; Neture - a NetLogo model that simulates how Nature works
;
; Equations in usage in the model are all taken from: 
; G.B. West, J.M. Brwon & B.J. Enquist (2001): A genereral model for ontogenetic growth. Nature 413, pp. 628-631
; For translation of concepts: 
; WBE (2001) = Neture
; B o        = basic_energy_input (average of mammalian species: 0.37 W/g^3/4, from 1; plant cells: 0.01147 W/g^3/4, from 3; B o = a x E c / m c;
;              bacteria: 0.0166 W/g^3/4, from 3)
;
; E c        = cellular_energy_content (mammalian tissue: 7 x 10^6 J / kg => 0.000021 J, from 1; plant tissue: 19.5 x 10^6 J / kg => 0.0001638, from 2;
;              bacterium: assuming m c / E c = const, 6.25 x 10^-10 / 3 x 10^-9 x 7 x 10^6 J / kg = 1.458 x 10^6 J / kg => 0.00000091146)
;
; m c        = cellular_mass (mammalian cell: 3 x 10^-9 g, from 1; plant cell: assuming m c / E c = cont, 19.5/7 x 3 x 10^-9 = 8.4 x 10^-9 g;
;              bacterium (E.coli): 6.25 x 10^-10 g, from 4)  
;
; M          = maximum_mass
;
; References: 
; 1 = G.B. West, J.M. Brwon & B.J. Enquist (2001): A genereral model for ontogenetic growth. Nature 413, pp. 628-631
; 2 = W. Larcher (2003): Physiological plant ecology. Springer
; 3 = J.F. Gilloly et al. (2001): Effects of size and temerperature on metabolic rate. Science 293, pp. 2248-2251 
; 4 = G. Elert: The Physics Factbook: Mass of a bacterium. http://hypertextbook.com/facts/2003/LouisSiu.shtml 

globals 
  [ time 
    color_list
    
    ; world-related
    ; energy
    total_energy_input
    unused_energy_input
    total_energy_producer_growth
    total_energy_decomposer_growth
    total_energy_in_producer_mass
    total_energy_in_decomposer_mass 
    total_energy_in_organic_matter
    total_energy_output_producer_maintenance
    total_energy_output_decomposer_maintenance
    total_energy_output_decomposer_movement
    
    total_mass_producers
    total_mass_decomposers
    total_organic_matter
    
     ; species-related
    mutation
    
    ; producer-related
    producersInserted?
    number_producer_species
    boundaries_birth_mass_producers
    boundaries_generative_fraction_producers
    boundaries_maximum_mass_producers
    boundaries_seed_dormancy_producers
    boundaries_germination_probability_producers
    
    ; decomposer-related
    decomposersInserted?
    number_decomposer_species
    boundaries_gene_transfer_probability_decomposers
    boundaries_movement/maintenance_ratio_decomposers
    boundaries_spore_metabolic_fraction_decomposers 
  ]

; producers take up energy from the patches, 
; they use energy for their metabolism, 
; they do not move, except for the time step
; following reproduction, moving producers is passive and not associated with energy cost
breed [ producers producer ]

; decomposers take up energy from the organic matter stored in the patches (i.e. mass of dead producers, consumers or dceomposers 
; they use energy for maintenance, movement and growth
breed [ decomposers decomposer ]

patches-own [ penergy usable_penergy penergy_change organic_matter mean_Ec/Mc_ratio ]

turtles-own 
  [ energy_for_maintenance energy_for_movement energy_for_growth 
    mass 
    birth_mass min_birth_mass max_birth_mass 
    maximum_mass min_maximum_mass max_maximum_mass
    generative_fraction min_generative_fraction max_generative_fraction 
    generative_mass no_seeds
    cellular_mass cellular_energy_content basic_energy_input 
  ]

producers-own 
  [ producer_species
    isSeed?
    time_in_seedbank
    seed_dormancy min_seed_dormancy max_seed_dormancy
    germination_probability min_germination_probability max_germination_probability  
  ]

decomposers-own 
  [ decomposer_species 
    isSpore?
    gene_transfer_probability min_gene_transfer_probability max_gene_transfer_probability
    movement/maintenance_ratio min_movement/maintenance_ratio max_movement/maintenance_ratio
    spore_metabolic_fraction min_spore_metabolic_fraction max_spore_metabolic_fraction
  ]

;===============================================================================================================

; setup procedures: 

to setup 
  ca
  setup-global-lists
  setup-patches     
  set mutation species_range  
  set producersInserted? false
  set decomposersInserted? false
  set time 0
end

to setup-global-lists
  set color_list (list (0) (15))
  repeat 1000 
    [ let new_color 10 * random 12 + 15 ; pure colors, not black
      set color_list lput new_color color_list
    ]
  set boundaries_birth_mass_producers 
     setup-species-boundaries birth_mass_new_producers min_birth_mass_producers max_birth_mass_producers
  set boundaries_birth_mass_producers fput min_birth_mass_producers boundaries_birth_mass_producers
  set boundaries_birth_mass_producers lput max_birth_mass_producers boundaries_birth_mass_producers
  set boundaries_generative_fraction_producers 
     setup-species-boundaries generative_fraction_new_producers min_generative_fraction_producers max_generative_fraction_producers
  set boundaries_generative_fraction_producers fput min_generative_fraction_producers boundaries_generative_fraction_producers
  set boundaries_generative_fraction_producers lput max_generative_fraction_producers boundaries_generative_fraction_producers
  set boundaries_maximum_mass_producers 
     setup-species-boundaries maximum_mass_new_producers min_maximum_mass_producers max_maximum_mass_producers 
  set boundaries_maximum_mass_producers fput min_maximum_mass_producers boundaries_maximum_mass_producers
  set boundaries_maximum_mass_producers lput max_maximum_mass_producers boundaries_maximum_mass_producers
  set boundaries_seed_dormancy_producers 
     setup-species-boundaries seed_dormancy_new_producers min_seed_dormancy_producers max_seed_dormancy_producers
  set boundaries_seed_dormancy_producers fput min_seed_dormancy_producers boundaries_seed_dormancy_producers
  set boundaries_seed_dormancy_producers lput max_seed_dormancy_producers boundaries_seed_dormancy_producers
  set boundaries_germination_probability_producers 
     setup-species-boundaries germination_probability_new_producers min_germination_probability_producers max_germination_probability_producers
  set boundaries_germination_probability_producers fput min_germination_probability_producers boundaries_germination_probability_producers
  set boundaries_germination_probability_producers lput max_germination_probability_producers boundaries_germination_probability_producers
  
  set boundaries_gene_transfer_probability_decomposers  
     setup-species-boundaries gene_transfer_probability_new_decomposers 
       min_gene_transfer_probability_decomposers max_gene_transfer_probability_decomposers
  set boundaries_gene_transfer_probability_decomposers 
       fput min_gene_transfer_probability_decomposers boundaries_gene_transfer_probability_decomposers
  set boundaries_gene_transfer_probability_decomposers 
       lput max_gene_transfer_probability_decomposers boundaries_gene_transfer_probability_decomposers
  set boundaries_movement/maintenance_ratio_decomposers  
     setup-species-boundaries movement/maintenance_ratio_new_decomposers 
       min_movement/maintenance_ratio_decomposers max_movement/maintenance_ratio_decomposers
  set boundaries_movement/maintenance_ratio_decomposers 
       fput min_movement/maintenance_ratio_decomposers boundaries_movement/maintenance_ratio_decomposers
  set boundaries_movement/maintenance_ratio_decomposers 
       lput max_movement/maintenance_ratio_decomposers boundaries_movement/maintenance_ratio_decomposers 
  set boundaries_spore_metabolic_fraction_decomposers  
     setup-species-boundaries spore_metabolic_fraction_new_decomposers 
       min_spore_metabolic_fraction_decomposers max_spore_metabolic_fraction_decomposers
  set boundaries_spore_metabolic_fraction_decomposers 
       fput min_spore_metabolic_fraction_decomposers boundaries_spore_metabolic_fraction_decomposers
  set boundaries_spore_metabolic_fraction_decomposers 
       lput max_spore_metabolic_fraction_decomposers boundaries_spore_metabolic_fraction_decomposers 
end 

to setup-patches 
  ask patches 
    [ set penergy (random 100)]
  repeat smoothness [ diffuse penergy 1 ]
  rescale
  ask patches 
    [ set usable_penergy penergy * penergy_multiplicator
      set organic_matter 1E-3 ; arbitrary low, just  to fill in some amount
      set mean_Ec/Mc_ratio 19500 ; initially producer-specific
    ]
  color-landscape
end

;===============================================================================================================

; go

to go
   tick
   
   ; patch procedures
   if changing-landscape? 
    [ diffuse penergy_change 1 ; this will diffuse "smoothness" number of times before the fitness is changed.
      if time > smoothness [update-landscape set time 0 ]
      set time time + 1 
    ]
   ask patches 
    [ set usable_penergy penergy * penergy_multiplicator
    ]
   set total_energy_input sum [usable_penergy] of patches
   
  ; prducer procedures
  if producersInserted?
    [ 
      ifelse (showProducers? = true) 
       [ ask producers with [hidden? = true]
          [show-turtle]
       ]
       [ ask producers with [hidden? = false]
          [hide-turtle]
       ]
        
     germinate-seeds
     take-up-usable-penergy
     set unused_energy_input sum [usable_penergy] of patches
     set total_energy_output_producer_maintenance sum [energy_for_maintenance] of producers
     set total_energy_producer_growth sum [energy_for_growth] of producers
     maintain-producers
     grow-producers
     reproduce-producers
     set total_mass_producers sum [mass] of producers
     set total_energy_in_producer_mass sum [mass / cellular_mass * cellular_energy_content] of producers
   ]
    
