globals [                
  clustering-coefficient                 
  clustering-coefficient-of-lattice                                 
  average-path-length
  average-path-length-of-lattice
  infinity
  acc_change
  apl_change  
  average_degree
  density
  component-size
  giant-component-size
  components
  go?
  proportion_cooperation_list
  tolerance_list
  average_hamming_distance_list
  cum_duration_fall
  duration_fall
  cooperation_history
  first_emergence_time_all_coop
  first_emergence_time_all_defect
  first_emergence_time_either
  phase
  cum_duration_rise
  duration_rise
  count_rise
  count_fall   
  mode_tolerance_list_history
  count_zero_block
  tol_dependent_degree_list   
]

turtles-own
[
  score
  tag-list
  tolerance
  average_hamming_distance
  dissimilarity_list
  new_disdissimilarity_list
  neighbor_list
  new_neighbor_list
  temp-score
  temp-strategy
  strategy-list 
  node-clustering-coefficient 
  distance-from-other-turtles
  target
  explored?
]

to setup
  clear-all
  set infinity 999
  set cum_duration_fall 0
  set duration_fall 0 
  set cum_duration_rise 0
  set duration_rise 0
  set cooperation_history [ ]
  set count_rise 0
  set count_fall 0  
  set mode_tolerance_list_history [ ] 
  set count_zero_block 0
  set-default-shape turtles "circle"  
  make-nodes-links
  no-display
  set clustering-coefficient-of-lattice clustering-coefficient
  set average-path-length-of-lattice average-path-length
  ask turtles [ 
    set neighbor_list [ who ] of link-neighbors 
    set new_neighbor_list sort neighbor_list  
    establish-color-setup
  ]  
  ask turtles [ similarity-perception ]  
  ;;if ( b/c = *** ) and ( network_plasticity = *** ) and ( closure_probability = *** ) [ 
    ;;file-open "E:\\exp***.txt"
  ;;] 
  update-plot
  display
end

to make-nodes-links
    make-nodes-net
    if ( erdos_renyi_probability = 0 or erdos_renyi_probability = 1 ) [ stop ]
    ask turtles [
      create-links-with turtles with [self > myself and random-float 1.0 <= erdos_renyi_probability ] [
        set color grey - 3
      ]
    ]
    let success? not any? turtles with [ count my-links = 0 ] 
    set success? do-calculations
    ifelse average-path-length = 999 [ 
      setup 
      clear-all-plots
    ] [
      ask turtles [
        set size ( 0.2 * count my-links )
      ]
      set success? do-calculations 
    ]
end  

to make-nodes-net
  crt num_of_agents [
    set tag-list [ ]
    let i 0
    while [ i < num-of-tag-item ]
    [ set tag-list fput random 2 tag-list
      set i i + 1
    ]    
    let j 0
    while [ j < num_of_agents ]
    [ let l num-of-tag-item
      set tolerance random ( l + 2 ) 
      set j j + 1
    ]    
    set dissimilarity_list [ ]
    set new_disdissimilarity_list [ ]
    set neighbor_list [ ]
    set new_neighbor_list [ ]
    set strategy-list [ ]
    set temp-score [ ]     
    layout-circle (sort turtles) max-pxcor - 1
  ]
end

to establish-color-setup 
  set color 1 + tolerance  
end


to go 
  set go? true 
  ask turtles [
    similarity-perception
  ]
  ask turtles [
    interaction-payoff
  ]
  ask turtles [
    tag-tolerance-update 
  ]
  ask turtles [ 
    select present_what
    ifelse count my-links != 0 [
      set size ( 0.2 * count my-links )    
    ] [
      set size 0.4
    ]
  ]
  tick
  if layout? [ layout ]
  let success? do-calculations
  update-plot
end

;;Text files can be exported in the following ways.
;;to write-to-file-network
  ;;file-print ( word "dl " "n=" num_of_agents " format=nodelist1" )
  ;;file-type ( word "data:" ) 
  ;;foreach sort turtles [ 
    ;;....
  ;;file-print ""
;;end

;;to write-to-file-attribute
  ;;file-print " "
  ;;foreach sort turtles [  
    ;;...
  ;;file-print " "    
;;end

to-report do-calculations
  ;; set up a variable so we can report if the network is disconnected
  let connected? true
    ;; find the path lengths in the network
  find-path-lengths
  let num-connected-pairs sum [length remove infinity (remove 0 distance-from-other-turtles)] of turtles
  ;; In a connected network on N nodes, we should have N(N-1) measurements of distances between pairs,
  ;; and none of those distances should be infinity.
  ;; If there were any "infinity" length paths between nodes, then the network is disconnected.
  ;; In that case, calculating the average-path-length doesn't really make sense.
  ifelse ( num-connected-pairs != (count turtles * (count turtles - 1) ))
  [
      set average-path-length infinity
      ;; report that the network is not connected
      set connected? false
  ]
  [
    set average-path-length (sum [sum distance-from-other-turtles] of turtles) / (num-connected-pairs)
  ]
  ;; find the clustering coefficient and add to the aggregate for all iterations
  find-clustering-coefficient
  ;; report whether the network is connected or not
  report connected?
end

to-report in-neighborhood? [ hood ]
  report ( member? end1 hood and member? end2 hood )
end

to find-clustering-coefficient
  ifelse all? turtles [count link-neighbors <= 1]
  [
    set clustering-coefficient 0
  ]
  [
    let total 0
    ask turtles with [ count link-neighbors <= 1]
      [ set node-clustering-coefficient "undefined" ]
    ask turtles with [ count link-neighbors > 1]
    [
      let hood link-neighbors
      set node-clustering-coefficient (2 * count links with [ in-neighborhood? hood ] /
                                         ((count hood) * (count hood - 1)) )
      ;; find the sum for the value at turtles
      set total total + node-clustering-coefficient
    ]
    ;; take the average
    set clustering-coefficient total / count turtles with [count link-neighbors > 1]
  ]
end

