Tabonuco Yagrumo Hybrid

;; To see the rest of this model, look in the System Dynamics Modeler
;; window.  (If the window isn't showing, you can open it from the
;; Tools menu.)

globals [ previous-carbon
          tabonuco-growth
          yagrumo-growth
          tabonuco-death
          yagrumo-death
          converted-to-tabonuco ]

breed [ tabonucos tabonuco ]
breed [ yagrumos yagrumo ]

to setup
  ca
  set-default-shape yagrumos "plant"
  set-default-shape tabonucos "tree"
  set previous-carbon 0
  system-dynamics-setup             ;; defined by System Dynamics Modeler
  agent-setup
  do-plot
end 

to go
  agent-go
  system-dynamics-go                ;; defined by System Dynamics Modeler
  do-plot
  set previous-carbon carbon
end 

;; Agent-Based rule setup for model.

to agent-setup
  ask n-of tabonuco-stock patches [ sprout-tabonucos 1 [ set color sky ] ]
  ask n-of yagrumo-stock patches with [ not any? turtles-here ] [ sprout-yagrumos 1 [ set color pink ] ]
end 


;; Agent-Based rules for the model
;; These are only run oncce per cycle of the model, and the order is important
;; Tabonuco trees get first shot at open patches.

to agent-go
  set yagrumo-growth agent-yagrumo-growth yagrumo-stock
  set tabonuco-growth agent-tabonuco-growth tabonuco-stock

  set tabonuco-death agent-tabonuco-death disturbance
  set yagrumo-death agent-yagrumo-death disturbance
  set converted-to-tabonuco agent-tabonuco-conversion tabonuco-outgrowth-rate
end 

to-report empty-patches
  report patches with [ not any? turtles-here ]
end 

;; Rules governing the conversion of yagrumo trees to tabonuco trees
;; Only yagrumo trees next to an existing tabonuco tree can be converted
;; and only tabonuco-outgrowth-rate are converted.

to-report agent-tabonuco-conversion [ rate ]
  let total-converted 0
  let convertables yagrumos with [ any? neighbors with [ any? tabonucos-here ] ]
  ask n-of (count convertables * rate) convertables
    [ set total-converted total-converted + 1
      set breed tabonucos set color sky ]
  report total-converted
end 


;; Rules governing the growth of Tabonuco trees
;; only trees with an empty patch next to them get a chance to reproduce
;; and only tabonuco-growth-rate of those trees can reproduce

to-report agent-tabonuco-growth [ current ]
  let total-grown 0
  let growable tabonucos with [ not all? neighbors [ any? turtles-here ] ]
  ask n-of ( count growable * tabonuco-growth-rate ) growable
    [ let seedpatch one-of neighbors with [ not any? turtles-here ]
      if ( seedpatch != nobody )
        [ ask seedpatch
            [ sprout-tabonucos 1 [ set color sky ]
              set total-grown total-grown + 1
            ]
        ]
    ]
    report total-grown
end 

;; Rules governing the growth of Yagrumo trees
;; only trees with an empty patch next to them get a chance to reproduce
;; and only tabonuco-growth-rate of those trees can reproduce

to-report agent-yagrumo-growth [ current ]
 let total-grown 0
  let growable yagrumos with [ not all? neighbors [ any? turtles-here ] ]
  ask n-of ( count growable  * yagrumo-growth-rate ) growable
    [ let seedpatch one-of neighbors with [ not any? turtles-here ]
      if ( seedpatch != nobody )
        [ ask seedpatch
            [ sprout-yagrumos 1 [ set color pink ]
              set total-grown total-grown + 1
            ]
        ]
    ]
    report total-grown
end 


;; Rules governing destruction of Tabonuco trees

to-report agent-tabonuco-death [ dist ]
  let total-dead 0
  ask n-of min (list (count tabonucos) ( tabonuco-stock * dist ) ) tabonucos
    [ set total-dead total-dead + 1
      die
    ]
  report total-dead
end 

;; Rules governing destruction of Yagrumo trees

to-report agent-yagrumo-death [ dist ]
  let total-dead 0
  ask n-of min (list (count yagrumos) ( yagrumo-stock * dist ) ) yagrumos
    [ set total-dead total-dead + 1
      die
    ]
  report total-dead
end 

to do-plot
  set-current-plot "output"
  set-current-plot-pen "carbon"
  plotxy ticks carbon
  set-current-plot-pen "nitrogen"
  plotxy ticks nitrogen
  set-current-plot "productivity"
  set-current-plot-pen "productivity"
  plotxy ticks productivity
  set-current-plot "trees"
  set-current-plot-pen "tabonuco"
  plotxy ticks amount-of-tabonuco
  set-current-plot-pen "yagrumo"
  plotxy ticks amount-of-yagrumo
end 

to-report pulse [ volume initial interval ]
  set interval abs interval
  let our-x ticks - initial
  let peak volume / dt
  let slope peak / ( dt / 2 )
  let offset abs our-x
  ;; if we have passed the initial pulse, then recalibrate
  ;; to the next pulse interval, if there IS an interval given
  if ( interval > 0 and our-x > ( dt / 2 ) )
    [ set offset  ( our-x mod interval )
      if ( offset > dt / 2 ) [ set offset 0 + offset - interval ]  ]
  ;; the down side of the pulse
  if ( offset >= 0 and offset <= dt / 2  )
     [ report peak - ( slope * offset ) ]
  ;; the upside of the pulse
  if ( offset < 0 and offset >= ( 0 - ( dt / 2 ) ) )
     [ report slope * min (list ( dt / 2 ) ( abs ( interval - offset ) ) ) ]
  report 0
end 

to test-pulse [ volume initial interval ]
  setup
  repeat 250 [
    let y pulse volume initial interval
    output-print y
    set-current-plot "productivity"
    plotxy ticks y
    tick-advance dt ]
end 


; Copyright 2006 Uri Wilensky.
; See Info tab for full copyright and license.