; adapted from models library by Lada Adamic (see copyright below)
; for the purposes of SI708/CSCS608
; also now contains major improvements by Eytan Bakshy

globals
[
  new-node  ;; the last node we created
  degrees   ;; this is an array that contains each node in
            ;; proportion to its degree
  num-infected
  tree-mode?
  time-to-90
]

turtles-own
[
  infected?        ;; true if agent has been infected
  infection-count  ;; the number of turtles a turtle has infected
]

;;;;;;;;;;;;;;;;;;;;;;;;
;;; 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 time-to-90 false
  set tree-mode? false
  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
    ]
  ]
  
  set num-infected 0

  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 100 [do-layout]
  ask turtles [set color gray
    set shape "circle"
    set size 2
    set infection-count 0
    set infected? false]
  
  ask links [set color gray]
  ask one-of turtles
  [ set infected? true
    set size 5
    set shape "target"
    set color yellow
  ]
end



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

; reset diffusion simulation
to reinfect-one
  clear-plot
  set num-infected 1
  set time-to-90 false
  reset-ticks
  
  ask turtles [
    set color gray + 2
    set shape "circle"
    set size 2
    set infection-count 0
    set infected? false
  ]
  ask links [
    set color gray + 2
  ]
  ask one-of turtles
  [ set infected? true
    set size 5
    set shape "target"
    set color yellow
  ]
end

;; toggle infection tree mode
;; when tree-mode is on, only links responsible for contagion and infected nodes
;; are displayed. tree-mode also affects layout
to toggle-tree
  ifelse tree-mode?
  [
    ask turtles with [not infected?] [show-turtle]
    ask links with [color != red - 1] [show-link]  
    set tree-mode? false
  ]
  [
    ask turtles with [not infected?] [hide-turtle]
    ask links with [color != red - 1] [hide-link]
    set tree-mode? true
  ]
end

to spread
  ;; infection can't take place while in infection tree mode
  ;; or if every agent has already been infected
  if all? turtles [infected?]
    [stop]
  if (count turtles with [infected?] > (num-nodes * .9)) and (time-to-90 = false) [
    set time-to-90 ticks
  ]
  ask turtles with [ infected? = true ]
  [
    ;; infect neighbors
    ask link-neighbors
    [ 
      if ( random-float 1 <= infect-rate )  ;; infect with probability p
      [
        if not infected?  ;; agents can be infected only once
        [
          set infected? true
          show-turtle
          set color red + 1
          ;; incremement infection-count of the node doing the infection
          ask myself [set infection-count infection-count + 1]
          ;; color the link with the node doing the infection
          ask link-with myself [set color red - 1 show-link]
          ;; increment the total number of infected agents
          set num-infected num-infected + 1
        ]
      ]
    ]

    ;; resize node so that the area is proportional to the current number of infections
    set size 1 * sqrt (infection-count + 1)
  ]
  
  do-plotting
  tick
end

;; 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 infected? false
    set new-node self ;; set the new-node global
  ]
end

to reset-node
    set color gray - 0.75
    set size 2.1
    set infected? false
    set infection-count 0
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


;;;;;;;;;;;;;;;;
;;; Plotting ;;;
;;;;;;;;;;;;;;;;

to do-plotting
     ;; plot the number of infected individuals at each step
     set-current-plot "Number infected"
     set-current-plot-pen "inf"
     plotxy ticks num-infected       
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
  ifelse tree-mode?
    [repeat 5 [layout-spring (turtles with [infected?]) (links with [color = red - 1]) 0.2 4 0.9]]
    [repeat 5 [layout-spring turtles links 0.2 4 0.9]]
  display
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

BUTTON
206
132
307
165
spread
spread
T
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
104
132
204
165
spread once
spread
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

MONITOR
219
165
336
210
time-to-90-percent
time-to-90
3
1
11

BUTTON
141
167
215
200
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

PLOT
8
213
280
415
Number infected
time
n
0.0
10.0
0.0
10.0
true
false
"" ""
PENS
"inf" 1.0 0 -2674135 true "" ""

SLIDER
150
97
285
130
infect-rate
infect-rate
0
1
0.15
0.01
1
NIL
HORIZONTAL

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

MONITOR
271
10
328
55
nodes
count turtles
3
1
11

BUTTON
4
132
102
165
reinfect one
reinfect-one
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

BUTTON
4
167
138
200
toggle infection tree
toggle-tree
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
1

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

A model of diffusion on networks that are generated through a process of growth and preferential attachment (also known as the Barbasi-Albert model).

## HOW IT WORKS

The model starts with two nodes connected by an edge.

At each step, a new node is added.  A new node picks an existing node to connect to randomly, but with some bias.  More specifically, a node's chance of being selected is directly proportional to the number of connections it already has, or its "degree." This is the mechanism which is called "preferential attachment."

## 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 gamma and press SETUP.

Adjust the INFECT-RATE value to determine the infectiousness of the spreading agent.

To REINFECT-ONE will infect a single individual while keeping the same topology - press "reinfect-one".

Now to allow the disease to spread, you can advance on time step at a time (each infected node will infect each of its neighbors with probability INFECT-RATE) with the SPREAD-ONCE button. To let the disease run its full course, you can click the SPREAD button.

## THINGS TO NOTICE

How is the rate of transmission affected as you change the model from a pure growth process (PROB-PREF = 0) to one in which rich-get-richer (PROB-PREF=1)?

## CREDITS AND REFERENCES

Copyright 2008 Uri Wilensky. Modified by Lada Adamic 2009.
 
This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/ or send a letter to Creative Commons, 559 Nathan Abbott Way, Stanford, California 94305, USA.
Commercial licenses are also available. To inquire about commercial licenses, please contact Uri Wilensky at uri@northwestern.edu.
@#$#@#$#@
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

link
true
0
Line -7500403 true 150 0 150 300

link direction
true
0
Line -7500403 true 150 150 30 225
Line -7500403 true 150 150 270 225

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 5.0.2
@#$#@#$#@
set layout? false
setup repeat 175 [ go ]
repeat 35 [ layout ]
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
default
0.0
-0.2 0 0.0 1.0
0.0 1 1.0 0.0
0.2 0 0.0 1.0
link direction
true
0
Line -7500403 true 150 150 90 180
Line -7500403 true 150 150 210 180

@#$#@#$#@
0
@#$#@#$#@