Forest Dynamic Model I - Rosindell et al 2010

extensions [table csv]
globals [rspec speciation specia spc spec  rspec0 Wvec V K W-vec 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]
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
  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 sp sp + 1
        set species sp
        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
    set rspec one-of spec
    set spec remove rspec spec
    if-else (r1 <= theta / (theta + K - 1)) [
      set speciation speciation + 1
      set specia fput rspec specia
      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 rspec0 one-of spec
      let color01 [color] of one-of trees with [species = rspec0]
      ask trees with [species = rspec] [
        set species rspec0
        set color color01
      ]
    ]
    set K K - 1
    set richness-counts map count table:values table:group-agents trees [ species ]
    set richness length richness-counts
    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 hist-frq-meta sort-by > map [ i -> i ] Wvec
    update-plots
    tick
  ]
end 


; Copyright 2023g Ruwan Punchi-Manage.
; See Info tab for full copyright and license.