Microbial Community Assembly

turtles-own [hatch-count]

to setup
  clear-all
  ;; create 10 early arrival turtles on the left side of the substrate (Green Species)
  species-arrival 10 -15 0 56

  ; Add any additional setup code here
  reset-ticks
end 

to go
  ;; add late arrival species if time has reached the desired number of ticks
  if ticks = late-arrival-interval [

    ;; create 10 late arrivals on the right side of the substrate (Blue species)
    species-arrival 10 0 15 84

    ;; create 10 late arrivals on the upper side of the substrate (Yellow species)
    species-arrival 10 15 0 44

    ;; create 10 late arrivals on the upper side of the substrate (Pink species)
    species-arrival 10 0 -15 16
  ]


 fight-or-not

 ;; Replicate all species
 replicate 84 0.5
 replicate 44 0.9
 replicate 16 0.5
 replicate 56 replication-rate-green


  let irreproducible-turtles turtles with [hatch-count = 4]
  ask irreproducible-turtles [
    set color gray
  ]


 tick
end 

;; Replicates turtles based on the replication rate. It stops hatching once a turtle has hatched 2 generations

to replicate [color-code replication-rate]
  ;; Calculate the number of replicating turtles based on the replication rate
  let replicating-turtles turtles with [color = color-code and hatch-count < 4 ]
  let replicating-turtle-count floor (count replicating-turtles * replication-rate)
  let selected-turtles n-of replicating-turtle-count replicating-turtles
  ask selected-turtles [
    fd 1
    hatch 1 [
      ; amplification
      rt random-float 360
      fd 1
    ]
    set hatch-count hatch-count + 1
  ]
end 


;; Function initializes 10 turtles in a circular shape with varying color and position

to species-arrival [num-turtles xposition yposition color-code]

  create-turtles num-turtles [
    let radius 0.5 ; Adjust the radius of the circle
    let angle (360 / num-turtles * who) ; Calculate the angle for each turtle

    ; Calculate the x and y coordinates based on the angle and radius
    let new-xcor radius * cos(angle)
    let new-ycor radius * sin(angle)

    setxy (xposition + new-xcor) (yposition + new-ycor)

    ;; Appearance of the species
    set color color-code
    set shape "circle"
    set size 0.5
    set hatch-count 0
  ]
end 

;; Kills an opponent bacteria if it enters a space dominanted by one of the species

to fight-or-not
  ask turtles [
    let neighborhood turtles in-radius 0.5
    let yellow-neighbors count neighborhood with [color = 44]
    let green-neighbors count neighborhood with [color = 56]
    let blue-neighbors count neighborhood with [color = 84]
    let pink-neighbors count neighborhood with [color = 16]

    ;; Check for blue neighborhood
    if color != 84 and blue-neighbors > 0 and (blue-neighbors / count neighborhood) > 0.5 [
      let death? random-float 1 < 0.9

      if death? [
        set color white
        die
      ]
    ]

    ;; Check for green neighborhood
    if color != 56 and green-neighbors > 0 and (green-neighbors / count neighborhood) > 0.5 [
      let death? random-float 1 < antagonistic-behavior

      if death? [
        set color white
        die
      ]
    ]

    ;; Check for yellow neighborhood
    if color != 44 and yellow-neighbors > 0 and (yellow-neighbors / count neighborhood) > 0.5 [
      let death? random-float 1 < 0.5

      if death? [
        set color white
        die
      ]
    ]

    ;; Check for pink neighborhood
    if color != 16 and pink-neighbors > 0 and (pink-neighbors / count neighborhood) > 0.5 [
      let death? random-float 1 < 0.5

      if death? [
        set color white
        die
      ]
    ]
  ]
end