;; Implements the Floyd Warshall algorithm for All Pairs Shortest Paths 
;; It is a dynamic programming algorithm which builds bigger solutions
;; from the solutions of smaller subproblems using memoization that
;; is storing the results.
;; It keeps finding incrementally if there is shorter path through
;; the kth node.
;; Since it iterates over all turtles through k,
;; so at the end we get the shortest possible path for each i and j.

to find-path-lengths
  ;; reset the distance list
  ask turtles
  [
    set distance-from-other-turtles []
  ]
  let i 0
  let j 0
  let k 0
  let node1 one-of turtles
  let node2 one-of turtles
  let node-count count turtles
  ;; initialize the distance lists
  while [i < node-count]
  [
    set j 0
    while [j < node-count]
    [
      set node1 turtle i
      set node2 turtle j
      ;; zero from a node to itself
      ifelse i = j
      [
        ask node1 [
          set distance-from-other-turtles lput 0 distance-from-other-turtles
        ]
      ]
      [
        ;; 1 from a node to it's neighbor
        ifelse [ link-neighbor? node1 ] of node2
        [
          ask node1 [
            set distance-from-other-turtles lput 1 distance-from-other-turtles
          ]
        ]
        ;; infinite to everyone else
        [
          ask node1 [
            set distance-from-other-turtles lput infinity distance-from-other-turtles
          ]
        ]
      ]
      set j j + 1
    ]
    set i i + 1
  ]
  set i 0
  set j 0
  let dummy 0
  while [k < node-count]
  [
    set i 0
    while [i < node-count]
    [
      set j 0
      while [j < node-count]
      [
        ;; alternate path length through kth node
        set dummy ( (item k [distance-from-other-turtles] of turtle i) +
                    (item j [distance-from-other-turtles] of turtle k))
        ;; is the alternate path shorter?
        if dummy < (item j [distance-from-other-turtles] of turtle i)
        [
          ask turtle i [
            set distance-from-other-turtles replace-item j distance-from-other-turtles dummy
          ]
        ]
        set j j + 1
      ]
      set i i + 1
    ]
    set k k + 1
  ]
end

to similarity-perception
  ifelse count link-neighbors = 0 [
    set average_hamming_distance 0
  ] [
    set neighbor_list [ who ] of link-neighbors
    set new_neighbor_list sort neighbor_list
    set dissimilarity_list [ ]
    let i 0
    while [ i < count link-neighbors ]
    [ 
      let b length filter [ ? = true ] ( map [ ?1 = 1 and ?2 = 0 ] [ tag-list ] of self [ tag-list ] of turtle item i new_neighbor_list ) 
      let c length filter [ ? = true ] ( map [ ?1 = 0 and ?2 = 1 ] [ tag-list ] of self [ tag-list ] of turtle item i new_neighbor_list )
      set dissimilarity_list lput ( b + c ) dissimilarity_list
      set i i + 1
    ]    
    set new_disdissimilarity_list dissimilarity_list
    set average_hamming_distance mean new_disdissimilarity_list
  ]
end

to interaction-payoff
  set score 0
  set temp-score [ ]
  set strategy-list [ ]
  let i 0
  while [ i < count link-neighbors ] [
    let partner turtle item i new_neighbor_list
    let ego self
    let p position [ who ] of ego [ new_neighbor_list ] of partner
    ask partner [
      ifelse [ tolerance ] of partner > item p [ new_disdissimilarity_list ] of partner [
        set temp-strategy true 
      ] [
        set temp-strategy false 
      ]
    ]
    ifelse [ tolerance ] of ego > item i [ new_disdissimilarity_list ] of ego [ 
      set [ temp-strategy ] of ego true
      set strategy-list lput 1 strategy-list
      ifelse [ temp-strategy ] of partner = true [
        set temp-score fput ( b/c - 1 ) temp-score 
      ] [
        set temp-score fput ( - 1 ) temp-score
      ] 
    ] [
      set [ temp-strategy ] of ego false
      set strategy-list lput 0 strategy-list
      ifelse [ temp-strategy ] of partner = true [
        set temp-score fput b/c temp-score 
      ] [
        set temp-score fput 0 temp-score
      ]     
    ]  
    set i i + 1
  ]
  set score sum temp-score 

end

;; Things to Notice 
;; There are two mutation rates, mu1 and mu2, in this model as below. 
;; The mutation rates are controlled as 0.01 for cultural perturbation and network perturbation, 
;; Given the codes actually used below, 
;; the following values were taken in our Behavior-Space experiments. 
;; At p=10, mu1=1/90; mu2=1/10 
;; At p=20, mu1=1/80; mu2=1/20 
;; At p=30, mu1=1/70; mu2=1/30 
;; At p=40, mu1=1/60; mu2=1/40 
;; At p=50, mu1=1/50; mu2=1/50
;; Without network plasticity, if the mutation rate is 1 given N=100, 1 agent errs in learning.
;; If network plasticity = 50 but the same mutation rate (0.01), 
;; the chance of cultural mutation will decrease, which accordingly reduces the emergence of mutant defectors (i.e. Conditional probability).
;; To avoid this issue, regardless of different levels of network plasticity,
;; 1 agent experiences cultural perturbation, and 1 agent experiences network perturbation at every generation.

