Helping Agents in Epidemics

globals [
  seed

 max-infected              ;; Maximum number of agents infected at a single time point
 max-infected-time         ;; time step at which the above occurs
end -time                  ;; time step at which the number of infected = 0 (DC: redundant due to step counter already output with csv file?)
 last-susceptible          ;; number of agents who were never infected. Subtracting from population size would give number of recovered at end.
 final-epi-size            ;; number of total people who got infected throughout the epidemic (N - last-susceptible)

 total-helper-infected     ;; total number of helpers that got infected throughout epidemic
 total-normal-infected     ;; total number of non-helpers infected throughout epidemic

 total-contacts             ;; interactions for every agent
 total-contact-list         ;; list of total contacts for each time step

 r0                        ;; r0 calculated by averaging number of people one indiv infects throughout time as infected
 length-infection          ;; average length of infection for initially infected agents

]

turtles-own [
initial-infected?          ;; turtle owned marker indicating if one of the initial infected agents
help                       ;; each helper's contribution depending on surroundings and maxhelp set by user, calc at each time step for each helper, normal setting = 0
totalInfected              ;; total number agents that a turtle infected thus far
helper-surrounding         ;; keeps track of how many helpers are around each sick individual at each time step
infected-surrounding       ;; keeps track of how many infected are around each helper at each time step
finish-infected            ;; (initial infected agents) how long initial agents were sick
]

to setup
  clear-all
  set seed new-seed
  random-seed seed
  resize-world 0 world-size 0 world-size

  set final-epi-size 0
  set total-helper-infected 0
  set total-normal-infected 0
  set total-contacts 0
  set total-contact-list []
  set max-infected 0
  set max-infected-time 0
  set end-time 0
  set last-susceptible 0
  turtle-creation

  ask patches [
    set pcolor 8
    if pxcor mod 2 = 1 and pycor mod 2 = 0 [set pcolor 9.9] if pxcor mod 2 = 0 and pycor mod 2 = 1 [set pcolor 9.9]]
  ask turtles [ set pen-mode "up"]

  reset-ticks
end 

to turtle-creation
  create-turtles N-H  [                               ;; create helpers
    set shape "person"
    set color black
    setxy random-xcor random-ycor
    set initial-infected? false
    ]
  if count turtles < N [                              ;; if helpers do not make up entire population, fill rest with default
    create-turtles (N - count turtles)[               ;; could theoretically put in more helpers than N, population size would be # helpers rather than N
      set color black
      setxy random-xcor random-ycor
      set initial-infected? false
    ]
  ]
  ask n-of N-I turtles [
    set initial-infected? true                        ;; initial infected
    set color red
  ]
end 

to go
  if count turtles with [color = red] = 0 [                         ;; check to see if epidemic over, do ending measurements
end -stats
    calculate-r0
    stop]

  tracking
  contacts
  targets-calc
  move
  infection-transmission
  help-calc
  recover
  update-plots
  tick-advance 1
end 

to tracking
  if count turtles with [color = red] > max-infected [              ;; keep writing over largest number of infected
    set max-infected count turtles with [color = red]               ;; record and write over time at which maximum number of infected achieved
    set max-infected-time ticks
  ]
end 

to targets-calc
  ask turtles with [color = red] [
    set helper-surrounding count turtles with [shape = "person" and color != red] in-radius hrad      ;;if sick, count number of helpers in help radius
  ]
  ask turtles with [color != red] [                                                                   ;; don't care about number of helpers surrounding the healthy or recovered
    set helper-surrounding 0
  ]
  ask turtles with [shape = "person" and color != red] [
    set infected-surrounding count turtles with [color = red] in-radius hrad
  ]
  ask turtles with [shape != "person"] [
    set infected-surrounding 0
  ]
  ask turtles with [shape = "person" and color = red] [
    set infected-surrounding 0
  ]
end 