    
  ; decomposer_procedures
  if decomposersInserted?
    [ ifelse (showDecomposers? = true) 
        [ ask decomposers with [hidden? = true]
          [show-turtle]
        ]
        [ ask decomposers with [hidden? = false]
          [hide-turtle]
        ]
      decompose-organic-matter
      set total_energy_output_decomposer_maintenance sum [energy_for_maintenance] of decomposers
      set total_energy_output_decomposer_movement sum [energy_for_movement] of decomposers
      set total_energy_decomposer_growth sum [energy_for_growth] of decomposers
      maintain-decomposers
      move-decomposers
      transfer-genes
      grow-decomposers
      divide-decomposers
      set total_mass_decomposers sum [mass] of decomposers
      set total_energy_in_decomposer_mass sum [mass / cellular_mass * cellular_energy_content] of decomposers
    ]
    
  set total_energy_in_organic_matter sum [organic_matter * mean_Ec/Mc_ratio] of patches
  set total_organic_matter sum [organic_matter] of patches
  
  color-landscape
  do-plots
end

;===============================================================================================================

; patch procedures

to rescale
   let highest max [ penergy ] of patches
   let lowest min [ penergy ] of patches
   ifelse (highest - lowest) = 0 
      [ask patches [set penergy 50
          set usable_penergy penergy * penergy_multiplicator] ]
      [ask patches [ set penergy range * (penergy - lowest) / (highest - lowest) + (99 - range) / 2
          set usable_penergy penergy * penergy_multiplicator] ]
end

to update-landscape 
  ask patches [set penergy penergy + penergy_change
               set usable_penergy penergy * penergy_multiplicator
               set penergy_change (random landscape-change-rate) ]
  rescale
end

to color-landscape
   ask patches 
     [ if patch_color = "showEnergy?"
         [ set pcolor scale-color green penergy 0 100]
       if patch_color = "showUsableEnergy?"  
         [ set  pcolor scale-color blue usable_penergy 0 (100 * penergy_multiplicator) ]
       if patch_color = "showOrganicMatter?"
         [ set pcolor scale-color yellow organic_matter 0 1E3 ]
     ]  
end

;===============================================================================================================

; general turtle procedures

to set-dead
  set mean_Ec/Mc_ratio (organic_matter * mean_Ec/Mc_ratio + mass * cellular_energy_content / cellular_mass) / (organic_matter + mass)
  set organic_matter organic_matter + mass
  die
end

to-report setup-species-boundaries [ value lower_boundary upper_boundary]
  let max_value (2 * value * 1 / (2 - species_range / 100))
  let min_value (2 * value - max_value)
  let boundary_list list (min_value) (max_value)
  while [min_value > lower_boundary] 
    [ set min_value min_value * (1 - species_range / 100)
      set boundary_list fput min_value boundary_list
    ]
  while [max_value < upper_boundary]
    [ set max_value max_value / (1 - species_range / 100)
      set boundary_list lput max_value boundary_list
    ]
  set boundary_list but-first boundary_list
  set boundary_list but-last boundary_list
  report boundary_list
end

to-report find-min/max-boundary [value boundary_list]
  let i 0
  let boundary item 0 boundary_list
  while [boundary < value]
    [ set i i + 1
      set boundary item i boundary_list
    ]
  let min/max list (item (i - 1) boundary_list) (item i boundary_list)  
  report min/max   
end

;===============================================================================================================

; producer procedures:

to insert-producers
  setup-producers number_producers xcor_producers ycor_producers
  set producersInserted? true
end

to setup-producers [no_producers i j]
  create-producers no_producers
    [ set shape "triangle 3"
      set size 0.3
      setxy i j
      set isSeed? false ; at the beginning seeds germinate immediately
      set birth_mass birth_mass_new_producers 
      set mass birth_mass
      set generative_fraction generative_fraction_new_producers
      set maximum_mass maximum_mass_new_producers
      set seed_dormancy seed_dormancy_new_producers
      set germination_probability germination_probability_new_producers
      set basic_energy_input 0.01147 * 60 * 60 * 24 ; assuming a time step of 1 d, the original W/g^3/4 have to be adjusted (s -> d)
      set cellular_energy_content  0.0001638
      set cellular_mass 8.4 * 10 ^ -9
      find-producer-min/max
      set producer_species find-my-producer-species 
        min_birth_mass max_birth_mass
        min_generative_fraction max_generative_fraction
        min_maximum_mass max_maximum_mass
        min_seed_dormancy max_seed_dormancy
        min_germination_probability max_germination_probability
      set color item producer_species color_list
    ]
end

to take-up-usable-penergy
  ask producers 
    [ set energy_for_maintenance 0
      let cellular_metabolic_rate basic_energy_input * cellular_mass / maximum_mass ^ (1 / 4)
      let no_of_cells mass / cellular_mass
      let maintenance_energy no_of_cells * cellular_metabolic_rate
      ifelse usable_penergy >= maintenance_energy
        [ set usable_penergy usable_penergy - maintenance_energy
          set energy_for_maintenance maintenance_energy  
        ]
        [ set-dead
        ]
      if mass < generative_fraction / 100 * maximum_mass
         [ set energy_for_growth 0 ]
      let a basic_energy_input * cellular_mass / cellular_energy_content
      let delta_mass a * mass ^ (3 / 4) * (1 - (mass / maximum_mass) ^ (1 / 4)) 
      let delta_no_of_cells delta_mass / cellular_mass
      let growth_energy delta_no_of_cells * cellular_energy_content
      if usable_penergy >= growth_energy
        [ set usable_penergy usable_penergy - growth_energy
          set energy_for_growth energy_for_growth + growth_energy
        ]
    ]
end

to maintain-producers
  ask producers
   [ set energy_for_maintenance 0 
   ]
end

to grow-producers 
  ask producers 
    [ if (mass < generative_fraction / 100 * maximum_mass and energy_for_growth > 0)
        [ let a basic_energy_input * cellular_mass / cellular_energy_content
          let delta_mass a * mass ^ (3 / 4) * (1 - ( mass / maximum_mass) ^ (1 / 4)) 
          set mass mass + delta_mass
        ]
    ]
end

to reproduce-producers
  ask producers with [isSeed? = false]
    [ if mass >= generative_fraction / 100 * maximum_mass
      [let possible_mating_partners other producers with [producer_species = [producer_species] of myself
          and distance myself <= pollination_range and mass >= generative_fraction / 100 * maximum_mass and energy_for_growth > 0]
       let mother_plant one-of possible_mating_partners  
       if is-producer? mother_plant ; and not nobody
        [ let father_birth_mass birth_mass
          let father_generative_fraction generative_fraction
          let father_maximum_mass maximum_mass
          let father_seed_dormancy seed_dormancy
          let father_germination_probability germination_probability
          ask mother_plant 
           [ let a basic_energy_input * cellular_mass / cellular_energy_content
             let delta_mass a * (mass + generative_mass) ^ (3 / 4) * (1 - ((mass + generative_mass) / maximum_mass) ^ (1 / 4)) 
             set generative_mass generative_mass + delta_mass
             let no_offspring 0 
             while [ generative_mass >= (no_seeds + 1) * birth_mass ]
               [ set no_seeds no_seeds + 1 
                 set no_offspring no_offspring + 1 
               ]
             if no_offspring > 0
               [ let delta_no_of_cells no_offspring * birth_mass / cellular_mass
                 let growth_energy delta_no_of_cells * cellular_energy_content
                 set energy_for_growth energy_for_growth + growth_energy
                 let mass_dependent_dispersal (log maximum_mass 10)
                 let seed_dependent_dispersal (log birth_mass 10)
                 hatch no_offspring 
                 [ set isSeed? true
                   set shape "square 3"
                   set size 0.2
                   set mass birth_mass ; mass at birth of mother plant
                   set generative_mass 0 ; reset
                   set no_seeds 0 ; reset
                   set birth_mass recombine birth_mass father_birth_mass
                   set birth_mass mutate birth_mass min_birth_mass_producers max_birth_mass_producers
                   set generative_fraction recombine generative_fraction father_generative_fraction
                   set generative_fraction mutate generative_fraction min_generative_fraction_producers max_generative_fraction_producers
                   set maximum_mass recombine maximum_mass father_maximum_mass
                   set maximum_mass mutate maximum_mass min_maximum_mass_producers max_maximum_mass_producers
                   set seed_dormancy recombine seed_dormancy father_seed_dormancy
                   set seed_dormancy mutate seed_dormancy min_seed_dormancy_producers max_seed_dormancy_producers
                   set germination_probability recombine germination_probability father_germination_probability
                   set germination_probability mutate germination_probability min_germination_probability_producers max_germination_probability_producers
                   
                   find-producer-min/max
                   set producer_species find-my-producer-species 
                     min_birth_mass max_birth_mass
                     min_generative_fraction max_generative_fraction
                     min_maximum_mass max_maximum_mass
                     min_seed_dormancy max_seed_dormancy
                     min_germination_probability max_germination_probability
                   set color item producer_species color_list 
                   rt random 360
                   jump random-float dispersal_range * (mass_dependent_dispersal - (seed_dependent_dispersal - 1)) ; - 1 gives both dependencies 
                   ; the same magnitude of order, note: if you change the birth_mass or maximum_mass boundaries this has to be replaced
                 ]
               ]
               if (mass + generative_mass >= 0.99 * maximum_mass)
                 [ set-dead ;determinate growth
                 ]  
             ]
        ] 
      ]  
    ]
end

to germinate-seeds
 ask producers with [isSeed? = true] 
        [ set time_in_seedbank time_in_seedbank + 1 
          if time_in_seedbank >= seed_dormancy 
            and random-float 100 < germination_probability 
            [ set isSeed? false
              set shape "triangle 3"
              set size 0.3
            ]
          if random-float 100 < seed_mortality [set-dead]  
        ] 
end