to tag-tolerance-update 
  let p random 100
  let m random-float 1.0
  ifelse ( p < network_plasticity and p >= 0 ) [
    ifelse mu1 > m [
      ifelse count link-neighbors != 0 [
        random_breaking_making 
      ] [
        random_making 
      ]
    ] [
      ifelse count link-neighbors != 0 [      
        breaking_if_outgroup_making_if_ingroup 
      ] [
        making_if_ingroup  
      ]
    ]
  ] [
    ifelse mu2 > m [
      ifelse count link-neighbors != 0 [
        set tag-list [ ]
        let j 0
        while [ j < num-of-tag-item ]
        [ set tag-list fput random 2 tag-list
          set j j + 1
        ] 
        set tolerance random ( num-of-tag-item + 2 ) 
      ] [
        stop 
      ]
    ] [
      ifelse count link-neighbors != 0 [
        let reference one-of link-neighbors
        let what-to-compare [score] of reference
        let self-score [score] of self        
        if what-to-compare > self-score [
          set tag-list [ ]
          set tag-list [ tag-list ] of reference
          ifelse tolerance > [ tolerance ] of reference [
            ifelse tolerance = 0 [
              set tolerance tolerance
            ] [
              set tolerance tolerance - 1
            ]
          ] [
            ifelse tolerance = [ tolerance ] of reference [
              set tolerance [ tolerance ] of reference
            ] [
              ifelse tolerance = num-of-tag-item + 1 [
                set tolerance tolerance
              ] [
                set tolerance tolerance + 1
              ]
            ]
          ]          
        ]   
      ] [
        stop 
      ]
    ]
  ]      
end

to random_breaking_making
  let node1 one-of link-neighbors
  let f [ who ] of node1
  let node3 self
  let g [ who ] of node3
  ifelse ( node1 = nobody ) [
    stop
  ] [
    let node2 one-of turtles with [ ( not link-neighbor? node3 ) and ( self != node3 )] 
    let h [ who ] of node2
    ask node3 [ create-link-with node2 [ set color green - 1 ] ]
    ask link [ who ] of node3 [ who ] of node1 [ die ]
    set [ new_neighbor_list ] of self fput h [ new_neighbor_list ] of self
    set [ new_neighbor_list ] of self sort remove f [ new_neighbor_list ] of self
    set [ new_neighbor_list ] of node2 sort fput g [ new_neighbor_list ] of node2  
    set [ new_neighbor_list ] of node1 sort remove g [ new_neighbor_list ] of node1      
  ] 
end

to random_making
  let node1 self
  let b [ who ] of node1
  let node2 one-of turtles with [ ( not link-neighbor? node1 ) and ( self != node1 ) ]
  let a [ who ] of node2
  ask node1 [ create-link-with node2 [ set color green - 1 ] ]
  set [ new_neighbor_list ] of self sort fput a [ new_neighbor_list ] of self
  set [ new_neighbor_list ] of node2 sort fput b [ new_neighbor_list ] of node2
end

