Forest Dynamic Model II- Rosindell et al. (2010)

extensions [table csv]
globals [V K W-vec rspec speciation specia spec Wvec index speciesi meta-speciesi JM meta-sp meta-time meta-a0  meta-j2 meta-a meta-set2 extinct-species number-of-meta-trees a initial-meta-richness dlocx dlocy 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 t]
breed [meta-trees meta-tree]
breed [trees tree]
meta-trees-own [species meta-species n-speciation-no]
trees-own [species h]
circles-own []
breed [circles a-circle]
patches-own[elevation]

to setup3
  clear-all
  set local-richness-counts map count table:values table:group-agents trees [species]
  set local-richness length local-richness-counts
  set sp 0
  set meta-sp 0
  set speciation 0
  set specia []
  set spec []
  set Wvec []
  set J (w1 + 1) * (w1 + 1)
  resize-world 0 w1 0 w1
  set JM 0
  set K J
  set t 0
  species-gen1
  set hist-frq-local sort-by > map count table:values table:group-agents trees [ species ]
  set rel-hist-frq-local map [ i -> i / count trees ] hist-frq-local
  set richness-counts map count table:values table:group-agents turtles [ species ]
  set richness length richness-counts
  set hist-frq-meta sort-by > map [ i -> i] Wvec
  update-plots
  reset-ticks
end 

to species-gen1
  set k1 -1
  while [k1 < w1 ] [
    set k1 k1 + 1
    set i1 -1
    while [i1 < w1 ] [
      set i1 i1 + 1
      create-trees 1 [
        setxy k1 i1
        set shape "circle"
        set size 1
        set num random-float 1
        set j1 j1 + 1
        set species (sp + 1)
        set sp sp + 1
        set color random-float -50
        set spec fput sp spec
      ]
    ]
  ]
  set local-richness sp
end 

to go3
  while [K > 0] [
    let r1 random-float 1
    if (length spec = 0 )[stop]
    set rspec one-of spec
    if-else (K > 1) [set t t - (ln (r1) / (K * (K - 1 )))]
    [set t 100000]
    if-else (tau >  t) [
      set spec remove rspec spec
      ask trees with [species = rspec] [
        set rspec one-of spec
        set species rspec
        set color [color] of one-of trees with [species = rspec]
      ]
      set K K - 1
      set t 0
      set richness-counts map count table:values table:group-agents turtles [ species ]
      set richness length richness-counts
      set hist-frq-local sort-by > map count table:values table:group-agents turtles [ species ]
      set rel-hist-frq-local map [ i -> i / count turtles ] hist-frq-local
      set hist-frq-meta sort-by > map [ i -> i ] Wvec
      update-plots
      tick
    ]
    [
      if (length spec = 0 )[stop]
      if-else (r1 <= theta / (theta + K - 1)) [
        set speciation speciation + 1
        set specia fput rspec specia
        set spec remove rspec spec
        let Wvec1 count trees with [species = rspec]
        set Wvec fput Wvec1 Wvec
        set sp sp + 1
        let color0 60 + random-float -50
        ask trees with [species = rspec] [
          set species sp
          set color color0
          ;set shape "arrow"
        ]
        set K K - 1
        set richness-counts map count table:values table:group-agents turtles [ species ]
        set richness length richness-counts
        set hist-frq-local sort-by > map count table:values table:group-agents turtles [ species ]
        set rel-hist-frq-local map [ i -> i / count turtles ] hist-frq-local
        set hist-frq-meta sort-by > map [ i -> i ] Wvec
        update-plots
        tick
      ]
      [
        if (length spec = 0 )[stop]
        set spec remove rspec spec
        let color01 [color] of one-of trees with [species = rspec]
        ask trees with [species = rspec] [
          set rspec one-of spec
          set species rspec
          set color color01
        ]
        set K K - 1
        set richness-counts map count table:values table:group-agents turtles [ species ]
        set richness length richness-counts
        set hist-frq-local sort-by > map count table:values table:group-agents turtles [ species ]
        set rel-hist-frq-local map [ i -> i / count turtles ] hist-frq-local
        set hist-frq-meta sort-by > map [ i -> i ] Wvec
        update-plots
        tick
      ]
    ]
  ]
end 

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