Ophiocordyceps Unilateralis Model

turtles-own [   ;Determines the variables that the ant can have.
    sick?
    sick-time
    ticks-since-here]

patches-own [  ;Determines the variables that the patches can have.
  countdown ]

globals
  [            ;This is where we define our variable
    chance-reproduce
    carrying-capacity
    plant-heal-time

]

to setup
  clear-all
  setup-constants    ;Runs the setup-constants command
  setup-turtles      ;Runs the setup-turtles command
  update-display     ;Runs the update-display command

  ask patches [      ;Sets up the "dirt" and gives all patches a random heal time for plants
    set pcolor brown
    set countdown random plant-heal-time
  ]

  ask n-of plants patches [ set pcolor green ] ;Asks random patches equal to the number of plants you've selected on the slider to become plants

  ask n-of(Initial-Infections) patches with [pcolor = green]
      [ set pcolor 12 ]                        ;Makes a percentage of the population infected, you are able to control this with the slider on the interface


  reset-ticks
end 

to setup-turtles                         ;Sets up the ants as an agent
  create-turtles number-of-ants
  [ set shape "bug"                      ;Changes the ants shape from a dot to an ant
     setxy random-xcor random-ycor       ;This creates the ants and places them randomly throughout the lattice
     set sick-time 0                     ;Makes sure that the ants do not start off infected
     set size 1.5                        ;Sets the size of the ants to be 1.5 times the size of the patches
      get-healthy ]                      ;Ensures the ants start off as healthy
end 

to get-sick                             ;This is a command to ensure the infected ants turn red
  set sick? true
  set color red
  set sick-time 0
end 

to get-healthy                          ;This is a command to ensure healthy ants turn black and don't gain the side effects of being sick
  set sick? false
  set sick-time 0
end 

to setup-constants
  set carrying-capacity 500                      ;Fixed Carrying Capacity of the model
  set chance-reproduce 0.5                       ;As there is not a functional queen, we are purely looking at foragers. To keep the population from plummiting we add a chance to reproduce
  set plant-heal-time (4 + random-float 6) * 7   ;As the model runs quite quickly, this command makes it so the heal time of the plant is converted to weeks. The process still takes 4 - 10 days but it is scaled to weeks for the sake of the model.
end 

to go
  ask turtles[                                         ;This is the checklist the ant goes through per tick, it ages, moves, and checks for infection.
    reproduce                                          ;Runs the reproduce command
    infect                                             ;Runs the infect command
    if sick? [ time-to-die ]                           ;If the ant is sick, it will run the time to die command
    if sick? [ set sick-time sick-time + 1 ]           ;If the ant is sick, starts up the command for sick time as a countdown for the time to die command

    ask turtles with [ not sick?] [                    ;If the turtle is healthy, then it just moves

      move

    ]


  ]
  ask turtles [                                                         ;This set of code is used to mimic the ant finding a plant in the wild to death grip
    if sick?[
      face min-one-of patches with [pcolor = green] [distance myself]   ;Asks the ant to face the direction of the closest green plant
      if pcolor = brown [                                               ;Asks the ant if the patch underneath is brown, if so then it must continue to move
        move ]
      if pcolor = green [                                               ;Asks the ant if the patch underneath is green, if so then it must stop and start the infect-plant command
        infect-plant]
      if pcolor = 12 [                                                  ;Forces the ant to stay stationary once the plant has turned red
        forward 0]
    ]
  ]
  ask patches with [pcolor = 12] [                                      ;Asks if the plant is infected, if so then start the heal plant command
    heal-plant]
  ;excel                                                                ;Allows for easy data collection
  tick
end 

to update-display                                                                      ;Just stops rainbow coloured ants from occuring
  ask turtles                                                                          ;Just asks the turtles what their health conditions are like. If they are healthy then they get coloured black, if sick then they are coloured red
      [set color ifelse-value sick? [ red ] [ black ] ]
end 