to find-producer-min/max
   let min/max find-min/max-boundary birth_mass boundaries_birth_mass_producers
   set min_birth_mass item 0 min/max
   set max_birth_mass item 1 min/max
   set min/max find-min/max-boundary generative_fraction boundaries_generative_fraction_producers
   set min_generative_fraction item 0 min/max
   set max_generative_fraction item 1 min/max
   set min/max find-min/max-boundary maximum_mass boundaries_maximum_mass_producers
   set min_maximum_mass item 0 min/max
   set max_maximum_mass item 1 min/max
   set min/max find-min/max-boundary seed_dormancy boundaries_seed_dormancy_producers
   set min_seed_dormancy item 0 min/max
   set max_seed_dormancy item 1 min/max
   
   set min/max find-min/max-boundary germination_probability boundaries_germination_probability_producers
   set min_germination_probability item 0 min/max
   set max_germination_probability item 1 min/max
end

to-report find-my-producer-species 
  [ my_min_birth_mass my_max_birth_mass 
    my_min_generative_fraction my_max_generative_fraction 
    my_min_maximum_mass my_max_maximum_mass
    my_min_seed_dormancy my_max_seed_dormancy
    my_min_germination_probability my_max_germination_probability
  ]
  let my_producer_species 0
  let another_producer_of_my_species one-of other producers with 
    [ min_birth_mass = my_min_birth_mass
      and max_birth_mass = my_max_birth_mass
      and min_generative_fraction =  my_min_generative_fraction 
      and max_generative_fraction = my_max_generative_fraction 
      and min_maximum_mass = my_min_maximum_mass
      and max_maximum_mass = my_max_maximum_mass
      and min_seed_dormancy = my_min_seed_dormancy
      and max_seed_dormancy = my_max_seed_dormancy
      and min_germination_probability = my_min_germination_probability
      and max_germination_probability = my_max_germination_probability
    ]
  ifelse (is-producer? another_producer_of_my_species) 
    [ set my_producer_species [producer_species] of another_producer_of_my_species
    ]
    [ if producersInserted? = true 
      [ set my_producer_species get-max-number-of-producer-species + 1]
    ]    
  report my_producer_species  
end 

to-report get-number-of-producer-species
let species_list [producer_species] of producers  
set species_list remove-duplicates species_list
set number_producer_species length species_list 
report number_producer_species
end

to-report get-max-number-of-producer-species
  let species_list [producer_species] of producers  
  set species_list remove-duplicates species_list
  let max_number_producer_species max species_list
  report max_number_producer_species 
end

;===============================================================================================================

; decomposer procedures

to insert-decomposers
  let i min-pxcor
  let j min-pycor
  while [i < max-pxcor + 1]
   [ while [j < max-pycor + 1]
      [ setup-decomposers i j
        set j j + 1
      ]
     set j min-pycor
     set i i + 1
   ]
  set decomposersInserted? true
end

to setup-decomposers [i j]
  create-decomposers number_decomposers
    [ set shape "bacterium"
      set size 0.5
      set isSpore? false
      setxy i j
      set basic_energy_input 0.0166 * 60 * 60 * 24 ; assuming a time step of 1 d, the original W/g^3/4 have to be adjusted (s -> d)
      set cellular_energy_content 0.00000091146
      set cellular_mass 6.25E-10
      set maximum_mass population_size * cellular_mass 
      set birth_mass 49.5 / 100 * maximum_mass 
      set mass birth_mass
      set generative_fraction 99
      set gene_transfer_probability gene_transfer_probability_new_decomposers 
      set movement/maintenance_ratio movement/maintenance_ratio_new_decomposers
      set spore_metabolic_fraction spore_metabolic_fraction_new_decomposers
      find-decomposer-min/max
      set decomposer_species find-my-decomposer-species 
        min_gene_transfer_probability max_gene_transfer_probability
        min_movement/maintenance_ratio max_movement/maintenance_ratio 
        min_spore_metabolic_fraction max_spore_metabolic_fraction 
      set color item (decomposer_species + 1) color_list
    ]
end

to decompose-organic-matter
  ask decomposers 
    [ if isSpore? = false and random-float 100 < decomposer_mortality
       [ set-dead ]
      
      ; maintenance
      let cellular_metabolic_rate basic_energy_input * cellular_mass / maximum_mass ^ (1 / 4)
      let no_of_cells mass / cellular_mass
      let maintenance_energy_bacterium no_of_cells * cellular_metabolic_rate
      let maintenance_energy_spore maintenance_energy_bacterium * spore_metabolic_fraction / 100 
      let energy_in_organic_matter organic_matter * mean_Ec/Mc_ratio
      set energy_for_maintenance 0
      ifelse energy_in_organic_matter >= maintenance_energy_bacterium
        [ if (isSpore? = true)
          [ set isSpore? false
            set shape "bacterium"
            set size 0.5
          ]
          set organic_matter organic_matter - maintenance_energy_bacterium / mean_Ec/Mc_ratio
          set energy_for_maintenance maintenance_energy_bacterium  
        ] 
        [ if (isSpore? = false) 
            [ transfer-my-genes
              set isSpore? true 
              set shape "square"
              set size 0.3
            ]
          let energy_in_spore mass / cellular_mass * cellular_energy_content  
          ifelse (energy_in_spore >= maintenance_energy_spore)
            [ set mass mass - maintenance_energy_spore / cellular_energy_content * cellular_mass
              set energy_for_maintenance maintenance_energy_spore
            ]
            [ set-dead
            ]
        ]
        
        if (isSpore? = false) 
          [ ; movement
            let movement_energy movement/maintenance_ratio * maintenance_energy_bacterium
            set energy_in_organic_matter organic_matter * mean_Ec/Mc_ratio
            set energy_for_movement 0
            if energy_in_organic_matter >= movement_energy
              [ set organic_matter organic_matter - movement_energy / mean_Ec/Mc_ratio
                set energy_for_movement movement_energy  
              ]
            
            ; growth
            let a basic_energy_input * cellular_mass / cellular_energy_content
            let delta_mass a * mass ^ (3 / 4) * (1 - (mass / maximum_mass) ^ (1 / 4)) 
            let delta_no_of_cells delta_mass / cellular_mass
            let growth_energy delta_no_of_cells * cellular_energy_content 
            set energy_in_organic_matter organic_matter * mean_Ec/Mc_ratio
            set energy_for_growth 0
            if energy_in_organic_matter >= growth_energy
              [ set organic_matter organic_matter - growth_energy / mean_Ec/Mc_ratio
                set energy_for_growth growth_energy  
              ]
          ]  
    ]
end

to maintain-decomposers
  ask decomposers
   [ set energy_for_maintenance 0 
   ]
end

to move-decomposers
  ask decomposers with [isSpore? = false]
    [ jump energy_for_movement * 1E-6
      set energy_for_movement 0
      let direction_change random 360
      rt direction_change
      jump passive_movement
      rt (- direction_change)
    ]  
end

to grow-decomposers 
  ask decomposers with [isSpore? = false]
    [ if (mass < generative_fraction / 100 * maximum_mass and energy_for_growth > 0)
        [ let a basic_energy_input * cellular_mass / cellular_energy_content
          let delta_mass a * mass ^ (3 / 4) * (1 - ( mass / maximum_mass) ^ (1 / 4)) 
          set mass mass + delta_mass
        ]
    ]
end

to divide-decomposers
  ask decomposers with [isSpore? = false]
    [ if (mass >= generative_fraction / 100 * maximum_mass and energy_for_growth > 0)
        [ set mass birth_mass
          set energy_for_maintenance 0
          set energy_for_movement 0
          set energy_for_growth 0
          hatch 1 
            [ rt random 360
            ]   
          
        ]
    ] 
end

to transfer-genes
  ask decomposers with [isSpore? = false]
     [ transfer-my-genes
     ]
end

to transfer-my-genes
    if (random 100 < gene_transfer_probability)
       [ let transfer_partner one-of other decomposers-here with [isSpore? = false and decomposer_species = [decomposer_species] of myself]
         if (is-decomposer? transfer_partner) 
         [ let gene_transfer_probability_partner [gene_transfer_probability] of transfer_partner
           let movement/maintenance_ratio_partner [movement/maintenance_ratio] of transfer_partner
           let spore_metabolic_fraction_partner [spore_metabolic_fraction] of transfer_partner
           
           let my_gene_transfer_probability gene_transfer_probability
           let my_movement/maintenance_ratio movement/maintenance_ratio
           let my_spore_metabolic_fraction spore_metabolic_fraction
           
           set gene_transfer_probability recombine gene_transfer_probability gene_transfer_probability_partner
           set gene_transfer_probability mutate gene_transfer_probability min_gene_transfer_probability_decomposers max_gene_transfer_probability_decomposers 
           set movement/maintenance_ratio recombine movement/maintenance_ratio movement/maintenance_ratio_partner
           set movement/maintenance_ratio mutate movement/maintenance_ratio min_movement/maintenance_ratio_decomposers max_movement/maintenance_ratio_decomposers
           set spore_metabolic_fraction recombine spore_metabolic_fraction spore_metabolic_fraction_partner
           set spore_metabolic_fraction mutate spore_metabolic_fraction min_spore_metabolic_fraction_decomposers max_spore_metabolic_fraction_decomposers
           find-decomposer-min/max
           set decomposer_species find-my-decomposer-species 
             min_gene_transfer_probability max_gene_transfer_probability
             min_movement/maintenance_ratio max_movement/maintenance_ratio 
             min_spore_metabolic_fraction max_spore_metabolic_fraction 
           set color item (decomposer_species + 1) color_list
           
