extensions [nw]

globals
[
  new-node  ;; the last node we created
  degrees   ;; this is an array that contains each node in
  is-connected
  giant-component-size
]


;;;;;;;;;;;;;;;;;;;;;;;;
;;; Setup Procedures ;;;
;;;;;;;;;;;;;;;;;;;;;;;;

to setup
  ;; (for this model to work with NetLogo's new plotting features,
  ;; __clear-all-and-reset-ticks should be replaced with clear-all at
  ;; the beginning of your setup procedure and reset-ticks at the end
  ;; of the procedure.)
  ca
  __clear-all-and-reset-ticks
  let partner nobody

  set-default-shape turtles "circle"
  set degrees []   ;; initialize the array to be empty
  ;; make the initial network of two turtles and an edge
  
  crt (m + 1)
  
  ask turtles [
    repeat m [set degrees lput self degrees] ; insert nodes into array
    
    ask other turtles with [not link-neighbor? myself] [
      create-link-with myself
    ]
  ]

  no-display
  repeat (num-nodes - m - 1) [
  crt 1 [
    set new-node self ;; set the new-node global
 
    repeat m [
      ifelse (random-float 1.0 <= prob-pref) ; if pref attachment
      [
        set partner new-node
        while [partner = new-node] [
          set partner one-of (degrees) 
          ask partner [
            if link-neighbor? self [  ; we can't link to someone we already share an edge with
              set partner new-node    ; so set to self so we redo
            ]
          ]
        ]
      ]
     [  ; if not pref attachment
     set partner one-of other turtles with [(not link-neighbor? new-node)]
     ]
     
    move-to partner
       fd 1
    create-link-with partner [set color green]
      set degrees lput new-node degrees
      set degrees lput partner degrees
    ]
  ]
  ]
  
  repeat (num-nodes / 2) [
    ask one-of turtles [
      create-link-with one-of other turtles with [(not link-neighbor? myself)]
    ]
  ]
  repeat 100 [do-layout]
  ask turtles [set color gray
    set shape "circle"
    set size 2
  ]
  
  ask links [set color gray]
  
  repeat 2000 [
    rewire
    do-layout
  ]
  
  repeat 5 [do-layout]
end

to-report do-calculations
    nw:set-snapshot turtles links
  ; check if network is connected
;  show "checking if connected"
  let giant-component first sort-by [length ?1 > length ?2] nw:weak-component-clusters
  ask turtles [set color gray]
  ask turtle-set giant-component [set color red]
  ask links [ set color [ color ] of end1 - 2]  ;; recolor all edges
  report (length giant-component = count turtles)
end


to rewire 
    let n1 nobody
    let n2 nobody
    let n3 nobody
    let d1 0
    let d2 0
    let d3 0
    let new-link nobody
    
    ask one-of links [
      ifelse (random-float 1.0 < 0.5) [
        set n1 end1
        set n2 end2
      ][
        set n1 end2
        set n2 end1
      ]
      
      set n3 one-of turtles with [(not link-neighbor? n1) and (self != n1)]
      set d1 (count [link-neighbors] of n1)
      set d2 (count [link-neighbors] of n2)
      set d3 (count [link-neighbors] of n3)
      
      if ((assortativity * (abs(d1 - d2) - abs(d1 - d3)) > 0) and (d2 > 1))[
        ask n1 [create-link-with n3 [set new-link self]]
        die
      ]
    ]
    
    set is-connected do-calculations
    if ((not is-connected) and (new-link != nobody)) [
           ask n1 [create-link-with n2]
           ask new-link [die]
        
    ]
          
end

to attack
  ask max-n-of num-remove turtles [count link-neighbors] [ die ]
  set is-connected do-calculations
end

;;;;;;;;;;;;;;;;;;;;;;;;;;
;;; Runtime Procedures ;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;

;; used for creating a new node
to make-node
  create-turtles 1  ;; don't know what this is - lada
  [
    set color gray + 2
    set size 0.5
    set new-node self ;; set the new-node global
  ]
end

;; Find a node to attach to
;; the degree of a node
;; 0 < gamma < 1 means gamma*100 percent of the 
;; time attach randomly, rest of the time attach
;; preferentially 


;;;;;;;;;;;;;;;;;;;;;;;
;;; Edge Operations ;;;
;;;;;;;;;;;;;;;;;;;;;;;

;; connects the two turtles
to make-edge [node1 node2]
  ask node1 [
    ifelse (node1 = node2) 
    [
      show "error: self-loop attempted"
    ]
    [
      create-link-with node2 [ set color green ]
     ;; position the new node near its partner
      setxy ([xcor] of node2) ([ycor] of node2)
      rt random 360
      fd 8
      set degrees lput node1 degrees
     set degrees lput node2 degrees
     ]
  ]
end