to breaking_if_outgroup_making_if_ingroup
  let node1 one-of link-neighbors 
  let b length filter [ ? = true ] ( map [ ?1 = 1 and ?2 = 0 ] [ tag-list ] of self [ tag-list ] of node1 ) 
  let c length filter [ ? = true ] ( map [ ?1 = 0 and ?2 = 1 ] [ tag-list ] of self [ tag-list ] of node1 )
  let dis1 ( b + c ) 
  ifelse dis1 >= [ tolerance ] of self [ 
    let f [ who ] of node1
    let node3 self
    let g [ who ] of node3
    ifelse ( node1 = nobody ) [ 
      stop
    ] [  
      let q random 100
      ifelse ( q < closure_probability and q >= 0 ) [
        set target one-of link-neighbors
        ifelse count [ link-neighbors ] of target >= 2 [
          let node2 one-of other [ link-neighbors ] of target 
          let a length filter [ ? = true ] ( map [ ?1 = 1 and ?2 = 0 ] [ tag-list ] of self [ tag-list ] of node2 ) 
          let d length filter [ ? = true ] ( map [ ?1 = 0 and ?2 = 1 ] [ tag-list ] of self [ tag-list ] of node2 )
          let dis2 ( a + d )       
          ifelse ( dis2 < [ tolerance ] of self ) and ( dis2 < [ tolerance ] of node2 ) [ 
            let h [ who ] of node2
            ask node3 [ create-link-with node2 [ set color white - 1 ] ]
            ask link [ who ] of node3 [ who ] of node1 [ die ]      
            set [ new_neighbor_list ] of self sort fput h [ new_neighbor_list ] of node3
            set [ new_neighbor_list ] of self sort remove f [ new_neighbor_list ] of self      
            set [ new_neighbor_list ] of node2 sort fput g [ new_neighbor_list ] of node2
            set [ new_neighbor_list ] of node1 sort remove g [ new_neighbor_list ] of node1               
          ] [
            stop
          ]
        ] [
          stop
        ]
      ] [
        let node2 one-of turtles with [ ( not link-neighbor? node3 ) and ( self != node3 ) and ( not member? self [ link-neighbors ] of link-neighbors ) ] 
        let a length filter [ ? = true ] ( map [ ?1 = 1 and ?2 = 0 ] [ tag-list ] of self [ tag-list ] of node2 ) 
        let d length filter [ ? = true ] ( map [ ?1 = 0 and ?2 = 1 ] [ tag-list ] of self [ tag-list ] of node2 )
        let dis2 ( a + d )       
        ifelse ( dis2 < [ tolerance ] of self ) and ( dis2 < [ tolerance ] of node2 ) [ 
          let h [ who ] of node2
          ask node3 [ create-link-with node2 [ set color blue - 1 ] ]
          ask link [ who ] of node3 [ who ] of node1 [ die ]      
          set [ new_neighbor_list ] of self sort fput h [ new_neighbor_list ] of self
          set [ new_neighbor_list ] of self sort remove f [ new_neighbor_list ] of self              
          set [ new_neighbor_list ] of node2 sort fput g [ new_neighbor_list ] of node2
          set [ new_neighbor_list ] of node1 sort remove g [ new_neighbor_list ] of node1                      
        ] [
          stop
        ] 
      ]
     ] 
   ] [
    stop
  ] 
end

to making_if_ingroup 
  let node1 self
  let b [ who ] of node1
  let node2 one-of turtles with [ ( not link-neighbor? node1 ) and ( self != node1 ) and ( not member? self [ link-neighbors ] of link-neighbors ) ]
  let a length filter [ ? = true ] ( map [ ?1 = 1 and ?2 = 0 ] [ tag-list ] of self [ tag-list ] of node2 ) 
  let d length filter [ ? = true ] ( map [ ?1 = 0 and ?2 = 1 ] [ tag-list ] of self [ tag-list ] of node2 )
  let dis2 ( a + d )       
  ifelse ( dis2 < [ tolerance ] of self ) and ( dis2 < [ tolerance ] of node2 ) [
    let c [ who ] of node2
    ask node1 [ create-link-with node2 [ set color blue - 1 ] ]
    set [ new_neighbor_list ] of self sort fput c [ new_neighbor_list ] of node1
    set [ new_neighbor_list ] of node2 sort fput b [ new_neighbor_list ] of node2
  ] [
    stop
  ]
  
end

to select [ present ]
  if ( present = "tolerance" ) [
    set color 1 + tolerance  
    set label-color 56
    set label tolerance
  ]
  if ( present = "strategy" ) [
    if count link-neighbors != 0 [
      set color 41 + ( 8 * sum strategy-list / count link-neighbors )
    ]
    set label-color 56
    set label tolerance
  ]
  if ( present = "av-hamming-d" ) [ 
    set color 129 - average_hamming_distance 
  ]
end

to-report occurrences [x the-list]
  report reduce
    [ifelse-value (?2 = x) [?1 + 1] [?1]] (fput 0 the-list)
end

to find-all-components
  set components []
  set giant-component-size 0

  ask turtles [ set explored? false ]
  ;; keep exploring till all turtles get explored
  loop
  [
    ;; pick a turtle that has not yet been explored
    let start one-of turtles with [ not explored? ]
    if start = nobody [ stop ]
    ;; reset the number of turtles found to 0
    ;; this variable is updated each time we explore an
    ;; unexplored turtle.
    set component-size 0
    ask start [ explore ]
    ;; the explore procedure updates the component-size variable.
    ;; so check, have we found a new giant component?
    if component-size > giant-component-size
    [
      set giant-component-size component-size
    ]
    set components lput component-size components
  ]
end

;; finds all turtles reachable from this turtle
to explore ;; turtle procedure
  if explored? [ stop ]
  set explored? true
  set component-size component-size + 1
  ask link-neighbors [ explore ]
end

to update-plot

  set-current-plot "tolerance distribution"
  set-plot-x-range 0 num-of-tag-item + 2
  set-plot-y-range 0 round ( count turtles / ( num-of-tag-item + 1 ) + 100 )
  set-histogram-num-bars ( num-of-tag-item + 2 )   
  histogram [ tolerance ] of turtles

  find-all-components
  set-current-plot "% of agents in the giant component"
  plotxy ticks (giant-component-size / (count turtles))
     
  let max-degree max [count link-neighbors] of turtles
  set-current-plot "degree distribution"
  plot-pen-reset  ;; erase what we plotted before
  set-plot-x-range 1 (max-degree + 1)  ;; + 1 to make room for the width of the last bar
  histogram [count link-neighbors] of turtles  

  set-current-plot "degree distribution (log-log)"
  plot-pen-reset
  let degree 1
  while [degree <= max-degree]
  [
    let matches turtles with [count link-neighbors = degree]
    if any? matches
      [ plotxy log degree 10
               log (count matches) 10 ]
    set degree degree + 1
  ]  
  