to Time-to-die                                                                         ;Used to kill off sick ants who haven't sucessfully completed the Death Grip
   if sick-time > (4 + random-float 6)                                                 ;This is how long it takes for the whole life cycle to occur 4-10 days. Thus if it has not successfully completed a stage in its life cycle then it shall die out
    [die]                                                                              ;Pretty self explanitory
end 

to reproduce                                                                           ;This is to stabalize the ant population, its a randomized birth rate.
  ask turtles with [not sick?] [                                                       ;Asks if the number of ants on the screen is less than the carrying capacity,
    if count turtles < carrying-capacity and random-float 250 < chance-reproduce       ;if so then all healthy ants have a chance to produce an offspring
    [ hatch 1[
      lt 45 fd 1                                                                       ;Movement pattern for the new ant
      get-healthy                                                                      ;Makes sure the new ant is healthy
      ]
    ]
  ]
end 

to move                                       ;Used to mimic ants movement
  rt random 100                               ;Right turn x amount
  lt random 100                               ;Left turn x amount
  forward 1                                   ;forward 1
end 

to infect                                               ;Infects ants that come into contact with plant
  ask turtles with [not sick?] [
    if pcolor = 12[                                     ;This asks all the turtles that are not sick if they are on an infected plant
      if random-float 100 < (10 + random-float 15)[     ;Statistical chance of being infected from the spores, this was taken from a study stating that 10 - 15% of the forager population was infected from the spores.
        get-sick                                        ;Starts the get-sick procedure
        forward 10                                      ;This is a feature added to stop the ant from being locked to the infected plant
    ]
    ]

  ]
end 

to infect-plant                                                     ;This is the code equivalent of the Death Grip
  ask one-of turtles [
    if sick?[                                                       ;This asks each of the ant if they are sick, if true then move onto the next line of code.
      if pcolor = green[                                            ;It then confirms if the patch the ant occupies is green, it cannot be red or brown as these are not viable plants
        if random-float 100 < (61.8 - (hyperparasite * 55.4)) [       ;This is the statistical chance of a proper a successful inoculation. There is a 64% chance of being successful without hyperparasites involed. If you select the hyperparasites to be in the model, it changes from a zero to a one. This allows for the subtraction of 55.4% success rate as the parasite is only has 8.6% success rate when hyperparasites are involved
            set pcolor 12]                                          ;Changes the green plant into an infected red plant
      ]
    ]
  ]
end 

to heal-plant                                ;Allows for the plant to become non contagious
  if pcolor = 12 [                           ;Asks if the patch colour is dark red
    ifelse countdown <= 0                    ;Asks if the countdown is less than or equal to zero, if true then it can run the next command
      [ set pcolor green                     ;Sets the patch color back to green
        set countdown plant-heal-time ]      ;Restarts the plant heal time to zero because it is no longer infected
      [ set countdown countdown - 1 ]        ;If the countdown was greater than zero, this command runs which just subtracts one from the countdown
  ]
end 

;to excel                                                           ;This section of the model is for data collection, It is greyed out so you don't make random excel files on your computer
  ;if ticks >= 300 [                                                ;Allows the model to run for 300 ticks prior to running the save command
    ;export-all-plots  (word "High " random-float 1.0 ".csv")       ;The premise is that this code will export the plot as a .csv file with the name "high" followed by a randomly generated number. We do this to ensure that the file is not overwritten within the folder.
    ;export-all-plots  (word "Medium " random-float 1.0 ".csv")
    ;export-all-plots  (word "Low " random-float 1.0 ".csv")
    ;export-all-plots  (word "Hyper-High " random-float 1.0 ".csv")
    ;export-all-plots  (word "Hyper-Medium " random-float 1.0 ".csv")
    ;export-all-plots  (word "Hyper-Low " random-float 1.0 ".csv")

    ;setup]                                                         ;Allows for the model to restart to insure a loop is created
;end