Forest Dynamic Model - Chisholm & Pacala 2010

extensions [table csv]
globals [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 habitat hist-frq-meta0 rel-hist-frq-meta0 hist-frq-local0 rel-hist-frq-local0 extinct-species-meta]
breed [meta-trees meta-tree]
breed [trees tree]
meta-trees-own [meta-species n-speciation-no]
trees-own [species h]
circles-own []
breed [circles a-circle]
patches-own[elevation niche]

to setup2
  clear-all
  set meta-richness-counts map count table:values table:group-agents meta-trees [ meta-species ]
  set meta-richness length meta-richness-counts
  set n-speciation 0
  set meta-set[]
  set meta-sp 0
  set JM (w1 + 1) * (w1 + 1)
  resize-world 0 (w1 + w2 + 20) 0 (w1 + w2 + 20)
  if (Hubbell-2001-Wright-Fisher? = true) [
    set speciation-rate theta / (2 * JM)
    set effective-meta-cmmunity-size JM]
  if (Moran? = true) [
    set speciation-rate theta / JM
    set effective-meta-cmmunity-size JM ^ 2 / 2]
  if (Etinne-Alonso-Hubbell?) [
    set speciation-rate theta / (theta + JM - 1)
    set effective-meta-cmmunity-size JM * (JM - 1) / 2]
  ;if (file-exists? "parent-species-speciation-species-time.csv")
  ;[
    ;carefully
    ;[file-delete "parent-species-speciation-species-time.csv"]
    ;[print error-message]
  ;]
  ;file-open "parent-species-speciation-species-time.csv"
  ;file-close
  ;if (file-exists? "Meta-Community-extinction-species-time.csv")
  ;[
    ;carefully
    ;[file-delete "Meta-Community-extinction-species-time.csv"]
    ;[print error-message]
  ;]
  ;file-open "Meta-Community-extinction-species-time.csv"
  ;file-close
  species-gen1
  ask patches with [count meta-trees-here > 0] [
    set niche 1 + random K
    set pcolor 5 * niche
  ]
  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 hist-frq-meta0 sort-by > map count table:values table:group-agents meta-trees-on patches with [niche = 1 AND count meta-trees-here > 0] [ meta-species ]
  set rel-hist-frq-meta0 map [ i -> i / count patches with [niche = 1 AND count meta-trees-here > 0] ] hist-frq-meta0
  set meta-time 0
  set meta-a0 1
  set n-speciation 0
  set extinct-species-meta 0
  set meta-j2 2
  set meta-a JM
  set a JL
  set sp 0
  set JL (w2 + 1) * (w2 + 1)
  if (Immigration-number? = True) [
    set theta2 immigration-rate * JL / (1 - immigration-rate) ]
  species-gen2
  ask patches with [count trees-here > 0] [
    set niche 1 + random K
    set pcolor 5 * niche
  ]
  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
  set hist-frq-local0 sort-by > map count table:values table:group-agents trees-on patches with [niche = 1 AND count trees-here > 0] [ species ]
  set rel-hist-frq-local0 map [ i -> i / count patches with [niche = 1 AND count trees-here > 0] ] hist-frq-local0
  ;if (file-exists? "Local-Extinction-Species-Extinction-Time.csv")
  ;[
    ;carefully
    ;[file-delete "Local-Extinction-Species-Extinction-Time.csv"]
    ;[print error-message]
  ;]
  ;file-open "Local-Extinction-Species-Extinction-Time.csv"
  ;file-close
  create-channel
  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-meta-trees 1 [
        setxy k1 i1
        set shape "circle"
        set size 1
        set num random-float 1
        set j1 j1 + 1
        if-else (num < (theta / (theta + j1 - 1 ))) [
          set meta-sp meta-sp + 1
          set meta-species meta-sp
          set color 0.5 * meta-species
        ]
        [
          set meta-species [meta-species] of one-of other meta-trees
          set meta-sp meta-sp
          set color 0.5 * meta-species
        ]
        ;file-open "Metacommunityset.csv"
        ;file-print (meta-species)
        ;file-close
      ]
    ]
  ]
  set initial-meta-richness meta-sp
end 

to species-gen2
  set k2 -1
  while [k2 < w2 ] [
    set k2 k2 + 1
    set i2 max-pxcor + 1
    while [i2 <= max-pxcor + 1 AND i2 >= max-pxcor - w2 + 1] [
      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 sp sp + 1
          set species sp
          set color 5 * species + 2
        ]
        [
          set species [species] of one-of other trees
          set sp sp
          set color 5 * species + 2
        ]
      ]
    ]
  ]
  set local-richness sp
end 

to go2
  forest-die-regenerate2
  count-down
  speciation
  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 hist-frq-meta0 sort-by > map count table:values table:group-agents meta-trees-on patches with [niche = 1 AND count meta-trees-here > 0] [ meta-species ]
  set rel-hist-frq-meta0 map [ i -> i / count patches with [niche = 1 AND count meta-trees-here > 0] ] hist-frq-meta0
  update-plots
  if (graphic? = true) [
    plot-genetic-tree-Meta-Community
    update-plot1
    update-plot4
  ]
  forest-die-regenerate3
  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
  set hist-frq-local0 sort-by > map count table:values table:group-agents trees-on patches with [niche = 1 AND count trees-here > 0] [ species ]
  set rel-hist-frq-local0 map [ i -> i / count patches with [niche = 1 AND count trees-here > 0] ] hist-frq-local0
  if (graphic? = true) [
    plot-genetic-tree-Local-Community
    update-plot2
    update-plot3
  ]
  update-plots
  tick
end 