  set average_degree ( count links * 2 ) / count turtles 
  set density ( 2 * count links ) / ( ( count turtles ) * ( count turtles - 1 ) )

  set apl_change average-path-length / average-path-length-of-lattice
  set acc_change clustering-coefficient / clustering-coefficient-of-lattice
  
  set-current-plot "average dissimilarity distribution"
  plot-pen-reset
  ifelse num-of-tag-item = 0 [
    set-plot-x-range 0 1
  ] [
    set-plot-x-range 0 num-of-tag-item
  ]
  set-plot-y-range 0 count turtles
  set-histogram-num-bars 10
  histogram [ average_hamming_distance ] of turtles 
  set tolerance_list [ tolerance ] of turtles
  set average_hamming_distance_list [ average_hamming_distance ] of turtles
  
  ifelse member? 0 modes tolerance_list and member? 1 modes tolerance_list [
    set mode_tolerance_list_history fput 0 mode_tolerance_list_history 
  ] [ 
    set mode_tolerance_list_history fput ( mean modes tolerance_list ) mode_tolerance_list_history 
  ]

  if ( length mode_tolerance_list_history > 2 ) [
    ifelse item 0 mode_tolerance_list_history = 0 and item 1 mode_tolerance_list_history = 0 and ( item 2 mode_tolerance_list_history != 0 ) [
      set count_zero_block count_zero_block + 1
    ] [
      set count_zero_block count_zero_block
    ]
  ]
  
  ifelse go? = true [
    set proportion_cooperation_list [ ]
    let j 0 ;; I don't know where there is something wrong....
    while [ j < count turtles ]
    [
      ;;  not divided by 8 any longer !
      if length [ neighbor_list ] of turtle j != 0 [
        set proportion_cooperation_list fput ( ( sum [ strategy-list ] of turtle j ) / length [ neighbor_list ] of turtle j ) proportion_cooperation_list 
      ]
      set j j + 1
    ] 
    set-current-plot "proportion of cooperation"
    plot ( sum proportion_cooperation_list ) / count turtles 
    set cooperation_history fput ( sum proportion_cooperation_list / count turtles ) cooperation_history
 
    if ( occurrences 1 cooperation_history = 1 and first cooperation_history = 1 ) [
      set first_emergence_time_all_coop ticks - 1 
      set first_emergence_time_either ticks - 1
      set phase 1
      set count_fall 1
    ] 
    if ( occurrences 0 cooperation_history = 1 and first cooperation_history = 0 ) [
      set first_emergence_time_all_defect ticks - 1 
      set first_emergence_time_either ticks - 1
      set phase 0 
      set count_rise 1
    ]
    if ( sum proportion_cooperation_list / count turtles > 0 and sum proportion_cooperation_list / count turtles < 1 ) and ( first_emergence_time_either = 0 ) [
      set phase 2
    ]        
  ] [ 
    set proportion_cooperation_list [ ]
    set cooperation_history [ ]
    set phase 2
  ]
  ifelse ( phase = 1 ) [
    ifelse ( sum proportion_cooperation_list / count turtles != 0 ) and ( ticks > first_emergence_time_either ) [ 
      set phase 1
      set cum_duration_fall cum_duration_fall + 1
      set duration_fall duration_fall + 1
      set count_rise count_rise
      set cum_duration_rise cum_duration_rise
      set duration_rise 0        
    ] [ 
      set phase 0
      set cum_duration_fall cum_duration_fall
      set duration_fall 0
      set count_rise count_rise + 1   
    ]   
  ] [
    if ( phase = 0 ) [ 
      ifelse ( sum proportion_cooperation_list / count turtles != 1 ) and ( ticks > first_emergence_time_either ) [ 
        set phase 0
        set cum_duration_rise cum_duration_rise + 1 
        set duration_rise duration_rise + 1
        set count_fall count_fall
        set cum_duration_fall cum_duration_fall
        set duration_fall 0        
      ] [
        set phase 1
        set cum_duration_rise cum_duration_rise
        set duration_rise 0 
        set count_fall count_fall + 1
      ]
    ]
  ]
  set-current-plot "duration dynamics" 
  set-current-plot-pen "cum_dur_fall"
  plot cum_duration_fall 
  set-current-plot-pen "dur_fall"
  plot duration_fall 
  set-current-plot-pen "cum_dur_rise"
  plot cum_duration_rise 
  set-current-plot-pen "dur_rise"
  plot duration_rise  

  if num-of-tag-item = 4 [
    set-current-plot "evolution of tolerance"
    let tot 0
    set-plot-y-range 0 1
    set-current-plot-pen "5"
    plot-pen-up plotxy ticks tot
    set tot tot + ( count turtles with [ tolerance = 5 ] / count turtles )
    plot-pen-down plotxy ticks tot
    set-current-plot-pen "4"
    plot-pen-up plotxy ticks tot
    set tot tot + ( count turtles with [ tolerance = 4 ] / count turtles )
    plot-pen-down plotxy ticks tot
    set-current-plot-pen "3"
    plot-pen-up plotxy ticks tot
    set tot tot + ( count turtles with [ tolerance = 3 ] / count turtles )
    plot-pen-down plotxy ticks tot
    set-current-plot-pen "2"
    plot-pen-up plotxy ticks tot
    set tot tot + ( count turtles with [ tolerance = 2] / count turtles )
    plot-pen-down plotxy ticks tot
    set-current-plot-pen "1"
    plot-pen-up plotxy ticks tot
    set tot tot + ( count turtles with [ tolerance = 1 ] / count turtles )
    plot-pen-down plotxy ticks tot
    set-current-plot-pen "0"
    plot-pen-up plotxy ticks tot
    set tot tot + ( count turtles with [ tolerance = 0 ] / count turtles )
    plot-pen-down plotxy ticks tot  
  ]

