Unified Forest Dynamic Model

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 neighbor-patch species0 neighbor-tree conspecifics species2 neighboring-tree specs time-spent-list abundance-list mean-time-spent mean-life-comm data extinct-species-meta]
breed [meta-trees meta-tree]
breed [trees tree]
meta-trees-own [meta-species n-speciation-no species-trait time-system]
trees-own [species h species-trait time-system]
circles-own []
breed [circles a-circle]
patches-own[occupied dis-patch]

to setup2
  clear-all
  ask patches [
    set pcolor black
    set occupied 0
  ]
  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 data []
  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
  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 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
  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
    ;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
   let random-patch one-of patches with [pycor <= w1 AND pycor >= 0 AND pxcor >= 0 AND pxcor <= w1 AND occupied = 0]
   create-meta-trees 1 [
    setxy [pxcor] of random-patch [pycor] of random-patch
    set shape "circle"
    set size 1
    set num random-float 1
    set j1 j1 + 1
    set species-trait random 2
    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
      ]
      ask patches [
        if-else (count turtles-here > 0) [
          set occupied 1
        ]
        [
          set occupied 0
        ]
      ]
      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] [
      let random-patch one-of patches with [pycor <= max-pycor AND pycor > max-pycor - w2 - 1 AND pxcor >= 0 AND pxcor <= w2 AND occupied = 0]
      set i2 i2 - 1
      create-trees 1 [
        set h s + 1
        setxy [pxcor] of random-patch [pycor] of random-patch
        set shape "circle"
        set size 1
        set num random-float 1
        set j2 j2 + 1
        set species-trait random 2
        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
        ]
      ]
      ask patches [
        if-else (count turtles-here > 0)[
          set occupied 1
        ]
        [
          set occupied 0
        ]
      ]
    ]
  ]
  set local-richness sp
end 

to go2
  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
  forest-die-regenerate2
  ask patches [
    if-else (count turtles-here > 0) [
      set occupied 1
    ]
    [
      set occupied 0
    ]
  ]
  count-down
  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
  neut-death-birth
  let disturbance-rate random-float 1
  if (disturbance-rate-per-year <= disturbance-rate) [
    tree-falls-gaps
  ]
  forest-die4
  forest-regenerate4
  if-else (graphics? = true) [
    update-plot1
    update-plots
    plot-genetic-tree-Meta-Community
    update-plots
    update-plot2
    update-plots
    plot-genetic-tree-Local-Community
    update-plots
  ]
  [ ]
  if (count trees <= Disturbance-Size) [
    stop
  ]
  time-spent-system
  update-plot9
  update-plot10
  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 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-else (random-number2 > speciation-rate) [
    ask one-of meta-trees [
      hatch 1
      setxy x-cor y-cor
    ]
  ]
  [
    speciation
  ]
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 time-system time-system + 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-die4
  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
  if-else (intra-specific-competition? = true) [
    ask one-of trees [
    set species species
    set 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 conspecifics count trees in-radius crowd-radius with [species = species0]
      if (conspecifics >= conspecific-crowd) [
        set di-locx xcor
        set di-locy ycor
        die
      ]
    ]
  ]
  [ ]
end 

to forest-regenerate4
  if (conspecifics >= conspecific-crowd) [
      if-else (limited-dispersal? = false) [
        ask one-of trees with [species != species0] [
          set time-system time-system + 1
          hatch 1
          set h  a
          setxy di-locx di-locy
        ]
      ]
      [
        ask patches with [pxcor = di-locx AND pycor = di-locy] [set neighbor-tree one-of trees in-radius dispersal-radius
        ]
        ask neighbor-tree [
          hatch 1
          setxy di-locx di-locy
        ]
      ]
    ]
end 

to tree-falls-gaps
  if (Disturbance-Size = 1) [
    let disturbance-patch one-of patches with [count trees-here >= 1 AND dis-patch = 0 AND pycor <= max-pycor - 1 AND pycor > max-pycor - w2 AND pxcor >= 1 AND pxcor <= w2 - 1]
    ask disturbance-patch [
      set dis-patch 1
    ]
    ask trees-on disturbance-patch [
      die
    ]
    ask disturbance-patch [
      set occupied 0
    ]
    if (Disturbance-Size > 1) [
      repeat Disturbance-Size - 1 [
        ask disturbance-patch [
          let neighboring-patch one-of neighbors with [occupied = 1 AND pycor <= max-pycor AND pycor > max-pycor - w2 - 1 AND pxcor >= 0 AND pxcor <= w2]
          ask neighboring-patch [
            ask trees-here [
              die
            ]
            set dis-patch 1
            set occupied 0
          ]
        ]
      ]
    ]