           ask transfer_partner 
             [ set gene_transfer_probability recombine gene_transfer_probability my_gene_transfer_probability 
               set gene_transfer_probability mutate gene_transfer_probability min_gene_transfer_probability_decomposers max_gene_transfer_probability_decomposers 
               set movement/maintenance_ratio recombine movement/maintenance_ratio my_movement/maintenance_ratio
               set movement/maintenance_ratio mutate movement/maintenance_ratio min_movement/maintenance_ratio_decomposers max_movement/maintenance_ratio_decomposers
               set spore_metabolic_fraction recombine spore_metabolic_fraction my_spore_metabolic_fraction 
               set spore_metabolic_fraction mutate spore_metabolic_fraction min_spore_metabolic_fraction_decomposers max_spore_metabolic_fraction_decomposers
               find-decomposer-min/max
               set decomposer_species find-my-decomposer-species 
                 min_gene_transfer_probability max_gene_transfer_probability
                 min_movement/maintenance_ratio max_movement/maintenance_ratio 
                 min_spore_metabolic_fraction max_spore_metabolic_fraction 
               set color item (decomposer_species + 1) color_list
             ]
         ]     
       ]
end

to find-decomposer-min/max
   let min/max find-min/max-boundary gene_transfer_probability boundaries_gene_transfer_probability_decomposers
   set min_gene_transfer_probability item 0 min/max
   set max_gene_transfer_probability item 1 min/max
   set min/max find-min/max-boundary movement/maintenance_ratio boundaries_movement/maintenance_ratio_decomposers
   set min_movement/maintenance_ratio item 0 min/max
   set max_movement/maintenance_ratio item 1 min/max
   set min/max find-min/max-boundary spore_metabolic_fraction boundaries_spore_metabolic_fraction_decomposers
   set min_spore_metabolic_fraction item 0 min/max
   set max_spore_metabolic_fraction item 1 min/max
end

to-report find-my-decomposer-species 
  [ my_min_gene_transfer_probability my_max_gene_transfer_probability  
    my_min_movement/maintenance_ratio my_max_movement/maintenance_ratio  
    my_min_spore_metabolic_fraction my_max_spore_metabolic_fraction 
  ]
  let my_decomposer_species 0
  let another_decomposer_of_my_species one-of other decomposers with 
    [ isSpore? = false
      and min_gene_transfer_probability = my_min_gene_transfer_probability 
      and max_gene_transfer_probability = my_max_gene_transfer_probability
      and min_movement/maintenance_ratio =  my_min_movement/maintenance_ratio  
      and max_movement/maintenance_ratio = my_max_movement/maintenance_ratio 
      and min_spore_metabolic_fraction = my_min_spore_metabolic_fraction
      and max_spore_metabolic_fraction = my_max_spore_metabolic_fraction 
    ]
  ifelse (is-decomposer? another_decomposer_of_my_species) 
    [ set my_decomposer_species [decomposer_species] of another_decomposer_of_my_species
    ]
    [ if decomposersInserted? = true 
      [ set my_decomposer_species get-max-number-of-decomposer-species + 1]
    ]    
  report my_decomposer_species  
end 

to-report get-number-of-decomposer-species
let species_list [decomposer_species] of decomposers  
set species_list remove-duplicates species_list
set number_decomposer_species length species_list 
report number_decomposer_species
end

to-report get-max-number-of-decomposer-species
  let species_list [decomposer_species] of decomposers  
  set species_list remove-duplicates species_list
  let max_number_decomposer_species max species_list
  report max_number_decomposer_species 
end

;===============================================================================================================

; auxilliary procedures

to-report recombine [val1 val2]
  let valueList list (val1) (val2)
  let minVal min valueList
  let maxVal max valueList 
  report minVal + random-float (maxVal - minVal)
end

to-report mutate [mutatable lower_boundary upper_boundary]
  if (random-float 100 < mutation_probability)
    [ set mutatable mutatable + (random-float 2 - 1) * mutation / 100 * mutatable
      if (mutatable < lower_boundary)
        [ set mutatable lower_boundary ]
      if (mutatable > upper_boundary)
        [set mutatable upper_boundary]  
    ]
  report mutatable  
end

to do-plots
  set-current-plot "Energetics: Energy input"   
  set-current-plot-pen "Energy input"
  plot total_energy_input
  set-current-plot-pen "Energy input used"
  plot total_energy_input - unused_energy_input 
  
  set-current-plot "Energetics: Energy stocks"   
  set-current-plot-pen "Energy in producers"
  plot total_energy_in_producer_mass 
  set-current-plot-pen "Energy in decomposers"
  plot total_energy_in_decomposer_mass 
  set-current-plot-pen "Energy in organic matter"
  plot total_energy_in_organic_matter 
  
;  set-current-plot "Energetics: Energy flows"   
;  let energy_input_used total_energy_input - unused_energy_input
;  set-current-plot-pen "Energy for producer growth"
;  plot total_energy_producer_growth / energy_input_used
;  set-current-plot-pen "Energy for decomposer growth"
;  plot total_energy_decomposer_growth / energy_input_used
;   set-current-plot-pen "Energy for producer maintenance"
;  plot total_energy_output_producer_maintenance / energy_input_used
;   set-current-plot-pen "Energy for decomposer maintenance"
;  plot total_energy_output_decomposer_maintenance / energy_input_used
;  set-current-plot-pen "Energy for decomposer movement"
;  plot total_energy_output_decomposer_movement / energy_input_used
  
  set-current-plot "Mass stocks"   
  set-current-plot-pen "Producer mass"
  plot total_mass_producers 
  set-current-plot-pen "Decomposer mass"
  plot total_mass_decomposers 
  set-current-plot-pen "Organic matter"
  plot total_organic_matter 
  
  set-current-plot "Count producers"   
  set-current-plot-pen "producers"
  plot count producers with [isSeed? = false]
  set-current-plot-pen "seeds"
  plot count producers with [isSeed? = true]
  
  set-current-plot "Count decomposers"   
  set-current-plot-pen "bacteria"
  plot count decomposers with [isSpore? = false] 
  set-current-plot-pen "spores"
  plot count decomposers with [isSpore? = true]
  
  let producer_species_list [producer_species] of producers  
  set producer_species_list remove-duplicates producer_species_list   
  set producer_species_list sort producer_species_list
  let x_range length producer_species_list
  
  set-current-plot "Producer species counts"
  ; The HISTOGRAM primitive doesn't support giving different bars
  ; different colors, so we roll our own histogramming code here.
  plot-pen-reset
  set-plot-x-range 0 x_range
  foreach producer_species_list 
    [ let producers_of_same_species producers with [producer_species = ?]
      let count_producers count producers_of_same_species
      if count_producers > 0 [set-plot-pen-color [color] of one-of producers_of_same_species]
      plot count_producers
    ]

  set-current-plot "Mass at birth"
  ; The HISTOGRAM primitive doesn't support giving different bars
  ; different colors, so we roll our own histogramming code here.
  plot-pen-reset
  set-plot-x-range 0 x_range
  foreach producer_species_list 
    [ let producers_of_same_species producers with [producer_species = ?]
      let birth_mass_min [min_birth_mass] of one-of producers_of_same_species 
      let birth_mass_max [max_birth_mass] of one-of producers_of_same_species 
      if is-number? birth_mass_max and is-number? birth_mass_min [set-plot-pen-color [color] of one-of producers_of_same_species]
      plot birth_mass_min 
      plot birth_mass_max
    ]
  
  set-current-plot "Maximum mass"
  ; The HISTOGRAM primitive doesn't support giving different bars
  ; different colors, so we roll our own histogramming code here.
  plot-pen-reset
  set-plot-x-range 0 x_range
  foreach producer_species_list 
    [ let producers_of_same_species producers with [producer_species = ?]
      let maximum_mass_min [min_maximum_mass] of one-of producers_of_same_species 
      let maximum_mass_max [max_maximum_mass] of one-of producers_of_same_species 
      if is-number? maximum_mass_max and is-number? maximum_mass_min [set-plot-pen-color [color] of one-of producers_of_same_species]
      plot maximum_mass_min 
      plot maximum_mass_max
    ]
  
  set-current-plot "Generative fraction"
  ; The HISTOGRAM primitive doesn't support giving different bars
  ; different colors, so we roll our own histogramming code here.
  plot-pen-reset
  set-plot-x-range 0 x_range
  foreach producer_species_list 
    [ let producers_of_same_species producers with [producer_species = ?]
      let generative_fraction_min [min_generative_fraction] of one-of producers_of_same_species 
      let generative_fraction_max [max_generative_fraction] of one-of producers_of_same_species 
      if is-number? generative_fraction_max and is-number? generative_fraction_min [set-plot-pen-color [color] of one-of producers_of_same_species]
      plot generative_fraction_min 
      plot generative_fraction_max
    ]
  
  set-current-plot "Seed dormancy"
  ; The HISTOGRAM primitive doesn't support giving different bars
  ; different colors, so we roll our own histogramming code here.
  plot-pen-reset
  set-plot-x-range 0 x_range
  foreach producer_species_list 
    [ let producers_of_same_species producers with [producer_species = ?]
      let seed_dormancy_min [min_seed_dormancy] of one-of producers_of_same_species 
      let seed_dormancy_max [max_seed_dormancy] of one-of producers_of_same_species 
      if is-number? seed_dormancy_max and is-number? seed_dormancy_min [set-plot-pen-color [color] of one-of producers_of_same_species]
      plot seed_dormancy_min 
      plot seed_dormancy_max
    ]
  set-current-plot "Germination probability"
  ; The HISTOGRAM primitive doesn't support giving different bars
  ; different colors, so we roll our own histogramming code here.
  plot-pen-reset
  set-plot-x-range 0 x_range
  foreach producer_species_list 
    [ let producers_of_same_species producers with [producer_species = ?]
      let germination_probability_min [min_germination_probability] of one-of producers_of_same_species 
      let germination_probability_max [max_germination_probability] of one-of producers_of_same_species 
      if is-number? germination_probability_max and is-number? germination_probability_min [set-plot-pen-color [color] of one-of producers_of_same_species]
      plot germination_probability_min 
      plot germination_probability_max
    ]
   