  let i 0 
  set tol_dependent_degree_list [ ]
  while [ i < 6 ] [
    let pool turtles with [ tolerance = i ]
    ifelse ( any? pool with [ length new_neighbor_list != 0 ] ) [ 
      set tol_dependent_degree_list lput mean [ length new_neighbor_list ] of turtles with [ tolerance = i ] tol_dependent_degree_list
    ] [ 
      set tol_dependent_degree_list lput 0 tol_dependent_degree_list
    ]
    set i i + 1
  ] 
  set tol_dependent_degree_list tol_dependent_degree_list
  
end

to layout
  if not layout? [ stop ]
  ;; the number here is arbitrary; more repetitions slows down the model, but too few gives poor layouts
  repeat 5 [
    do-layout
    ;; so we get smooth animation
    display 
  ]
end

to do-layout
  layout-spring (turtles with [any? link-neighbors]) links 0.2 8 1 
end
@#$#@#$#@
GRAPHICS-WINDOW
225
33
449
278
17
17
6.1143
1
10
1
1
1
0
0
0
1
-17
17
-17
17
1
1
1
ticks

CC-WINDOW
5
546
971
641
Command Center
0

SLIDER
1
46
128
79
num_of_agents
num_of_agents
10
100
50
1
1
NIL
HORIZONTAL

BUTTON
110
12
223
45
go
go
T
1
T
OBSERVER
NIL
NIL
NIL
NIL

BUTTON
0
12
109
45
setup
setup
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL

SLIDER
1
113
129
146
num-of-tag-item
num-of-tag-item
0
10
4
1
1
NIL
HORIZONTAL

SWITCH
131
92
221
125
layout?
layout?
1
1
-1000

BUTTON
130
55
221
88
redo layout
layout
T
1
T
OBSERVER
NIL
NIL
NIL
NIL

MONITOR
456
483
506
532
apl
average-path-length
3
1
12

PLOT
1
282
223
410
degree distribution
degree
# of nodes
1.0
10.0
0.0
10.0
true
false
PENS
"default" 1.0 1 -16777216 true

MONITOR
599
432
661
481
NIL
density
3
1
12

SLIDER
-2
146
130
179
erdos_renyi_probability
erdos_renyi_probability
0
1
0.12
0.01
1
NIL
HORIZONTAL

PLOT
452
154
704
282
tolerance distribution
tolerance level
# of agents
0.0
11.0
0.0
20.0
true
false
PENS
"default" 1.0 1 -16777216 true

CHOOSER
130
128
222
173
present_what
present_what
"tolerance" "strategy" "av-hamming-d"
1

SLIDER
1
79
129
112
b/c
b/c
2
10
4
0.1
1
NIL
HORIZONTAL

SLIDER
1
248
113
281
mu1
mu1
0
1
0.0125
0.0001
1
NIL
HORIZONTAL

PLOT
225
282
450
411
proportion of cooperation
time
proportion
0.0
50.0
0.0
1.0
true
false
PENS
"default" 1.0 0 -4699768 true

MONITOR
599
482
661
531
p_coop
mean proportion_cooperation_list
4
1
12

PLOT
225
412
451
532
average dissimilarity distribution
average hamming distance
# of agents
0.0
10.0
0.0
20.0
true
false
PENS
"default" 1.0 1 -16777216 true

SLIDER
1
214
223
247
closure_probability
closure_probability
0
100
40
1
1
%
HORIZONTAL

PLOT
0
412
224
532
degree distribution (log-log)
log of (degree)
log of (# of agents)
0.0
0.3
0.0
1.0
true
false
PENS
"default" 0.5 2 -16777216 true

SLIDER
1
180
225
213
network_plasticity
network_plasticity
0
100
20
1
1
%
HORIZONTAL

MONITOR
455
432
506
481
acc
clustering-coefficient
17
1
12

MONITOR
508
483
597
532
apl change
average-path-length / average-path-length-of-lattice
17
1
12

MONITOR
507
432
597
481
acc change
clustering-coefficient / clustering-coefficient-of-lattice
17
1
12

PLOT
451
10
798
156
duration dynamics
time
rhythm
0.0
50.0
0.0
10.0
true
true
PENS
"cum_dur_fall" 1.0 0 -2674135 true
"dur_fall" 1.0 1 -8990512 true
"cum_dur_rise" 1.0 0 -11053225 true
"dur_rise" 1.0 1 -1664597 true

MONITOR
798
108
952
157
1st_emergence_all_coop
first_emergence_time_all_coop
17
1
12

MONITOR
799
10
950
59
# of 0 to 1 cycle
count_rise
17
1
12

MONITOR
798
59
951
108
# of 1 to 0 cycle
count_fall
17
1
12

PLOT
703
156
958
283
% of agents in the giant component
time
% agents
0.0
50.0
0.0
1.0
true
false
PENS
"default" 1.0 0 -13791810 true

