Forest Dynamic Model - Bell (2000)

extensions [table csv]
globals [meta-sp extinct-species n-speciation spi local-s K1 i1 K2 i2 hist-frq-local rel-hist-frq-local local-richness local-richness-counts count-dead-trees immigrant-trees count-new-trees n crowding conspecifics di-locx di-locy neighbor-patch JL1]
breed [meta-trees meta-tree]
breed [trees tree]
meta-trees-own [species]
trees-own [species h]
patches-own [occupied]
circles-own []
breed [circles a-circle]

to setup2
  clear-all
  set meta-sp 0
  set JMS (w1 + 1) * (w1 + 1)
  resize-world 0 (w1 + w2 + 20) 0 (w1 + w2 + 20)
  ;set hist-frq-meta sort-by > map count table:values table:group-agents meta-trees [ meta-species ]
  ;set rel-hist-frq-meta map [ i -> i / JM ] hist-frq-meta
  set extinct-species 0
  set n-speciation 0
  set JL initial-local-richness * Ni
  set K (w2 + 1) * (w2 + 1)
  set w2 w2
  set n 0
  set di-locx 0
  set di-locy max-pycor
  ask patches with [pycor <= max-pycor AND pycor >= w1 + 20 AND pxcor >= 0 AND pxcor <= w2] [
    set pcolor gray
    set occupied 0 ]
  species-generator-1
  species-generator-4
  set hist-frq-local sort-by > map count table:values table:group-agents turtles with [ycor >= w1 + 20] [species]
  set rel-hist-frq-local map [ i -> i / JL ] hist-frq-local
  set local-richness local-s
  set count-dead-trees 0
  set immigrant-trees 0
  set count-new-trees 0
  create-channel
  reset-ticks
end 

to species-generator-1
  set k1 -1
  while [k1 < w1 ] [
    set k1 k1 + 1
    set i1 -1
    while [i1 < w1 ] [
      set i1 i1 + 1
      create-meta-trees 1 [
        let random-patch one-of patches with [pycor <= w1 AND pycor >= 0 AND pxcor >= 0 AND pxcor <= w1 AND occupied = 0]
        setxy [pxcor] of random-patch [pycor] of random-patch
        set shape "circle"
        set size 1
        set species (meta-sp + 1)
        set meta-sp meta-sp + 1
        set color species
        ask patch-here [set occupied 1]
      ]
    ]
  ]
end 

to species-generator-4
  set k2 1
  while [k2 <= initial-local-richness] [
    set k2 k2 + 1
    set i2 max-pxcor + 1
    set local-s local-s + 1
    repeat Ni [
      let random-patch one-of patches with [pycor <= max-pycor AND pycor >= w1 + 20 AND pxcor >= 0 AND pxcor <= w2 AND occupied = 0]
      create-trees 1 [
        set i2 i2 - 1
        set shape "circle"
        set size 1
        set species local-s
        setxy [pxcor] of random-patch [pycor] of random-patch
        set color local-s
        ask patch-here [set occupied 1]
        ]
      ]
    ]
end 

to go2
  test-capacity
  death-rates
  birth-rates
  immigration
  set JL1 count turtles-on patches with [pycor <= max-pycor AND pycor >= w1 + 20 AND pxcor >= 0 AND pxcor <= w2]
  set hist-frq-local sort-by > map count table:values table:group-agents turtles with [pycor > w1 + 20] [ species ]
  set rel-hist-frq-local map [ i -> i / JL1 ] hist-frq-local
  set local-richness-counts map count table:values table:group-agents turtles with [pycor >= w1 + 20] [species ]
  set local-richness length local-richness-counts
  update-plots
  tick
end 

to immigration
  let random-number3 random-float 1
  if (immigration-rate > random-number3) [
      replace-previous-immigrant
      move-immigrant
      immigration-through-channel
    ask one-of meta-trees [
      hatch 1
      let random-patch one-of patches with [pycor <= max-pycor AND pycor >= w1 + 20 AND pxcor >= 0 AND pxcor <= w2 AND occupied = 0]
      setxy [pxcor] of random-patch [pycor] of random-patch
      ask patch-here [set occupied 1]
    ]
    set immigrant-trees immigrant-trees + 1
  ]
end 

to birth-rates
 let random-number1 random-float 1
    if (b > random-number1) [
      set count-new-trees count-new-trees + 1
    ask one-of turtles with [ycor >= w1 + 20] [
        hatch 1
        let random-patch one-of patches with [pycor <= max-pycor AND pycor >= w1 + 20 AND pxcor >= 0 AND pxcor <= w2 AND occupied = 0]
        setxy [pxcor] of random-patch [pycor] of random-patch
        ask patch-here [set occupied 1]
        ]
      ]
end 

to death-rates
 let random-number2 random-float 1
  if (d > random-number2) [
    ask one-of turtles with [ycor >= w1 + 20] [
      set di-locx xcor
      set di-locy ycor
      die]
    set count-dead-trees count-dead-trees + 1
  ]
end 

to create-channel
  ask patches [
    if (pxcor > w2 / 2 AND pxcor < ((w2 / 2) + 2) AND pycor > w1 AND pycor < w1 + 20) [
      set pcolor gray
    ]
  ]
end 

to immigration-through-channel
  create-circles 1 [
    set color ticks
    set heading 0
    set size 1
    setxy ((w2 + 2) / 2) (w1 + 1)
   ]
end 

to move-immigrant
  ask circles [ fd 4]
end 

to replace-previous-immigrant
  ask circles with [ycor > (w1 + 13) ] [die]
end 

to update-plot2
set-current-plot "Species Abundance Distribution Local Community"
set n 1
while [n <= meta-sp] [
create-temporary-plot-pen (word n)
set-current-plot-pen (word n)
set-plot-pen-color 5 * n + 4
plotxy ticks count trees with [ycor >= w1 + 20 AND species = n]
set n n + 1
plot-pen-down
]
end 

to test-capacity
  if (count turtles with [ycor >= w1 + 20] > K - 5) [
    ask one-of turtles with [ycor >= w1 + 20] [die]
    ]
  ask patches [
    if (count turtles-here > 0) [
      set occupied 1
    ]
    if (count turtles-here = 0) [
      set occupied 0
    ]
  ]
end 

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