    let decomposer_species_list [decomposer_species] of decomposers  
    set decomposer_species_list remove-duplicates decomposer_species_list   
    set decomposer_species_list sort decomposer_species_list
    set x_range length decomposer_species_list
    
    set-current-plot "Gene transfer probability"
    ; The HISTOGRAM primitive doesn't support giving different bars
    ; different colors, so we roll our own histogramming code here.
    plot-pen-reset
    set-plot-x-range 0 x_range
    foreach decomposer_species_list 
      [ let decomposers_of_same_species decomposers with [decomposer_species = ?]
        let gene_transfer_probability_min [min_gene_transfer_probability] of one-of decomposers_of_same_species 
        let gene_transfer_probability_max [max_gene_transfer_probability] of one-of decomposers_of_same_species 
        if is-number? gene_transfer_probability_max and is-number? gene_transfer_probability_min 
          [set-plot-pen-color [color] of one-of decomposers_of_same_species]
        plot gene_transfer_probability_min 
        plot gene_transfer_probability_max  
      ]
    
    set-current-plot "Movement/maintenance ratio"
    ; The HISTOGRAM primitive doesn't support giving different bars
    ; different colors, so we roll our own histogramming code here.
    plot-pen-reset
    set-plot-x-range 0 x_range
    foreach decomposer_species_list 
      [ let decomposers_of_same_species decomposers with [decomposer_species = ?]
        let movement/maintenance_ratio_min [min_movement/maintenance_ratio] of one-of decomposers_of_same_species 
        let movement/maintenance_ratio_max [max_movement/maintenance_ratio] of one-of decomposers_of_same_species 
        if is-number? movement/maintenance_ratio_max and is-number? movement/maintenance_ratio_min 
          [set-plot-pen-color [color] of one-of decomposers_of_same_species]
        plot movement/maintenance_ratio_min 
        plot movement/maintenance_ratio_max  
      ]
      
    set-current-plot "Spore metabolic fraction"
    ; The HISTOGRAM primitive doesn't support giving different bars
    ; different colors, so we roll our own histogramming code here.
    plot-pen-reset
    set-plot-x-range 0 x_range
    foreach decomposer_species_list 
      [ let decomposers_of_same_species decomposers with [decomposer_species = ?]
        let spore_metabolic_fraction_min [min_spore_metabolic_fraction] of one-of decomposers_of_same_species 
        let spore_metabolic_fraction_max [max_spore_metabolic_fraction] of one-of decomposers_of_same_species 
        if is-number? spore_metabolic_fraction_max and is-number? spore_metabolic_fraction_min 
          [set-plot-pen-color [color] of one-of decomposers_of_same_species]
        plot spore_metabolic_fraction_min plot spore_metabolic_fraction_max  
      ]
  
    set-current-plot "Decomposer species counts"
    ; The HISTOGRAM primitive doesn't support giving different bars
    ; different colors, so we roll our own histogramming code here.
    plot-pen-reset
    set-plot-x-range 0 x_range
    foreach decomposer_species_list 
      [ let decomposers_of_same_species decomposers with [decomposer_species = ?]
        let count_decomposers count decomposers_of_same_species
        if count_decomposers > 0 [set-plot-pen-color [color] of one-of decomposers_of_same_species]
        plot count_decomposers
      ]
     
end

; experiments

to-report monocultureReached?
  ifelse decomposersinserted? = true and number_producer_species = 1
      [report true]
      [report false]
end

@#$#@#$#@
GRAPHICS-WINDOW
185
10
627
473
4
4
48.0
1
10
1
1
1
0
1
1
1
-4
4
-4
4
1
1
1
ticks

SLIDER
5
162
177
195
species_range
species_range
0
100
10
1
1
NIL
HORIZONTAL

SLIDER
2
315
174
348
mutation_probability
mutation_probability
0
100
0
1
1
NIL
HORIZONTAL

BUTTON
186
497
249
530
setup
setup
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL

BUTTON
249
497
312
530
go
go
T
1
T
OBSERVER
NIL
NIL
NIL
NIL

SLIDER
6
37
178
70
smoothness
smoothness
0
50
10
1
1
NIL
HORIZONTAL

SLIDER
6
64
178
97
range
range
0
100
100
1
1
NIL
HORIZONTAL

SWITCH
4
159
175
192
changing-landscape?
changing-landscape?
1
1
-1000

SLIDER
5
129
178
162
landscape-change-rate
landscape-change-rate
0
200
200
1
1
NIL
HORIZONTAL

SLIDER
147
798
288
831
number_producers
number_producers
0
20
4
2
1
NIL
HORIZONTAL

PLOT
1216
384
1557
534
Mass at birth
species
birth mass
0.0
10.0
0.0
0.01
true
false
PENS
"min birth mass" 1.0 1 -16777216 true
"max birth mass" 5.0 1 -16777216 true

PLOT
1216
532
1559
682
Maximum mass
species
maximum mass
0.0
10.0
0.0
0.3
true
false
PENS
"default" 1.0 1 -16777216 true

MONITOR
656
590
802
635
count producers
count producers with [isSeed? = false]
0
1
11

PLOT
1216
58
1559
208
Count producers
time
number producers
0.0
10.0
0.0
10.0
true
true
PENS
"producers" 1.0 0 -2674135 true
"seeds" 1.0 0 -5825686 true

MONITOR
656
546
801
591
No. producer species
get-number-of-producer-species
0
1
11

SLIDER
5
97
178
130
penergy_multiplicator
penergy_multiplicator
0
10000
1500
100
1
NIL
HORIZONTAL

SLIDER
1
458
174
491
dispersal_range
dispersal_range
0
10
0.2
0.1
1
NIL
HORIZONTAL

BUTTON
432
495
571
528
insert decomposers
insert-decomposers
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL

MONITOR
800
590
947
635
count decomposers
count decomposers with [isSpore? = false]
0
1
11

PLOT
1558
58
1900
208
Count decomposers
time
NIL
0.0
10.0
0.0
20.0
true
true
PENS
"bacteria" 1.0 0 -2674135 true
"spores" 1.0 0 -5825686 true

CHOOSER
5
194
177
239
patch_color
patch_color
"showEnergy?" "showUsableEnergy?" "showOrganicMatter?"
0

SWITCH
3
393
174
426
showProducers?
showProducers?
0
1
-1000

SWITCH
5
559
172
592
showDecomposers?
showDecomposers?
1
1
-1000

SLIDER
2
425
174
458
pollination_range
pollination_range
0
10
10
1
1
NIL
HORIZONTAL

SLIDER
2
282
173
315
species_range
species_range
0
100
10
1
1
NIL
HORIZONTAL

TEXTBOX
10
10
160
35
Landscape:
20
65.0
1

TEXTBOX
7
253
157
278
Species:
20
0.0
1

TEXTBOX
7
364
157
389
Producers:
20
105.0
1

TEXTBOX
10
532
160
557
Decomposers:
20
15.0
1

SLIDER
445
830
599
863
number_decomposers
number_decomposers
1
10
1
1
1
NIL
HORIZONTAL

INPUTBOX
5
592
172
652
population_size
10000000000
1
0
Number

MONITOR
994
196
1169
241
Energy input
total_energy_input
3
1
11

MONITOR
997
611
1170
656
Energy deocmposer movement
total_energy_output_decomposer_movement
3
1
11

MONITOR
994
240
1170
285
Unused energy input
unused_energy_input
3
1
11

MONITOR
995
445
1171
490
Energy producer growth
total_energy_producer_growth
3
1
11

MONITOR
995
524
1170
569
Energy producer maintenance
 total_energy_output_producer_maintenance
3
1
11

MONITOR
994
312
1169
357
Energy producer mass
total_energy_in_producer_mass
3
1
11

MONITOR
993
357
1169
402
Energy decomposer mass
total_energy_in_decomposer_mass
3
1
11

MONITOR
993
401
1169
446
Energy organic matter
total_energy_in_organic_matter
3
1
11

MONITOR
996
569
1170
614
Energy decomposer maintenance
total_energy_output_decomposer_maintenance
3
1
11

MONITOR
996
486
1171
531
Energy decomposer growth
total_energy_decomposer_growth
3
1
11

MONITOR
940
56
1074
101
Mass of producers
total_mass_producers
3
1
11

MONITOR
941
101
1073
146
Mass of decomposers
total_mass_decomposers
3
1
11

MONITOR
941
145
1074
190
Organic matter
total_organic_matter
3
1
11

PLOT
660
229
996
379
Energetics: Energy input
time
energy
0.0
10.0
0.0
10.0
true
true
PENS
"Energy input" 1.0 0 -11221820 true
"Energy input used" 1.0 0 -8630108 true

PLOT
660
379
996
529
Energetics: Energy stocks
energy stock
time
0.0
10.0
0.0
10.0
true
true
PENS
"Energy in producers" 1.0 0 -10899396 true
"Energy in decomposers" 1.0 0 -2674135 true
"Energy in organic matter" 1.0 0 -1184463 true

SLIDER
5
652
172
685
passive_movement
passive_movement
0
5
0.1
0.1
1
NIL
HORIZONTAL

MONITOR
802
546
947
591
No. decomposer species
get-number-of-decomposer-species
0
1
11

TEXTBOX
668
201
818
226
Energetics:
20
115.0
1

TEXTBOX
667
10
817
40
Masses:
20
0.0
1

PLOT
661
47
941
197
Mass stocks
time
mass
0.0
10.0
0.0
10.0
true
true
PENS
"Producer mass" 1.0 0 -13840069 true
"Decomposer mass" 1.0 0 -2674135 true
"Organic matter" 1.0 0 -1184463 true

PLOT
1218
206
1559
383
Producer species counts
species
count
0.0
10.0
0.0
10.0
true
false
PENS
"Producer species counts" 1.0 1 -16777216 true