PLOT
452
282
962
413
evolution of tolerance
time
proportion
0.0
50.0
0.0
1.0
true
true
PENS
"5" 1.0 0 -13345367 true
"4" 1.0 0 -1184463 true
"3" 1.0 0 -4079321 true
"2" 1.0 0 -7171555 true
"1" 1.0 0 -5298144 true
"0" 1.0 0 -16382462 true

SLIDER
114
248
223
281
mu2
mu2
0
1
0.05
0.0001
1
NIL
HORIZONTAL

@#$#@#$#@


@#$#@#$#@
default
true
0
Polygon -7500403 true true 150 5 40 250 150 205 260 250

airplane
true
0
Polygon -7500403 true true 150 0 135 15 120 60 120 105 15 165 15 195 120 180 135 240 105 270 120 285 150 270 180 285 210 270 165 240 180 180 285 195 285 165 180 105 180 60 165 15

arrow
true
0
Polygon -7500403 true true 150 0 0 150 105 150 105 293 195 293 195 150 300 150

box
false
0
Polygon -7500403 true true 150 285 285 225 285 75 150 135
Polygon -7500403 true true 150 135 15 75 150 15 285 75
Polygon -7500403 true true 15 75 15 225 150 285 150 135
Line -16777216 false 150 285 150 135
Line -16777216 false 150 135 15 75
Line -16777216 false 150 135 285 75

bug
true
0
Circle -7500403 true true 96 182 108
Circle -7500403 true true 110 127 80
Circle -7500403 true true 110 75 80
Line -7500403 true 150 100 80 30
Line -7500403 true 150 100 220 30

butterfly
true
0
Polygon -7500403 true true 150 165 209 199 225 225 225 255 195 270 165 255 150 240
Polygon -7500403 true true 150 165 89 198 75 225 75 255 105 270 135 255 150 240
Polygon -7500403 true true 139 148 100 105 55 90 25 90 10 105 10 135 25 180 40 195 85 194 139 163
Polygon -7500403 true true 162 150 200 105 245 90 275 90 290 105 290 135 275 180 260 195 215 195 162 165
Polygon -16777216 true false 150 255 135 225 120 150 135 120 150 105 165 120 180 150 165 225
Circle -16777216 true false 135 90 30
Line -16777216 false 150 105 195 60
Line -16777216 false 150 105 105 60

car
false
0
Polygon -7500403 true true 300 180 279 164 261 144 240 135 226 132 213 106 203 84 185 63 159 50 135 50 75 60 0 150 0 165 0 225 300 225 300 180
Circle -16777216 true false 180 180 90
Circle -16777216 true false 30 180 90
Polygon -16777216 true false 162 80 132 78 134 135 209 135 194 105 189 96 180 89
Circle -7500403 true true 47 195 58
Circle -7500403 true true 195 195 58

circle
false
0
Circle -7500403 true true 0 0 300

circle 2
false
0
Circle -7500403 true true 0 0 300
Circle -16777216 true false 30 30 240

cow
false
0
Polygon -7500403 true true 200 193 197 249 179 249 177 196 166 187 140 189 93 191 78 179 72 211 49 209 48 181 37 149 25 120 25 89 45 72 103 84 179 75 198 76 252 64 272 81 293 103 285 121 255 121 242 118 224 167
Polygon -7500403 true true 73 210 86 251 62 249 48 208
Polygon -7500403 true true 25 114 16 195 9 204 23 213 25 200 39 123

cylinder
false
0
Circle -7500403 true true 0 0 300

dot
false
0
Circle -7500403 true true 90 90 120

face happy
false
0
Circle -7500403 true true 8 8 285
Circle -16777216 true false 60 75 60
Circle -16777216 true false 180 75 60
Polygon -16777216 true false 150 255 90 239 62 213 47 191 67 179 90 203 109 218 150 225 192 218 210 203 227 181 251 194 236 217 212 240

face neutral
false
0
Circle -7500403 true true 8 7 285
Circle -16777216 true false 60 75 60
Circle -16777216 true false 180 75 60
Rectangle -16777216 true false 60 195 240 225

face sad
false
0
Circle -7500403 true true 8 8 285
Circle -16777216 true false 60 75 60
Circle -16777216 true false 180 75 60
Polygon -16777216 true false 150 168 90 184 62 210 47 232 67 244 90 220 109 205 150 198 192 205 210 220 227 242 251 229 236 206 212 183

fish
false
0
Polygon -1 true false 44 131 21 87 15 86 0 120 15 150 0 180 13 214 20 212 45 166
Polygon -1 true false 135 195 119 235 95 218 76 210 46 204 60 165
Polygon -1 true false 75 45 83 77 71 103 86 114 166 78 135 60
Polygon -7500403 true true 30 136 151 77 226 81 280 119 292 146 292 160 287 170 270 195 195 210 151 212 30 166
Circle -16777216 true false 215 106 30

flag
false
0
Rectangle -7500403 true true 60 15 75 300
Polygon -7500403 true true 90 150 270 90 90 30
Line -7500403 true 75 135 90 135
Line -7500403 true 75 45 90 45