;;;;;;;;;;;;;;
;;; Layout ;;;
;;;;;;;;;;;;;;
;; resize-turtles, change back and forth from size based on degree to a size of 1

;; spring layout of infection tree while in tree mode
;; otherwise, layout all nodes and links
to do-layout

   
   repeat 5 [layout-spring turtles links 0.2 4 0.9]
  display
end

to highlight-giant-component
  nw:set-snapshot turtles links
  ; nw:weak-component-clusters gives you a list of all the components in the network,
  ; each component being itself represented as a list. The get the biggest component
  ; (this "giant" one), we sort them in reverse size order and take the first one.
  let giant-component first sort-by [length ?1 > length ?2] nw:weak-component-clusters
  if length giant-component > giant-component-size [
    set giant-component-size length giant-component
    ask turtles [ set color gray + 2 ]
    ask turtle-set giant-component [ set color red ]
  ]
  ask links [ set color [ color ] of end1 - 2]  ;; recolor all edges
end


; *** NetLogo 3.1.3 Model Copyright Notice ***
;
; Copyright 2005 by Uri Wilensky.  All rights reserved.
;
; Permission to use, modify or redistribute this model is hereby granted,
; provided that both of the following requirements are followed:
; a) this copyright notice is included.
; b) this model will not be redistributed for profit without permission
;    from Uri Wilensky.
; Contact Uri Wilensky for appropriate licenses for redistribution for
; profit.
;
; To refer to this model in academic publications, please use:
; Wilensky, U. (2005).  NetLogo Preferential Attachment model.
; http://ccl.northwestern.edu/netlogo/models/PreferentialAttachment.
; Center for Connected Learning and Computer-Based Modeling,
; Northwestern University, Evanston, IL.
;
; In other publications, please use:
; Copyright 2005 Uri Wilensky.  All rights reserved.
; See http://ccl.northwestern.edu/netlogo/models/PreferentialAttachment
; for terms of use.
;
; *** End of NetLogo 3.1.3 Model Copyright Notice ***
@#$#@#$#@
GRAPHICS-WINDOW
340
10
730
421
45
45
4.18
1
10
1
1
1
0
0
0
1
-45
45
-45
45
0
0
1
ticks
30.0

BUTTON
6
25
72
58
NIL
setup
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

SWITCH
176
26
266
59
plot?
plot?
0
1
-1000

SWITCH
81
26
171
59
layout?
layout?
0
1
-1000

BUTTON
152
99
226
132
layout
do-layout
T
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

SLIDER
151
61
254
94
m
m
1
5
1
1
1
NIL
HORIZONTAL

SLIDER
4
61
148
94
num-nodes
num-nodes
5
200
200
1
1
NIL
HORIZONTAL

SLIDER
3
97
148
130
prob-pref
prob-pref
0
1
1
0.01
1
NIL
HORIZONTAL

MONITOR
271
10
328
55
nodes
count turtles
3
1
11

CHOOSER
77
133
215
178
assortativity
assortativity
-1 1
1

SLIDER
5
194
177
227
num-remove
num-remove
0
20
10
1
1
NIL
HORIZONTAL

BUTTON
179
194
248
227
NIL
attack
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

@#$#@#$#@
## WHAT IS IT?

A model to test robustness of assortative and disassortative networks.

## HOW TO USE IT

The NUM-NODES slider controls the size of the network.

The PROB-PREF parameter determines whether the attachment is preferential. With probability PROB-PREF, the node will chose to attach to existing nodes in proportion to their degree. With probability (1 - PROB-PREF) it will attach to any existing node with equal probability.

Choose num-nodes and PROB-PREF and press SETUP.

The network will first be setup using a growth process, and then will rewire for a while to become assortative (ASSORTATIVITY = 1 from the dropdown menu), or disassortative (ASSORTATIVITY = 10)

Once it's done, you can do a targeted ATTACK, taking out the NUM-REMOVE highest degree nodes. 

## THINGS TO NOTICE

How does the assorativity affect how resilient the network is to targeted attack?

## CREDITS AND REFERENCES

Copyright 2012 Lada Adamic, adapted from the NetLogo models library written by Uri Wilensky.
@#$#@#$#@
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flag
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line half
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square
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@#$#@#$#@
NetLogo 5.0.2
@#$#@#$#@
set layout? false
setup repeat 175 [ go ]
repeat 35 [ layout ]
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
default
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@#$#@#$#@
0
@#$#@#$#@