PLOT
1558
208
1900
384
Decomposer species counts
species
counts
0.0
10.0
0.0
700.0
true
false
PENS
"default" 1.0 1 -16777216 true

INPUTBOX
8
894
148
954
min_birth_mass_producers
0.0050
1
0
Number

INPUTBOX
148
894
289
954
max_birth_mass_producers
1
1
0
Number

INPUTBOX
8
982
148
1042
min_generative_fraction_producers
60
1
0
Number

INPUTBOX
147
983
289
1043
max_generative_fraction_producers
100
1
0
Number

INPUTBOX
8
1073
147
1133
min_maximum_mass_producers
2
1
0
Number

INPUTBOX
144
1073
290
1133
max_maximum_mass_producers
200
1
0
Number

SLIDER
8
864
289
897
birth_mass_new_producers
birth_mass_new_producers
min_birth_mass_producers + precision (1 / 200 * (max_birth_mass_producers - min_birth_mass_producers)) 3 
max_birth_mass_producers - precision (1 / 200 * (max_birth_mass_producers - min_birth_mass_producers)) 3
0.03
precision (1 / 200 * (max_birth_mass_producers - min_birth_mass_producers)) 3
1
NIL
HORIZONTAL

SLIDER
8
953
289
986
generative_fraction_new_producers
generative_fraction_new_producers
min_generative_fraction_producers + round 1 / 100 * (max_generative_fraction_producers - min_generative_fraction_producers)
max_generative_fraction_producers - round 1 / 100 * (max_generative_fraction_producers - min_generative_fraction_producers)
80
round 1 / 100 * (max_generative_fraction_producers - min_generative_fraction_producers)
1
NIL
HORIZONTAL

SLIDER
8
1042
290
1075
maximum_mass_new_producers
maximum_mass_new_producers
min_maximum_mass_producers + round (1 / 100 * (max_maximum_mass_producers - min_maximum_mass_producers)) 
max_maximum_mass_producers - round (1 / 100 * (max_maximum_mass_producers - min_maximum_mass_producers))
20
round (1 / 100 * ( max_maximum_mass_producers - min_maximum_mass_producers))
1
NIL
HORIZONTAL

BUTTON
312
496
433
529
insert producers
insert-producers
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL

SLIDER
7
831
147
864
xcor_producers
xcor_producers
min-pxcor
max-pxcor
3
1
1
NIL
HORIZONTAL

SLIDER
147
832
288
865
ycor_producers
ycor_producers
min-pycor
max-pycor
0
1
1
NIL
HORIZONTAL

SLIDER
288
863
599
896
gene_transfer_probability_new_decomposers
gene_transfer_probability_new_decomposers
min_gene_transfer_probability_decomposers + 0.1
max_gene_transfer_probability_decomposers - 0.1
5
0.1
1
NIL
HORIZONTAL

SLIDER
291
952
600
985
movement/maintenance_ratio_new_decomposers
movement/maintenance_ratio_new_decomposers
min_movement/maintenance_ratio_decomposers + 0.01
max_movement/maintenance_ratio_decomposers - 0.01
1.99
0.01
1
NIL
HORIZONTAL

SLIDER
289
1042
600
1075
spore_metabolic_fraction_new_decomposers
spore_metabolic_fraction_new_decomposers
min_spore_metabolic_fraction_decomposers + 0.1
max_spore_metabolic_fraction_decomposers - 0.1
1
0.1
1
NIL
HORIZONTAL

INPUTBOX
289
895
444
955
min_gene_transfer_probability_decomposers
0.1
1
0
Number

INPUTBOX
444
894
599
954
max_gene_transfer_probability_decomposers
10
1
0
Number

INPUTBOX
289
984
444
1044
min_movement/maintenance_ratio_decomposers
0.01
1
0
Number

INPUTBOX
445
985
600
1045
max_movement/maintenance_ratio_decomposers
2
1
0
Number

INPUTBOX
290
1074
445
1134
min_spore_metabolic_fraction_decomposers
0.1
1
0
Number

INPUTBOX
444
1074
599
1134
max_spore_metabolic_fraction_decomposers
5
1
0
Number

PLOT
1216
682
1559
832
Generative fraction
species
NIL
0.0
10.0
0.0
10.0
true
false
PENS
"default" 1.0 1 -16777216 true

PLOT
1558
384
1902
534
Gene transfer probability
species
NIL
0.0
10.0
0.0
6.0
true
false
PENS
"default" 1.0 1 -16777216 true

PLOT
1558
534
1902
684
Movement/maintenance ratio
species
NIL
0.0
10.0
0.0
1.5
true
false
PENS
"default" 1.0 1 -16777216 true

TEXTBOX
1222
20
1413
53
Producer species:
20
0.0
1

TEXTBOX
1564
22
1781
50
Decomposer species:
20
0.0
1

TEXTBOX
15
744
416
792
Species parameters:
32
0.0
1

PLOT
1560
682
1902
832
Spore metabolic fraction
species
spore metabolic fraction
0.0
10.0
0.0
1.0
true
false
PENS
"default" 1.0 1 -16777216 true

SLIDER
5
684
172
717
decomposer_mortality
decomposer_mortality
0
3
1.8
0.1
1
NIL
HORIZONTAL

SLIDER
9
1132
292
1165
seed_dormancy_new_producers
seed_dormancy_new_producers
min_seed_dormancy_producers + 5
max_seed_dormancy_producers - 5
10
30
1
NIL
HORIZONTAL

INPUTBOX
9
1165
146
1225
min_seed_dormancy_producers
5
1
0
Number

INPUTBOX
144
1165
292
1225
max_seed_dormancy_producers
390
1
0
Number

SLIDER
9
1224
292
1257
germination_probability_new_producers
germination_probability_new_producers
min_germination_probability_producers + 1
max_germination_probability_producers - 1
2
1
1
NIL
HORIZONTAL

INPUTBOX
8
1257
147
1317
min_germination_probability_producers
1
1
0
Number

INPUTBOX
146
1257
293
1317
max_germination_probability_producers
51
1
0
Number

SLIDER
1
491
174
524
seed_mortality
seed_mortality
0
50
1
1
1
NIL
HORIZONTAL

MONITOR
656
634
801
679
count seeds
count producers with [isSeed? = true]
0
1
11

MONITOR
800
634
946
679
count spores
count decomposers with [isSpore? = true]
17
1
11

PLOT
1216
832
1559
982
Seed dormancy
species
seed dormancy
0.0
10.0
0.0
10.0
true
false
PENS
"default" 1.0 1 -16777216 true

PLOT
1218
980
1560
1130
Germination probability
species
germination probability
0.0
10.0
0.0
10.0
true
false
PENS
"default" 1.0 1 -16777216 true

@#$#@#$#@
WHAT IS IT? 
-----------
Neture is a NetLogo model that simulates how Nature works. 

Neture simulates a terrestrial ecosystem at the interface of ecology and evolution. 
The model embraces the three main ecosystem components: (1) the landscape environment, (2) the producers, and (3) the decomposers. It assembles processes that operate on a local spatial scale,  endure decades, but progress with daily time steps.


HOW IT WORKS
------------ 
Producer and decomposer species are both defined by a set of attributes. For an organism to belong to a certain species its attributes have to stay within the species-specific range. Exchange of genes leads to recombination of attributes. Mutation of attributes may take place - thereby giving rise to evolution and speciation. 

As all living things in Neture producers and decomposers have energy supply either from sunlight or from organic matter and undergo metabolism for their maintenance, growth and reproduction. In Neture maintenance and growth metabolism is governed by "universal scaling laws" given by West, Brown & Enquist (2001) and Gilloly et al. (2001). Additional parameters with respect to plants and bacteria were obtained from Larcher (2003) and Elert, respectively.

(1) The landscape environment supplies energy to the biotic subsystem of producers. Allowance is made for spatial and/or temporal heterogeneity of the energy supplied across the landscape. 

(2) The producers - or say - plants take up energy in the form of sunlight from the environment and use it for their metabolism. 
A producer (species) is defined by its mass at birth, its maximum mass at maturity, the  fraction of maximum mass at which generative reporduction starts, the seed dormancy and the germination probability. 
Generative reproduction between a father and a mother plant takes place in the pollination range around the father plant. Supposing that lighter seeds are dispersed farther, the range of dispersal is made negatively dependent on the log mass at birth. Further assuming that heavier plants are taller and thus disperse their seeds farther, the dispersal range is made dependent on the log maximum mass. The effects considered to be additive are finally adjustable by you.
The dispersed seeds enter the soil seed bank, reside there at least for the species-specific seed dormancy and exhibit hardly any metabolism during that time (compare Solbrig 1980). After seed dormancy has passed by a seed germinates with a certain daily probability or it dies with the user-defined probability which summarizes effects of (biotic) soil mixing and predation on seed viability (Solbrig 1980).     
An established producer either dies when its maintenance requirements are not fulfilled or when it has reached 99% of its maximum mass (determinate growth). Its residues enter the organic matter pool of the landscape patch, where it died.

(3) The decomposers are simulated as populations of bacteria that behave like single bacterium cells. This strategy for scaling down from the  producer to the decomposer level shall cope with the consequences of the body sizes being distinct between the two groups. 
A decomposer (species) is defined by its "spore" metabolic fraction, by the gene transfer probability and the movement to maintenance ratio. 
When organic matter is scarce, bacteria tend to transform either into GASP phenotypes with reduced metabolism or into spores with negligible metabolism (Colwell & Huq 1994, Storz & Hengge-Aronis 2000). Their metabolism is fed by stored reserves and is used merely for maintenance. Under those threatening conditions bacteria are simulated to transfer genes and eventually develop mutations. When maintenance requirements cannot be satisfied any longer, the enduring form dies from starvation.  
With plenty of organic matter bacteria are assumed to transfer genes with the  probability set by the user. 
Bacteria are at the bottom trophic level of the soil food web (Chapin (III.), Matson & Mooney 2002). Since true integration of higher trophic levels is beyond the scope of this model, their effect on bacteria populations is simulated as a decomposer mortality to be set by you. 
Soil bacteria tend to form microfilms along soil macropores; they are considered to be translocated primarily by the activity of the soil meso- and macrofauna (Chapin (III.), Matson & Mooney 2002). You can choose the extent of this passive movement. Apart from that the movement to maintenance ratio allows to simulate effects of active movement. 
The residues of dead bacteria or spores enter the organic matter pool of the landscape patch - thereby forming sort of a closed loop.