    if-else (light-sensitivity = true) [
      repeat Disturbance-Size [
        let non-empty-patch one-of patches with [count trees-here > 1 AND pycor <= max-pycor AND pycor > max-pycor - w2 - 1 AND pxcor >= 0 AND pxcor <= w2]
        let empty-patch one-of patches with [count trees-here = 0 AND dis-patch = 1 AND pycor <= max-pycor AND pycor > max-pycor - w2 - 1 AND pxcor >= 0 AND pxcor <= w2]
        ask empty-patch [
          set neighboring-tree one-of trees with [species-trait = 1] in-radius dispersal-radius
          if-else (neighboring-tree = true) [
            ask neighboring-tree [
              hatch 1 [
                ;set time-system time-system + 1
                setxy [pxcor] of empty-patch [pycor] of empty-patch
              ]
            ]
          ]
          [
          set neighboring-tree one-of trees in-radius dispersal-radius
            ask neighboring-tree [
              hatch 1 [
                setxy [pxcor] of empty-patch [pycor] of empty-patch
              ]
            ]
          ]
          set dis-patch 0
          set occupied 1
        ]
      ]
    ]
    [repeat Disturbance-Size [
        let non-empty-patch one-of patches with [count trees-here > 1 AND pycor <= max-pycor AND pycor > max-pycor - w2 - 1 AND pxcor >= 0 AND pxcor <= w2]
        let empty-patch one-of patches with [count trees-here = 0 AND dis-patch = 1 AND pycor <= max-pycor AND pycor > max-pycor - w2 - 1 AND pxcor >= 0 AND pxcor <= w2]
        ask one-of trees [
          hatch 1 [
            setxy [pxcor] of empty-patch [pycor] of empty-patch
          ]
        ]
        ask empty-patch [
        set dis-patch 0
        set occupied 1
        ]
      ]
    ]
  ]
end 

to neut-death-birth
  let rando-patch one-of patches with [pycor <= max-pycor AND pycor > max-pycor - w2 - 1 AND pxcor >= 0 AND pxcor <= w2]
  ask trees-on rando-patch [
    die
  ]
  let random-number4 random-float 1
  if-else (random-number4 > immigration-rate) [
    ask one-of trees [
      hatch 1
      setxy [pxcor] of rando-patch [pycor] of rando-patch
    ]
  ]
  [
    set species2 one-of [meta-species] of meta-trees
    replace-previous-immigrant
    move-immigrant
    immigration-through-channel
    create-trees 1 [
      set species species2
      set h  a
      set shape "circle"
      set size 1
      setxy [pxcor] of rando-patch [pycor] of rando-patch
    ]
  ]
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 time-spent-system
  ask trees [set time-system time-system + 1]
  ask meta-trees [set time-system time-system + 1]
  set specs 0
  set time-spent-list []
  set abundance-list []
  set mean-time-spent []
  set mean-life-comm []
  set data []
  while [specs <= max [species] of trees] [
    let time-spent-list0 sum [time-system] of trees with [species = specs]
    let abundance count trees with [species = specs]
    set time-spent-list fput time-spent-list0 time-spent-list
    if (abundance > 0) [
      set abundance-list fput abundance abundance-list
      let mean-time-spent0 time-spent-list0 / abundance
      set mean-time-spent fput mean-time-spent0 mean-time-spent
      let data0 (list mean-time-spent0 abundance)
      set data fput data0 data
      let mean-life-community mean [time-system] of trees
      set mean-life-comm n-values 300 [i -> mean-life-community]
    ]
    set specs specs + 1
  ]
end 

to update-plot9
  set-current-plot "Average Life Time Vs. Abundance (Y vs. X)"
  clear-plot
  create-temporary-plot-pen (word "pen-0")
  set-current-plot-pen "pen-0"
  set-plot-pen-mode 2
  foreach data [[pt1] -> plotxy item 1 pt1 item 0 pt1]
  update-plots
end 

to update-plot10
  set-current-plot "Average Life Time Vs. Abundance (Y vs. X)"
  create-temporary-plot-pen (word "pen-1")
  set-current-plot-pen "pen-1"
  set-plot-pen-mode 0
  foreach (mean-life-comm) plot
  update-plots
end 

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