Network Corona Model

turtles-own [infected? infecttime immtime fam hub? city everinfected? outside?]
globals [maxinfected separated? ld? totturt]
links-own [active? strength offset second?]

to Setup
  clear-all
  clear-turtles
  clear-plot
  set maxinfected 0
  set separated? false
  set ld? false

  if network = "lattice" [
    ask n-of numtur patches [
      sprout 1[
        nodeprops
      ]
    ]
    ask-concurrent turtles[
      create-links-with up-to-n-of knowsize other turtles in-radius radius with [count my-links < knowsize + 1][
        activelinkprops
      ]
    ]

  ]

  if network = "Clustered" [
    ask n-of (numtur / knowsize) patches [
      sprout knowsize[
        nodeprops
      ]
      ask up-to-n-of outsidelinks turtles-here [set outside? true]
    ]
    ask turtles[
      create-links-with other turtles-here [activelinkprops]
    ]
    ask turtles[
            fd 1
    ]
  ]


 if network = "ER" [
  create-turtles numtur [
      nodeprops    ]

    ask turtles [
      setxy random-float max-pxcor random-float max-pycor
    ]
    ask turtles [
      create-links-with up-to-n-of knowsize other turtles in-radius radius with [count my-links < knowsize][activelinkprops]
    ]
  ]

 if network = "star" [
    create-turtles numtur [
      nodeprops
    ]

    ask one-of turtles [set hub? true]
    layout-circle turtles with [hub? = false]  40
    layout-circle turtles with [hub? = true] 0

    ask turtles with [hub? = true][
      create-links-with other turtles [activelinkprops]
    ]
  ]

  ask turtles [ set everinfected? false]
  set totturt count turtles
  reset-ticks
end 

to nodeprops
  set shape "circle"
  set size 0.5
  set color yellow
  set infected? false
  set immtime 0
  set hub? false
  set outside? false
end 

to activelinkprops
  set active? true
  set strength 1
  set color white
  set offset random knowsize
  set second? false
end 

to seed
  ask n-of initial turtles[
    set color red
    set infected? true
    set everinfected? true
    set infecttime 0
  ]
end 

to Go
  linkupdate
  ask turtles with [infected? = true][
    ask in-link-neighbors with [[active?] of link-with myself and infected? = false and immtime = 0][
      if (transmission / 100 > random-float 1) [
        set color red
        set infected? true
        set everinfected? true
        ;set infecttime 0
      ]
    ]
    set infecttime infecttime + 1
    if infecttime > removed [
      ifelse (mort / 100 > random-float 1) [
        die
      ]
      [
        set infected? false
        set infecttime 0
        set color yellow
        set immtime immunity
      ]
    ]
  ]
  ask turtles [
    if immtime > 0 [
      set immtime immtime - 1
      if immtime = 0 [set color yellow]
    ]
  ]
  ask turtles with [immtime > 0][set color blue]
  if maxinfected < count turtles with [infected?] [
    set maxinfected count turtles with [infected?]
  ]
  if count turtles with [infected?] < 1 [stop]
 ;set infections count turtles with [infected?]



  tick
end 

to-report infections
  report count turtles with [everinfected?]
end 

to linkupdate
  if ld? = false [
    ask links[
      ifelse ((ticks + offset) mod strength = 0) [
        set active? true
        set color white
      ]
      [
        set active? false
        set color black
      ]
    ]
  ]
end 

to Rearrange
  layout-tutte turtles with [not outside?] links with [second?] 45

  ;layout-circle turtles with [hub?] 45
  ;ask turtles with [hub? = false][
   ; face one-of in-link-neighbors with [hub?]
    ;fd 1
  ;]
end 

to Hubs
   ask n-of numhubs turtles[
      set hub? true
      set shape "star"
      set size 1
    ]
  if numhubs != 1 [
    ask turtles with [outside? and hub? = false][
      create-link-with one-of turtles with [hub?][
        set active? true
        set color white
        set strength freqsecond
        set second? true
        set offset random (freqsecond + wends)
        if strength < 1 [set strength 1]
    ]
      set fam [who] of in-link-neighbors with [hub?]
    ]
  ]
  if numhubs = 1 [
    ask turtles with [hub?] [create-links-with other turtles[
      set active? true
      set color white
      set strength freqsecond - 4 + (random 8)
      if strength < 1 [set strength 1]
    ]
  ]
    layout-circle turtles with [hub? = false ] 39
    ask turtles with [hub? = false] [
      set heading random 360
      fd 5
    ]
    ask turtles with [hub?][
      set xcor ((max [xcor] of in-link-neighbors) - (min [xcor] of in-link-neighbors)) / 2
      set ycor ((max [ycor] of in-link-neighbors) - (min [ycor] of in-link-neighbors)) / 2
    ]
  ]
end 