HOW TO USE IT
-------------
Before you start a model run please choose a SPECIES_RANGE, which defines the % deviation a species attribute is allowed to have before an organism is considered to belong to a different species. The default is 10%. 

(1) Landscape environment: You may wish to manage settings of the landscape right before you start a model run, but it is also possible to change those settings later. 
The SMOOTHNESS and RANGE sliders allow for spatial heterogeeneity.   
The SMOOTHNESS slider alters the patch-to-patch change in the energy supply. 
When the RANGE slider is set to zero you are dealing with a homogeneous landscape, when RANGE is set to the maximum 100 the energy supply is made heterogeneous and varies between 0 and 100.
Turning on the CHANGING-LANDSCAPE? switch leads to temporal heterogeneity.
The LANDSCAPE-CHANGE-RATE slider alters the speed with which the energy supply changes.
The PENERGY_MULTIPLICATOR slider allows to adjust the energy input to realistic units. 
With the PATCH_COLOR chooser you can color the landscape by the energy, the usable energy or by the organic matter. 
 
As usual pressing the SETUP button prepares for a model run. 

(2) Producers: Afterwards you may populate the landscape with producers by pressing the 
INSERT PRODUCERS button. Before doing so you can set the NUMBER_PRODUCERS and the location of producers (XCOR_PRODUCERS, YCOR_PRODUCERS) to be inserted. Below are sliders for setting the attributes of the producers within the min-/max-limits given by the inputs. External effects on the behavior of producers are on sliders located on the left hand side (POLLINATION_RANGE, DISPERSAL_RANGE, SEED_MORTALITY). Seeds are being displayed on the landscape as empty squares, whereas established producers are shown as empty triangles. Producers belonging to different species are depicted in different colors. 

(3) Decomposers: Subsequently, it is required to insert decomposers. You can do so by pressing the INSERT_DECOMPOSERS button. The landscape is then homogeneously populated with NUMBER_DECOMPOSERS representing the number of decomposers to be inserted per patch.  Once again you can choose decomposer attributes within limits using the sliders at the bottom. Sliders for introducing external effects, such as PASSIVE_MOVEMENT and DECOMPOSER_MORTALITY, are located on the left hand side. 
Spores are being displayed as filled squares, while fully active decomposers are displayed using a bacterium-like shape. As with producers the color of a decomposer depends on the species which it belongs to. 

After you have made those arrangements start the model run by pressing the GO button. 
Have fun to watch the unfolding mass and enery dynamics on top-level monitors and plots. 

At any time you can initiate evolutionary processes and speciation by setting the MUTATION_PROBABILITY to a non-zero value. Enjoy watching the attributes of new species and their population dynamics on species-specific plots located at the very right. 


THINGS TO TRY AND NOTICE
----------------
I am still at the beginning of model exploration. Initially, my principal interest was to find regions of species coexistence in the vast multi-dimensional parameter space. 
This is what I would recommend you to try first as well. Developing hypotheses about species coexistence and testing them with Behavior Space experiments will give you many opporutinities to learn how Neture works. 

Here are some basic results and ideas that emerged from them: 
I was unsuccessful to detect regions of producer species coexistence by varying the energy supply in planned two-species experiments on a homogeneous landscape (-> Is spatial or temporal heterogeneity a sine qua non for coexistence and diversity?). Almost always the species with higher maximum mass won. There was one exception from that: At very low energy supplies even the first generation of heavier plants was not able to reproduce and died already.  
Next I tried to compensate the consequences of higher maximum mass in terms of dispersal by reducing the mass at birth for the heavier species in experiments. I thought that might change the outcome of the competition. But unfortunately, this did not change anything. The heavier species remained the winner. 
My next attempt was to study the effects of the external factor "dispersal range" on the experimental results. Although reduced dispersal range was likely to increase  intra-species competition, it did not alter the outcome of the competition. 
Returning to the above mentioned exception I conducted an experiment with extreme landscape heterogeneity (RANGE = 100). The idea here was that the competition by the heavier species would be excluded on very low energy patches. It did not work out that way - since even dispersal of seeds by the heavier species drove the lighter species to extinction. I thought further that some extra space would be necessary to prevent seed dispersal from reaching those patches and achieving protection. Whatsoever, I have not tried it yet. 
Nonetheless, I was finally successful and found a region of species coexistence, but the result was surprising and unexpected in many respects: The region was located at a high energy supply. Lighter plants resided on patches with high energy supply, while low energy patches were populated by heavier plants. I can send you the experimental settings. So do not hesitate to ask me at uwegrueters@users.sourceforge.net . 

Otherwise try to find this region yourself. Can you explain why this happens at all? 
Since it is well known that high species richness is frequently associated with infertile conditions, try also to find regions of coexistence in the domain of overall low energy supply.

However, this all involves filling spatial niches with species. But is there a way to fill temporal niches with species as well? Recall that seed dormancy may open up such possibilities. Play around with that parameter and try to address the above question.
Extend the search for species coexistence also to the realms of temporal landscape heterogeneity (by turning on the changing-landscape? switch). The potentials of filling temporal niches seem promising, since the energy used often falls remarkably behind the available energy when temporal fluctuation is allowed for.

Try to do similar planned experiments with inserted decomposer species. An option might be to let "non-sporulating" species of higher active motility compete with spore-forming species that are merely moved passively. 

When you think you have learned enough about how Neture works, give up the initial constraints and allow evolution and speciation to enter the scene. I would recommend to insert a number of  diverging producer and decomposer species, let a dynamic equilibrium develop and then - by setting the MUTATION_PROBABILITY non-zero - let the "evolutionary damn burst". This setting will alter your search fundamentally: Try now to find regions of maximum species packaging or - in other words - regions of maximum species richness and diversity. 

Please send me your insights of how Neture works together with the experimental settings from which you gained your insights. My e-mail address is: uwegrueters@users.sourceforge.net 


EXTENDING THE MODEL
-------------------
Here are just few hints:
- Based on your insights make Neture as diverse as Nature. 
- Integrate an above-ground consumer food web. 
- Integrate a sol food web consisting of nematodes, micro-arthropods, enchythraeids and earthworms. West, Brown & Enquist (2001) and Gilloly et al. (2001), respectively, have parameters for other groups of organisms as well. Let actions of these animals afffect the bacterial populations directly (by predation) and indirectly (by soil mixing).    
- Think about alternatives for scaling down from producers to decomposers - alternatives, that take into account spatial heterogeneity in the decomposers' world.


NETLOGO FEATURES
----------------
Code for the implementation of the landscape was taken from the NetLogo User Community model "Fitness_Landscape". http://ccl.northwestern.edu/netlogo/models/community/Fitness_Landsacape
The species counts and species attributes plots followed the example given in the "Echo"  model contained in the NetLogo Models Librariy. 
http://ccl.northwestern.edu/netlogo/models/Echo

RELATED MODELS
--------------
UIBM - the Universal Individual-Based Model.
Project website: http://uibm-de.sourceforge.net
Project administrator: Dr. Uwe Grueters, uwegrueters@users.sourceforge.net

REFERENCES
----------------------
- West G.B., Brwon J.M. & Enquist B.J.(2001): A genereral model for ontogenetic growth. 	Nature 413, pp. 628-631

- Gilloly J.F. et al. (2001): Effects of size and temerperature on metabolic rate. 
Science 293, pp. 2248-2251 

- Larcher W. (2003): Physiological plant ecology. Springer

- Elert G.: The Physics Factbook: Mass of a bacterium. http://hypertextbook.com/facts/2003/LouisSiu.shtm

- Solbrig O.T. (1980): Demography and evolution in plant populations. University of California Press  

- Colwell R.R. & Huq A. (1994: Chapter 9: Vibrios in the environment: Viable but non-culturalble Vibrio cholerae. pp. 117-135
In: Wachsmuth K., Blake P.A. & Olsvik Ø. (1994): Vibrio cholerae and cholera: molecular to global perspectives. ASM Press

- Storz G. & Hengge-Aronis R. (2000): Bacterial stress responses. ASM Press

- Chapin (III.) F.S. , Matson P.A., Mooney H.A. (2002): Principles of terrestrial ecosystem ecology. Birkhäuser


COPYRIGHT NOTICE
----------------
In academic publications any references to this model should refer to: 
- Grueters U. (2011): Neture - a NetLogo model that simulates how Nature works. http://ccl.northwestern.edu/netlogo/models/community/Neture

In all other publications please use:
Copyright 2011 Dr. Uwe Grueters. All rights reserved. 

