Peanut Field Spread of Aspergillus flavus and Aflatoxin Contamination

breed [peanuts peanut]
breed [spores spore]
patches-own [soil-infected?]
peanuts-own [plant-infected? pod-count kernel-count kernel-af]

to setup
  clear-all
  setup-soil
  setup-spores

  reset-ticks
end 

to setup-soil
  ask patches [ set pcolor brown set soil-infected? FALSE]

  ;make a square field of peanut plants
  ask patches with [ abs pxcor < 13 and abs pycor < 13 ]
    [sprout-peanuts 1 [ set shape "peanut_plant"  set size .25 set pod-count  0 set kernel-af 0] ;setting up our peanut plants. Note that each plants has no pods at the beginning
  ]
end 

to setup-spores ;here each patch can be infected or not. We color it orange.
  ask n-of (infected_patches * (32 ^ 2) / 100) patches [sprout-spores 1 [set shape "aspergillus" set size 0.5 set pcolor orange]]
end 

to go
  ask peanuts [set size size + 0.005] ;allow our peanut plants to grow each tick, which represent 1 day
  infect-patches; spores infect the soil
  infect-from-patches ; the soil infects the peanut plants
  move-spores
  add_pods ;as peanuts grow, they produce pods in the soil
  infect_kernels ;kernels become infected when a plant is infected and and it's vulnerable due to environmental stress

  if ticks >= Season_length [ stop ] ; assume peanut harvest after 9-120 days
  tick
end 

to move-spores
  ask spores [
    right random 360
    forward 0.1
  ]
end 

to infect-patches
  ask patches with [ any? spores-here]
    [set pcolor orange]
end 

to infect-from-patches
; note that infection of plants is a stochastic process. However, the probability depends partly on whether pesticides are used to prevent plant disease and other pests in the first place
  ask peanuts [
    ifelse (pcolor = orange) and (pesticide-use = false) and (random 100 < 50) ;we assume plant infection is more likely if pesticides are not used.
    [
      set shape "peanut_plant_infected"
      set plant-infected?  true

    ]
    [
    if (pcolor = orange) and (pesticide-use = true) and (random 100 < 5)
      [
        set shape "peanut_plant_infected"
        set plant-infected?  true
      ]

    ]]
end 

to add_pods ;we add pods based on how many days we are into the growing season. The pods start to develop at day forty
  ask peanuts[
  (ifelse
    ticks < 40
    [set pod-count 0]
    ticks = 40
    [set pod-count 10]
    ticks mod 5 = 0
      [
        if heat-stress = true [set pod-count pod-count + 1]   ;water stressed plants will add pods more slowly
        if heat-stress = false [set pod-count pod-count + 2]
      ]
   )


               ]
  ask peanuts [set kernel-count pod-count * 2]
end 

to infect_kernels ;infection of peanut kernels depends on both use of water stress of the the plant and pesticide use. With more water stress, plants produce fewer phytolexins
                  ;and other defenses against aflatoxigenic fungi
  ask peanuts[
  if plant-infected? = true[
    (ifelse
      (heat-stress = false) and (pesticide-use = true)
      [set kernel-af 1 ]

       (heat-stress = false) and (pesticide-use = false)
      [set kernel-af  20  ]

      (heat-stress = true) and (pesticide-use = true)
      [set kernel-af 50 ]

      (heat-stress = true) and (pesticide-use = false)
      [set kernel-af 100 ]
  )]]
end