Spreading groups of bots in social networks

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

;Finally, the model is constructed by Alon Sela (2016)

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

]

turtles-own
[
  infected?        ;; true if agent has been 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.)
  __clear-all-and-reset-ticks
  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


  make-node ;; add the very first node

  let first-node new-node  ;; remember that its the first node

  ;; the following few lines create a cycle of length 5
  ;; this is just an arbitrary way to start a network

  let prev-node new-node
  repeat 4 [
    make-node ;; second node
    make-edge new-node prev-node ;; make the edge
    set degrees lput prev-node degrees
    set degrees lput new-node degrees
    set prev-node new-node
  ]
  make-edge new-node first-node

  set time 0
  set num-infected 0
  set previous-num-infected 0

  repeat (num-nodes / 2) [create-preferential-net]


  set spreading-group n-of (num-nodes * spreading-group-percent / 100 )turtles
  ask spreading-group [set color orange set size 1]
  repeat spreadingGroupRepet [create-spreading-group]

  repeat (num-nodes / 2 - 4) [create-preferential-net]
display
end 

to create-preferential-net
    no-display
    make-node  ;; add one new node

    ;; it's going to have m edges
    repeat m [
      let partner find-partner new-node      ;; find a partner for the new node
      ask partner [set color gray + 2]    ;; set color of partner to gray
      make-edge new-node partner     ;; connect it to the partner we picked before
    ]
    if layout? [ do-layout ]
    if plot? [ do-plotting ]
end 

to create-spreading-group
  ask spreading-group
    [let first-node [who] of one-of spreading-group
      let second-node [who] of one-of spreading-group
      if (first-node != second-node)
        [if not is-link? link first-node second-node [
          ask turtle first-node [
            set size 2
            create-link-with turtle second-node[
              set color orange
              set thickness 0.5]
          ]
        ]
        ]
    ]
  repeat 5 [layout-spring (spreading-group) (links with [color = red]) 5 0.5 0.5]
end 





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

; reset diffusion simulation

to reinfect-once
  clear-plot
  reset-ticks
  set num-infected num-infected-init
  set time 0
  set previous-num-infected 0
  ask turtles [set color grey
    set infected? false
    set size 1]

  if (reinfect-type = "random")
  [ask n-of num-infected-init turtles
    [set color red
      set size 2
      set infected? true
    ]
  ]

  if (reinfect-type = "group")
  [ask n-of num-infected-init spreading-group
    [set color red
      set size 2
      set infected? true
    ]
  ]

  if (reinfect-type = "eigenval-centrality")
  [ask max-n-of num-infected-init turtles [nw:eigenvector-centrality]
    [set color red
      set size 2
      set infected? true
    ]
  ]

  if (reinfect-type = "PageRank-Centrality")
    [ask max-n-of num-infected-init turtles [ nw:page-rank]
      [set color red
        set size 2
        set infected? true
      ]
    ]
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 ] [show-link]
    set tree-mode? false
  ]
  [
    ask turtles with [not infected?] [hide-turtle]
    ask links with [color != red] [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]

  ask turtles with [ infected? = true ]
  [let mysize [size] of turtle who
    let prob 0
    ;; infect neighbors
    ask link-neighbors with [infected? = false]
    [ifelse (Retention-loss = true)
      [set prob p * mysize]
      [set prob p]
    if ( random-float 1 <= prob)  ;; infect with probability p or with prob p * size
      [ set infected? true
        show-turtle
        set color red
      ;; color the link with the node doing the infection
        ask link-with myself [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


  let tmp count turtles with [infected? = true]
  ifelse (tmp = previous-num-infected)
  [stop]
  [set  previous-num-infected tmp]

  forgetness
  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 



;; 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

to-report find-partner [node1]
  ;; set a local variable called ispref that
  ;; determines if this link is going to be
  ;; preferential of not
  let ispref (random-float 1 >= gamma)

  ;; initialize partner to be the node itself
  ;; this will have to be changed
  let partner node1

  ;; if preferential attachment then choose
  ;; from our degrees array
  ;; otherwise chose one of the turtles at random
  ifelse ispref
  [
    set partner one-of degrees
   ]
   [
     set partner one-of turtles
     ]

   ;; but need to check that partner chosen isn't
   ;; the node itself and also isn't a node that
   ;; our node is already connected to
   ;; if this is the case, it will try another
   ;; partner and try again
  let checkit true
  while [checkit] [
    ask partner [
      ifelse ((link-neighbor? node1) or (partner = node1))
        [
          ifelse ispref
          [
            set partner one-of degrees
           ]
           [
             set partner one-of turtles
           ]
            set checkit true
         ]
         [
           set checkit false
         ]
       ]
    ]
  report partner
end 

;;;;;;;;;;;;;;;;;;;;;;;
;;; 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 grey + 2 ]
     ;; 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 (spreading-group) (links) 5 0.5 0.5]]
    [repeat 5 [layout-spring turtles links 0.2 4 3]]
  display
end 

to forgetness
  ask turtles
    [set size size / size-reduction
      if size < 0.1 [set infected? false]
    ]
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 ***