to Separate
  ask turtles [
    ifelse (xcor > max-pxcor / 2) [
      set heading 90
      fd 2
      set city  "1"
    ]
    [
      set heading 270
      fd 2
      set city "2"
   ]
  ]

  if (separator = "4")[
    ask turtles [
      ifelse (ycor > max-pycor / 2) [
        set heading 0
        fd 2
      ]
      [
        set heading 180
        fd 2
        if city = "1" [set city  "3"]
        if city = "2" [set city  "4"]
      ]
    ]
  ]


  ask turtles with [city = "1"][
    ask my-links [if ([city] of other-end) != "1" [die]]
    create-links-with up-to-n-of Secondlink other turtles with [city = "1"] in-radius radius [
      set active? true
      set color white
      set strength freqsecond
     ; - 4 + (random 8)
    ]
  ]

  ask turtles with [city = "2"][
    ask my-links [if ([city] of other-end) != "2" [die]]
    create-links-with up-to-n-of Secondlink other turtles with [city = "2"] in-radius radius [
      set active? true
      set color white
      set strength freqsecond
     ; - 4 + (random 8)
    ]
  ]
  ask turtles with [city = "3"][
    ask my-links [if ([city] of other-end) != "3" [die]]
    create-links-with up-to-n-of Secondlink other turtles with [city = "3"] in-radius radius [
      set active? true
      set color white
      set strength freqsecond
     ; - 4 + (random 8)
    ]
  ]
  ask turtles with [city = "4"][
    ask my-links [if ([city] of other-end) != "4" [die]]
    create-links-with up-to-n-of Secondlink other turtles with [city = "4"] in-radius radius [
      set active? true
      set color white
      set strength freqsecond
     ; - 4 + (random 8)
    ]
  ]

  ask up-to-n-of Secondlink turtles with [city = "1"][create-link-with one-of turtles with [city != "1"][activelinkprops]]
  ask up-to-n-of Secondlink turtles with [city = "2"][create-link-with one-of turtles with [city != "2"][activelinkprops]]
  ask up-to-n-of Secondlink turtles with [city = "3"][create-link-with one-of turtles with [city != "3"][activelinkprops]]
  ask up-to-n-of Secondlink turtles with [city = "4"][create-link-with one-of turtles with [city != "4"][activelinkprops]]


  set separated? true
end 

to ConnectHubs
  ask turtles with [hub?] [
    create-link-with one-of other turtles with [hub?][
      set active? true
      set strength freqsecond
     ; - 4 + (random 8)
    ]
  ]
end 

to Lockdown
  ifelse ld? [set ld? false][set ld? true]
  if separated? = false and ld? [
    ask up-to-n-of (linksbroken / 100 * count links) links [
      set active? false
      set color black
    ]
  ]
  if separated? = false and ld? = false [
    ask links [
      set active? true
      set color white
    ]
  ]

  ;if separated? = true [
   ; ask turtles[
    ;  if
end 

to Lockdown2
  ifelse ld? [set ld? false][set ld? true]
  if separated? = false and ld? [
    ask up-to-n-of (linksbroken / 100 * count links with [second?]) links with [second?] [
      set active? false
      set color black
    ]
  ]
  if separated? = false and ld? = false [
    ask links [
      set active? true
      set color white
    ]
  ]
end 

to StaggeredLock
  if ticks mod 4 = 0 [
    Lockdown
  ]
end 

to Secondary
  ask turtles with [outside?] [
    create-links-with n-of Secondlink other turtles with [outside?] [
      set strength freqsecond
      set offset random (freqsecond + wends)
      set second? true
      ]

  ]
  linkupdate
  histogram [count my-links with [active?]] of turtles
end