Permission to use, modify or redistribute this model is hereby granted, provided that both of the following requirements are followed:
a) this copyright notice is included.
b) this model will not be redistributed for profit without permission from Uwe Grueters. Contact Uwe Grueters at uwegrueters@users.sourceforge.net for appropriate licenses related to redistribution for profit.
@#$#@#$#@
default
true
0
Polygon -7500403 true true 150 5 40 250 150 205 260 250

airplane
true
0
Polygon -7500403 true true 150 0 135 15 120 60 120 105 15 165 15 195 120 180 135 240 105 270 120 285 150 270 180 285 210 270 165 240 180 180 285 195 285 165 180 105 180 60 165 15

arrow
true
0
Polygon -7500403 true true 150 0 0 150 105 150 105 293 195 293 195 150 300 150

bacterium
true
0
Circle -7500403 true true 103 207 95
Circle -7500403 true true 103 -3 95
Rectangle -7500403 true true 105 45 195 255

box
false
0
Polygon -7500403 true true 150 285 285 225 285 75 150 135
Polygon -7500403 true true 150 135 15 75 150 15 285 75
Polygon -7500403 true true 15 75 15 225 150 285 150 135
Line -16777216 false 150 285 150 135
Line -16777216 false 150 135 15 75
Line -16777216 false 150 135 285 75

bug
true
0
Circle -7500403 true true 96 182 108
Circle -7500403 true true 110 127 80
Circle -7500403 true true 110 75 80
Line -7500403 true 150 100 80 30
Line -7500403 true 150 100 220 30

butterfly
true
0
Polygon -7500403 true true 150 165 209 199 225 225 225 255 195 270 165 255 150 240
Polygon -7500403 true true 150 165 89 198 75 225 75 255 105 270 135 255 150 240
Polygon -7500403 true true 139 148 100 105 55 90 25 90 10 105 10 135 25 180 40 195 85 194 139 163
Polygon -7500403 true true 162 150 200 105 245 90 275 90 290 105 290 135 275 180 260 195 215 195 162 165
Polygon -16777216 true false 150 255 135 225 120 150 135 120 150 105 165 120 180 150 165 225
Circle -16777216 true false 135 90 30
Line -16777216 false 150 105 195 60
Line -16777216 false 150 105 105 60

car
false
0
Polygon -7500403 true true 300 180 279 164 261 144 240 135 226 132 213 106 203 84 185 63 159 50 135 50 75 60 0 150 0 165 0 225 300 225 300 180
Circle -16777216 true false 180 180 90
Circle -16777216 true false 30 180 90
Polygon -16777216 true false 162 80 132 78 134 135 209 135 194 105 189 96 180 89
Circle -7500403 true true 47 195 58
Circle -7500403 true true 195 195 58

circle
false
0
Circle -7500403 true true 0 0 300

circle 2
false
0
Circle -7500403 true true 0 0 300
Circle -16777216 true false 30 30 240

circle 3
false
0
Circle -7500403 false true 15 15 270

cow
false
0
Polygon -7500403 true true 200 193 197 249 179 249 177 196 166 187 140 189 93 191 78 179 72 211 49 209 48 181 37 149 25 120 25 89 45 72 103 84 179 75 198 76 252 64 272 81 293 103 285 121 255 121 242 118 224 167
Polygon -7500403 true true 73 210 86 251 62 249 48 208
Polygon -7500403 true true 25 114 16 195 9 204 23 213 25 200 39 123

cylinder
false
0
Circle -7500403 true true 0 0 300

dot
false
0
Circle -7500403 true true 90 90 120

face happy
false
0
Circle -7500403 true true 8 8 285
Circle -16777216 true false 60 75 60
Circle -16777216 true false 180 75 60
Polygon -16777216 true false 150 255 90 239 62 213 47 191 67 179 90 203 109 218 150 225 192 218 210 203 227 181 251 194 236 217 212 240

face neutral
false
0
Circle -7500403 true true 8 7 285
Circle -16777216 true false 60 75 60
Circle -16777216 true false 180 75 60
Rectangle -16777216 true false 60 195 240 225

face sad
false
0
Circle -7500403 true true 8 8 285
Circle -16777216 true false 60 75 60
Circle -16777216 true false 180 75 60
Polygon -16777216 true false 150 168 90 184 62 210 47 232 67 244 90 220 109 205 150 198 192 205 210 220 227 242 251 229 236 206 212 183

fish
false
0
Polygon -1 true false 44 131 21 87 15 86 0 120 15 150 0 180 13 214 20 212 45 166
Polygon -1 true false 135 195 119 235 95 218 76 210 46 204 60 165
Polygon -1 true false 75 45 83 77 71 103 86 114 166 78 135 60
Polygon -7500403 true true 30 136 151 77 226 81 280 119 292 146 292 160 287 170 270 195 195 210 151 212 30 166
Circle -16777216 true false 215 106 30

flag
false
0
Rectangle -7500403 true true 60 15 75 300
Polygon -7500403 true true 90 150 270 90 90 30
Line -7500403 true 75 135 90 135
Line -7500403 true 75 45 90 45

flower
false
0
Polygon -10899396 true false 135 120 165 165 180 210 180 240 150 300 165 300 195 240 195 195 165 135
Circle -7500403 true true 85 132 38
Circle -7500403 true true 130 147 38
Circle -7500403 true true 192 85 38
Circle -7500403 true true 85 40 38
Circle -7500403 true true 177 40 38
Circle -7500403 true true 177 132 38
Circle -7500403 true true 70 85 38
Circle -7500403 true true 130 25 38
Circle -7500403 true true 96 51 108
Circle -16777216 true false 113 68 74
Polygon -10899396 true false 189 233 219 188 249 173 279 188 234 218
Polygon -10899396 true false 180 255 150 210 105 210 75 240 135 240

house
false
0
Rectangle -7500403 true true 45 120 255 285
Rectangle -16777216 true false 120 210 180 285
Polygon -7500403 true true 15 120 150 15 285 120
Line -16777216 false 30 120 270 120

leaf
false
0
Polygon -7500403 true true 150 210 135 195 120 210 60 210 30 195 60 180 60 165 15 135 30 120 15 105 40 104 45 90 60 90 90 105 105 120 120 120 105 60 120 60 135 30 150 15 165 30 180 60 195 60 180 120 195 120 210 105 240 90 255 90 263 104 285 105 270 120 285 135 240 165 240 180 270 195 240 210 180 210 165 195
Polygon -7500403 true true 135 195 135 240 120 255 105 255 105 285 135 285 165 240 165 195

line
true
0
Line -7500403 true 150 0 150 300

line half
true
0
Line -7500403 true 150 0 150 150

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

sheep
false
0
Rectangle -7500403 true true 151 225 180 285
Rectangle -7500403 true true 47 225 75 285
Rectangle -7500403 true true 15 75 210 225
Circle -7500403 true true 135 75 150
Circle -16777216 true false 165 76 116

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

square 3
false
0
Rectangle -7500403 false true 45 45 255 255

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

triangle 3
true
0
Polygon -7500403 false true 45 255 255 255 150 0 45 255

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

x
false
0
Polygon -7500403 true true 270 75 225 30 30 225 75 270
Polygon -7500403 true true 30 75 75 30 270 225 225 270

@#$#@#$#@
NetLogo 4.1
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
<experiments>
  <experiment name="coexistence" repetitions="2" runMetricsEveryStep="true">
    <setup>setup

set xcor_producers -3
set birth_mass_new_producers 0.01
set maximum_mass_new_producers 10
insert-producers

set xcor_producers 3
set birth_mass_new_producers 0.03
set maximum_mass_new_producers 20
insert-producers
insert-decomposers</setup>
    <go>go</go>
    <exitCondition>monocultureReached?</exitCondition>
    <metric>count producers with [producer_species = 0]</metric>
    <metric>count producers with [producer_species = 1]</metric>
    <enumeratedValueSet variable="species_range">
      <value value="10"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="min_gene_transfer_probability_decomposers">
      <value value="0.1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="patch_color">
      <value value="&quot;showEnergy?&quot;"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="showProducers?">
      <value value="true"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="species_range">
      <value value="10"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="xcor_producers">
      <value value="3"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="max_spore_metabolic_fraction_decomposers">
      <value value="5"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="showDecomposers?">
      <value value="false"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="min_seed_dormancy_producers">
      <value value="5"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="min_movement/maintenance_ratio_decomposers">
      <value value="0.01"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="spore_metabolic_fraction_new_decomposers">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="min_birth_mass_producers">
      <value value="0.0050"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="germination_probability_new_producers">
      <value value="2"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="birth_mass_new_producers">
      <value value="0.03"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="changing-landscape?">
      <value value="false"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="seed_dormancy_new_producers">
      <value value="10"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="max_movement/maintenance_ratio_decomposers">
      <value value="2"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="penergy_multiplicator">
      <value value="1500"/>
      <value value="2000"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="passive_movement">
      <value value="0.1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="generative_fraction_new_producers">
      <value value="80"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="max_seed_dormancy_producers">
      <value value="390"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="max_maximum_mass_producers">
      <value value="200"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="max_germination_probability_producers">
      <value value="51"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="max_birth_mass_producers">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="number_producers">
      <value value="4"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="pollination_range">
      <value value="10"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="range">
      <value value="100"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="min_germination_probability_producers">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="gene_transfer_probability_new_decomposers">
      <value value="5"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="smoothness">
      <value value="10"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="landscape-change-rate">
      <value value="200"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="movement/maintenance_ratio_new_decomposers">
      <value value="1.99"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="mutation_probability">
      <value value="0"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="number_decomposers">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="seed_mortality">
      <value value="1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="decomposer_mortality">
      <value value="1.8"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="min_spore_metabolic_fraction_decomposers">
      <value value="0.1"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="max_gene_transfer_probability_decomposers">
      <value value="10"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="dispersal_range">
      <value value="0.2"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="ycor_producers">
      <value value="0"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="min_maximum_mass_producers">
      <value value="2"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="population_size">
      <value value="10000000000"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="maximum_mass_new_producers">
      <value value="20"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="min_generative_fraction_producers">
      <value value="60"/>
    </enumeratedValueSet>
    <enumeratedValueSet variable="max_generative_fraction_producers">
      <value value="100"/>
    </enumeratedValueSet>
  </experiment>
</experiments>
@#$#@#$#@
@#$#@#$#@
default
0.0
-0.2 0 1.0 0.0
0.0 1 1.0 0.0
0.2 0 1.0 0.0
link direction
true
0
Line -7500403 true 150 150 90 180
Line -7500403 true 150 150 210 180

@#$#@#$#@
0
@#$#@#$#@