flower
false
0
Polygon -10899396 true false 135 120 165 165 180 210 180 240 150 300 165 300 195 240 195 195 165 135
Circle -7500403 true true 85 132 38
Circle -7500403 true true 130 147 38
Circle -7500403 true true 192 85 38
Circle -7500403 true true 85 40 38
Circle -7500403 true true 177 40 38
Circle -7500403 true true 177 132 38
Circle -7500403 true true 70 85 38
Circle -7500403 true true 130 25 38
Circle -7500403 true true 96 51 108
Circle -16777216 true false 113 68 74
Polygon -10899396 true false 189 233 219 188 249 173 279 188 234 218
Polygon -10899396 true false 180 255 150 210 105 210 75 240 135 240

house
false
0
Rectangle -7500403 true true 45 120 255 285
Rectangle -16777216 true false 120 210 180 285
Polygon -7500403 true true 15 120 150 15 285 120
Line -16777216 false 30 120 270 120

leaf
false
0
Polygon -7500403 true true 150 210 135 195 120 210 60 210 30 195 60 180 60 165 15 135 30 120 15 105 40 104 45 90 60 90 90 105 105 120 120 120 105 60 120 60 135 30 150 15 165 30 180 60 195 60 180 120 195 120 210 105 240 90 255 90 263 104 285 105 270 120 285 135 240 165 240 180 270 195 240 210 180 210 165 195
Polygon -7500403 true true 135 195 135 240 120 255 105 255 105 285 135 285 165 240 165 195

line
true
0
Line -7500403 true 150 0 150 300

line half
true
0
Line -7500403 true 150 0 150 150

pentagon
false
0
Polygon -7500403 true true 150 15 15 120 60 285 240 285 285 120

person
false
0
Circle -7500403 true true 110 5 80
Polygon -7500403 true true 105 90 120 195 90 285 105 300 135 300 150 225 165 300 195 300 210 285 180 195 195 90
Rectangle -7500403 true true 127 79 172 94
Polygon -7500403 true true 195 90 240 150 225 180 165 105
Polygon -7500403 true true 105 90 60 150 75 180 135 105

plant
false
0
Rectangle -7500403 true true 135 90 165 300
Polygon -7500403 true true 135 255 90 210 45 195 75 255 135 285
Polygon -7500403 true true 165 255 210 210 255 195 225 255 165 285
Polygon -7500403 true true 135 180 90 135 45 120 75 180 135 210
Polygon -7500403 true true 165 180 165 210 225 180 255 120 210 135
Polygon -7500403 true true 135 105 90 60 45 45 75 105 135 135
Polygon -7500403 true true 165 105 165 135 225 105 255 45 210 60
Polygon -7500403 true true 135 90 120 45 150 15 180 45 165 90

square
false
0
Rectangle -7500403 true true 30 30 270 270

square 2
false
0
Rectangle -7500403 true true 30 30 270 270
Rectangle -16777216 true false 60 60 240 240

star
false
0
Polygon -7500403 true true 151 1 185 108 298 108 207 175 242 282 151 216 59 282 94 175 3 108 116 108

target
false
0
Circle -7500403 true true 0 0 300
Circle -16777216 true false 30 30 240
Circle -7500403 true true 60 60 180
Circle -16777216 true false 90 90 120
Circle -7500403 true true 120 120 60

tree
false
0
Circle -7500403 true true 118 3 94
Rectangle -6459832 true false 120 195 180 300
Circle -7500403 true true 65 21 108
Circle -7500403 true true 116 41 127
Circle -7500403 true true 45 90 120
Circle -7500403 true true 104 74 152

triangle
false
0
Polygon -7500403 true true 150 30 15 255 285 255

triangle 2
false
0
Polygon -7500403 true true 150 30 15 255 285 255
Polygon -16777216 true false 151 99 225 223 75 224

truck
false
0
Rectangle -7500403 true true 4 45 195 187
Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194
Rectangle -1 true false 195 60 195 105
Polygon -16777216 true false 238 112 252 141 219 141 218 112
Circle -16777216 true false 234 174 42
Rectangle -7500403 true true 181 185 214 194
Circle -16777216 true false 144 174 42
Circle -16777216 true false 24 174 42
Circle -7500403 false true 24 174 42
Circle -7500403 false true 144 174 42
Circle -7500403 false true 234 174 42

turtle
true
0
Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210
Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105
Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105
Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87
Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210
Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99

wheel
false
0
Circle -7500403 true true 3 3 294
Circle -16777216 true false 30 30 240
Line -7500403 true 150 285 150 15
Line -7500403 true 15 150 285 150
Circle -7500403 true true 120 120 60
Line -7500403 true 216 40 79 269
Line -7500403 true 40 84 269 221
Line -7500403 true 40 216 269 79
Line -7500403 true 84 40 221 269

x
false
0
Polygon -7500403 true true 270 75 225 30 30 225 75 270
Polygon -7500403 true true 30 75 75 30 270 225 225 270

@#$#@#$#@
NetLogo 4.0.2
@#$#@#$#@
setup
repeat 5 [rewire-one]
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
default
0.0
-0.2 0 1.0 0.0
0.0 1 1.0 0.0
0.2 0 1.0 0.0
link direction
true
0
Line -7500403 true 150 150 30 225
Line -7500403 true 150 150 270 225

@#$#@#$#@