to forest-die-regenerate2
  set N count meta-trees
  set meta-richness-counts map count table:values table:group-agents meta-trees [ meta-species ]
  set meta-richness length meta-richness-counts
  ask one-of meta-trees [
    set x-cor xcor
    set y-cor ycor
    set habitat [niche] of patch x-cor y-cor
    set meta-species meta-species
    let meta-species0 meta-species
    set number-of-meta-trees count meta-trees with [meta-species = meta-species0]
    if (number-of-meta-trees = 1)[
      set extinct-species-meta extinct-species-meta + 1
      ;file-open "Meta-Community-extinction-species-time.csv"
      ;file-write (meta-species)
      ;file-write (ticks)
      ;file-print ""
      ;file-close
    ]
    die
  ]
  set random-number2 random-float 1
  if (random-number2 > speciation-rate)[
    ask one-of meta-trees-on patches with [niche = habitat] [
      hatch 1
      setxy x-cor y-cor
    ]
  ]
end 

to count-down
  set time time + 1
end 

to speciation
  if  (random-number2 <= speciation-rate) [
    set n-speciation n-speciation + 1
    set meta-sp meta-sp + 1
    ask one-of meta-trees [
      let parent-of-speciation meta-species
      hatch 1
      set n-speciation-no n-speciation
      set meta-j2 meta-j2 + 1
      set meta-species meta-sp
      set color  0.5 * (a0 + 1 + meta-j2)
      setxy x-cor y-cor
      ;file-open "parent-species-speciation-species-time.csv"
      ;file-write (parent-of-speciation)
      ;file-write (meta-species)
      ;file-write (ticks)
      ;file-print ""
      ;file-close
    ]
  ]
end 

to forest-die-regenerate3
  set N count trees
  count-down
  set remove-set []
  set local-richness-counts map count table:values table:group-agents trees [species]
  set local-richness length local-richness-counts
  repeat D [ask one-of trees [
    set species species
    let species0 species
    set number-of-local-trees count trees with [species = species0]
    if (number-of-local-trees = 1)[
      set extinct-species extinct-species + 1
      ;file-open "Local-Extinction-Species-Extinction-Time.csv"
      ;file-write (species0)
      ;file-write (ticks)
      ;file-print ""
      ;file-close
    ]
    set di-locx xcor
    set di-locy ycor
    set habitat [niche] of patch x-cor y-cor
    die
    ]
    let random-number3 random-float 1
    if-else (immigration-rate < random-number3) [
      ask one-of trees-on patches with [niche = habitat] [
        hatch 1
        set h  a
        setxy di-locx di-locy
      ]
    ]
    [
      replace-previous-immigrant
      move-immigrant
      immigration-through-channel
      create-trees 1 [
        set species one-of [meta-species] of meta-trees
        set h  a
        set shape "circle"
        set size 1
        setxy di-locx di-locy
      ]
    ]
  ]
end 

to update-plot1
  set-current-plot "Species Abundance Distribution Meta 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 meta-trees with [meta-species = n]
    set n n + 1
    plot-pen-down
  ]
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-Meta-Community
  set meta-sp-count 0
  set-current-plot "Generic-Tree Meta Community"
  while [meta-sp-count <= meta-sp] [
    create-temporary-plot-pen (word meta-sp-count)
    set-current-plot-pen (word meta-sp-count)
    set-plot-pen-color 5 * meta-sp-count + 4
    let N-sp count (meta-trees with [meta-species = meta-sp-count])
    if (N-sp > 0) [
      plotxy ticks meta-sp-count
      plot-pen-down
    ]
    set meta-sp-count meta-sp-count + 1
  ]
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 

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-plot3
  set-current-plot "Relative species abundance of niches in local community"
  let n2 1
  clear-plot
  while [n2 <= K] [
    create-temporary-plot-pen (word "habitat " n2)
    set-current-plot-pen (word "habitat " n2)
    set-plot-pen-color 5 * n2 + 4
    set-plot-pen-mode 0
    set hist-frq-local0 sort-by > map count table:values table:group-agents trees-on patches with [niche = n2 AND count trees-here > 0] [ species ]
    set rel-hist-frq-local0 map [ i -> i / count patches with [niche = n2 AND count trees-here > 0] ] hist-frq-local0
    foreach (reverse sort rel-hist-frq-local0) plot
    set n2 n2 + 1
    plot-pen-down
  ]
end 

to update-plot4
  set-current-plot "Relative species abundance of niches in meta-community"
  let n3 1
  clear-plot
  while [n3 <= K] [
    create-temporary-plot-pen (word "habitat " n3)
    set-current-plot-pen (word "habitat " n3)
    set-plot-pen-color 5 * n3 + 4
    set-plot-pen-mode 0
    set hist-frq-meta0 sort-by > map count table:values table:group-agents trees-on patches with [niche = n3 AND count trees-here > 0] [ species ]
    set rel-hist-frq-meta0 map [ i -> i / count patches with [niche = n3 AND count trees-here > 0] ] hist-frq-meta0
    foreach (reverse sort rel-hist-frq-meta0) plot
    set n3 n3 + 1
    plot-pen-down
  ]
end 

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