Forest Dynamic Model - Hubbell (1980)

extensions [table csv]
globals [x-cor1 y-cor1 richness1 count-neighbors splist splist2 random-sp sp-id index meta-sp meta-time meta-a0  meta-j2 meta-a meta-set2 extinct-species number-of-meta-trees a initial-meta-richness random-number2 number time num j x-cor y-cor N richness a0 n-speciation local-set local-di-set local-off-set set-species-who-di set-species-who-off sp hist-frq rel-hist-frq s local-set0 remove-set richness-counts species-who-di di-locx di-locy species-who-off set1-species-who-off meta-set effective-meta-cmmunity-size number-of-local-trees item-x meta-set-new meta-sp-count sp-count j1 i1 k1 j2 i2 k2 meta-richness-counts meta-richness local-richness-counts local-richness hist-frq-meta rel-hist-frq-meta hist-frq-local rel-hist-frq-local]
breed [meta-trees meta-tree]
breed [trees tree]
breed [spec a-spec]
turtles-own [species]
meta-trees-own [meta-species n-speciation-no]
trees-own [species h]
spec-own [species]
circles-own []
breed [circles a-circle]
patches-own[elevation]
;extensions [ r ]

to setup2
  clear-all
  set a JL
  set sp 0
  set JL (w2 + 1) * (w2 + 1)
  resize-world 0 w2 0 w2
  species-gen2
  set extinct-species 0
  set hist-frq-local sort-by > map count table:values table:group-agents trees [ species ]
  set rel-hist-frq-local map [ i -> i / JL ] hist-frq-local
  reset-ticks
end 

to species-gen2
  set k2 -1
  while [k2 < w2 ] [
    set k2 k2 + 1
    set i2 -1
    while [i2 < w2] [
      set i2 i2 + 1
      create-trees 1 [
        set h s + 1
        setxy k2 i2
        set shape "circle"
        set size 1
        set num random-float 1
        set j2 j2 + 1
        if-else (num < (theta2 / (theta2 + j2 - 1 ))) [
          set species (sp + 1)
          set label species
          set sp sp + 1
          set color 5 * species + 2
        ]
        [
          set species [species] of one-of other trees
          set sp sp
          set label species
          set color 5 * species + 2
        ]
      ]
    ]
  ]
  set local-richness sp
  set richness1 local-richness
end 

to go2
  count-down
  intraspecific-competition
  ;halt-process
  set hist-frq-local sort-by > map count table:values table:group-agents turtles [ species ]
  set rel-hist-frq-local map [ i -> i / JL ] hist-frq-local
  set richness1 length remove-duplicates [species] of turtles
  set extinct-species local-richness - richness1
  ;update-plot2
  ;plot-genetic-tree-Local-Community
  update-plots
  tick
end 

to count-down
  set time time + 1
end 

to intraspecific-competition
  set random-sp one-of trees
  ask random-sp [
    set x-cor xcor
    set y-cor ycor
    set sp-id species
    set splist remove-duplicates [species] of trees in-radius spacing-distance
    if (length splist < richness1)[
      ask one-of trees with [member? species splist = false] [
        hatch 1
        setxy x-cor y-cor
      ]
      die
    ]
  ]
end 

to halt-process
  ask turtles [
    set splist2 remove-duplicates [species] of trees in-radius 1
    if (member? species splist2 = false) [stop]
  ]
end 

to update-plot2
  set-current-plot "Species Abundance Distribution Local Community"
  set n 1
  while [n <= 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 [species = n]
    set n n + 1
    plot-pen-down
  ]
end 

to plot-genetic-tree-Local-Community
  set sp-count 0
  set-current-plot "Generic-Tree Local Community"
  while [sp-count <= sp] [
    create-temporary-plot-pen (word sp-count)
    set-current-plot-pen (word sp-count)
    set-plot-pen-color 5 * sp-count + 4
    let N-sp count (trees with [species = sp-count])
    if (N-sp > 0) [
      plotxy ticks sp-count
      plot-pen-down
    ]
    set sp-count sp-count + 1
  ]
end 


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