are motionless. The houses are here just for graphic reasons.
 
breed [ viruses virus]

breed [ houses house ]

;; lifetime is a virus variable
viruses-own [ lifetime ]

;;;;;;;;;
;;Setup;;
;;;;;;;;;

to setup
  
  clear-all
  random-seed 10005
  reset-ticks
  set treatment-level 1
  initialize
  
end

;;;;;;;;;;;;;;;;;;
;;Initialization;;
;;;;;;;;;;;;;;;;;;

to initialize
  
  let city_size 0
  
  if Size_of_the_city = " Small " [ set city_size 0 ]
  if Size_of_the_city = " Medium " [ set city_size 4 ]
  if Size_of_the_city = " Big " [ set city_size 6 ]
  
  ;; Houses are situated in green patches, black represents the "healthy" population and blue the water.
  ask patches[
    set pcolor green
    if  ((pxcor - 1) mod ( 10 - city_size )) = 0 or ((pxcor + 1) mod ( 10 - city_size )) = 0 or ((pycor - 1) mod ( 10 - city_size ) ) = 0 or ((pycor + 1) mod ( 10 - city_size )) = 0 [
     set pcolor black 
    ]
    if  (pxcor mod ( 10 - city_size )) = 0 or (pycor mod ( 10 - city_size )) = 0 [
     set pcolor blue 
    ]
  ]
  
  ;; In the beginning, one virus is created in the center. Its shape is a dot and color black.
  create-viruses 1
  ask viruses [
    setxy 0 0 
    set color black
    set shape "dot"
    set size 1
  ]
  
  ;; Houses are created randomly on green patches and their color is brown.
  let x 0
  while [x < 200] [
    let GreenPatches one-of patches with [ pcolor = green ]
    create-houses 1 [ 
      set x x + 1
      set shape "house"
      set color brown
      set size 2
      setxy [pxcor] of GreenPatches [pycor] of GreenPatches
    ] 
  ]
  
end

;;;;;;
;;GO;;
;;;;;;

to go
  
  ;; Viruses start by moving and contaminating the "healthy" population. Afterwards, the functions immunize, mutate and contagion activate themselves.
  ;; The viruses start dying after 300 ticks so that the epidemic can develop.
  ;; Once the infected population is zero, the program stops.
  tick
  ask viruses[ 
    move
    contaminate
    ]
  immunize
  mutate
  contagion
  let infected-pop ((count patches with [ pcolor = yellow ]) / (count patches with [ pcolor = yellow or pcolor = black or pcolor = white]))
  if ticks > 300[
    stop-virus
    if infected-pop = 0 [ stop ]
  ]
   
end

;;;;;;;;;;;;;;;;
;;Virus motion;;
;;;;;;;;;;;;;;;;

to move
  
  let destination one-of neighbors with [pcolor = blue  ]
  move-to destination
  
end

;;;;;;;;;;;;;;;;;;;;;;;
;;Virus contamination;;
;;;;;;;;;;;;;;;;;;;;;;;

to contaminate
  
  ;; Black turns into yellow depending on alpha. Yellow represents the "infected" population.
  ask neighbors4 [
      if pcolor = black [
       let i random-float 1
       if i <= alpha [
         set pcolor yellow
       ]  
     ] 
   ]
  
end

;;;;;;;;;;;;;;;;;;;
;;Virus contagion;;
;;;;;;;;;;;;;;;;;;;

to contagion
  
  ;; Each patch wich is contaminated may release a virus with probability beta.
  let bluePatch one-of patches with [pcolor = blue]
  if any? patches with [pcolor = yellow] [
    set bluePatch one-of patches with [pcolor = blue and count neighbors4 with [ pcolor = yellow ] > 0 ]]
  let number-of-contamined count patches with [ pcolor = yellow ]
  let t 0
  while [t < number-of-contamined ]  [  
    let i random-float 1
    if i <= beta [
      create-viruses 1 [
        setxy [pxcor] of bluePatch [pycor] of bluePatch 
        set color black 
        set shape "dot"
        set size 1]
    ]
  set t t + 1
  ]
  
end

;;;;;;;;;;;;;;;;;;;;
;;Death of a virus;;
;;;;;;;;;;;;;;;;;;;;

to stop-virus
  set treatment-level 1
  if water-treatment = " None " [ set treatment-level 1 ]
  if water-treatment = " Medium " [ set treatment-level 2 ]
  if water-treatment = " High " [ set treatment-level 3 ]
  ;; The virus dies after some time naturally ( 100 ticks ). If the water treatment level is increased, then the virus dies more quickly.
  ask viruses with [color = black] [
    set lifetime lifetime + 1
    if lifetime > (100 / (treatment-level * treatment-level)) [die]
    ]
  
end

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;Immunization of the population;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to immunize
  
  let immunity 1
  if population-prescription = " None " [ set immunity 1 ]
  if population-prescription =  " Water-bottles " [ set immunity 2 ]
  if population-prescription = " Vaccines " [ set immunity 3 ]
  
  ;; Yellow turns into white after some time. White represents the "immune" population.
  ;; This immunity has a price.
  ask patches with [ pcolor = yellow ][
    set lifetime-patch lifetime-patch + 1
    if lifetime-patch > 200 / immunity [
      set pcolor white
      set cost cost + 1 * (immunity * immunity )
      ]
  ]
  
end

;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;Mutation of the population;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;

to mutate
  
  let immunity 1
  if population-prescription = " None " [ set immunity 1 ]
  if population-prescription =  " Water-bottles " [ set immunity 2 ]
  if population-prescription = " Vaccines " [ set immunity 3 ]
  
  ;; White turns into black after some time. The population is "healthy" but not "immune" anymore.
  ask patches with [ pcolor = white ][
  set lifetime-patch lifetime-patch + 1
  if lifetime-patch > immunity * 80 [    set pcolor black
    set lifetime-patch 0
    ]
  ]
  
end

 
@#$#@#$#@
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setup
setup
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go
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Infected Population Percentage
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PLOT
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Infected Population - Time
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"" ""
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Number of Viruses
count viruses
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INPUTBOX
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alpha
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INPUTBOX
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beta
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water-treatment
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@#$#@#$#@
## 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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@#$#@#$#@
NetLogo 5.0.5
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
<experiments>
  <experiment name="experiment" repetitions="1" runMetricsEveryStep="true">
    <setup>setup</setup>
    <go>go</go>
    <timeLimit steps="10000"/>
    <metric>ticks</metric>
    <metric>((count patches with [ pcolor = yellow ]) / (count patches with [ pcolor = yellow or pcolor = black or pcolor = white]))</metric>
    <metric>count viruses</metric>
    <metric>cout</metric>
    <enumeratedValueSet variable="taille_ville">
      <value value="0"/>
      <value value="1"/>
      <value value="6"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="treatment-level">
      <value value="1"/>
      <value value="1"/>
      <value value="3"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="immunity">
      <value value="1"/>
      <value value="1"/>
      <value value="3"/>
    </enumeratedValueSet>
  </experiment>
</experiments>
@#$#@#$#@
@#$#@#$#@
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@#$#@#$#@
0
@#$#@#$#@