to contacts
  ask turtles [
    set total-contacts total-contacts + count turtles in-radius infrad
  ]
set total-contact-list lput total-contacts total-contact-list
end 

to move


 if interaction-type = "random-move" [                                                      ;; all turtles move randomly
   ask turtles [
     right (random-float 2 * 90 ) - 90
    fd 1
   ]
 ]

 if interaction-type = "helper-seek" [
   ask turtles with [shape = "person" and color = red] [                                    ;; sick helpers move randomly
     right (random-float 2 * 90 ) - 90
     fd 1
   ]

   ask turtles with [shape = "default"][                                                    ;; non-helpers move randomly
     right (random-float 2 * 90 ) - 90
     fd 1
   ]
   ask turtles with [shape = "person" and color != red][                                    ;; non-sick helpers seek the sick
    ifelse any? turtles with [color = red][
      let target min-one-of turtles with [color = red] [distance myself]                    ;; move toward nearest sick person
      face target
      fd 1
    ]
    [
      right (random-float 2 * 90 ) - 90                                                     ;; if no one is sick, move normally
      fd 1
    ]
   ]
 ]

 if interaction-type = "helper-smart-seek" [                                                ;; non-helpers move randomly
   ask turtles with [shape = "default"][
     right (random-float 2 * 90 ) - 90
     fd 1
   ]
   ask turtles with [shape = "person" and color = red] [                                    ;; sick helpers move randomly
     right (random-float 2 * 90 ) - 90
     fd 1
   ]
   ask turtles with [shape = "person" and color != red][                                    ;; non-sick helpers seek...
     ifelse any? turtles with [color = red and (helper-surrounding = 0)][
       let possible-targets turtles with [color = red]
       let targets possible-targets with [helper-surrounding = 0]
       let target min-one-of targets [distance myself]                                      ;; nearest sick agent without a helper (helper-surrounding = 0)
       face target
       fd 1
     ]
     [
       right (random-float 2 * 90 ) - 90                                                    ;; if all helpers busy or all are non-sick, move randomly
       fd 1
     ]
   ]
 ]

 if interaction-type = "infected-seek"[
   ask turtles with [shape = "default" and color != red] [                                 ;; ask normal agents to move randomly
     right (random-float 2 * 90 ) - 90
     fd 1
   ]
   ask turtles with [shape = "person" and color != red] [                                  ;; ask non-sick helpers to move randomly
     right (random-float 2 * 90 ) - 90
     fd 1
   ]
   ask turtles with [color = red] [
     ifelse any? turtles with [shape = "person" and color != red] [                        ;; ask infected to seek nearest non-sick helper
       let target min-one-of turtles with [shape = "person" and color != red] [distance myself]
       face target
       fd 1
     ]
     [
       right (random-float 2 * 90 ) - 90                                                   ;; if no non-sick helpers, move randomly
       fd 1
     ]
   ]
 ]

 if interaction-type = "infected-smart-seek" [
   ask turtles with [shape = "default" and color != red] [                                ;; ask normal non-sick agents to move randomly
     right (random-float 2 * 90 ) - 90
     fd 1
   ]
   ask turtles with [shape = "person" and color != red] [                                 ;; ask helper non-sick agents to move randomly
     right (random-float 2 * 90 ) - 90
     fd 1
   ]
   ask turtles with [color = red] [                                                       ;; ask infected to seek nearest helper who isn't already helping someone else
     ifelse any? turtles with [shape = "person" and color != red and (infected-surrounding = 0)] [
       let possible-targets turtles with [shape = "person" and color != red]
       let targets possible-targets with [infected-surrounding = 0]
       let target min-one-of targets [distance myself]
       face target
       fd 1
     ]
     [
       right (random-float 2 * 90 ) - 90                                                 ;; if no non-sick helpers free, move randomly
       fd 1
     ]
   ]
 ]

if interaction-type = "dual-smart-seek" [
  ask turtles with [shape = "default" and color != red] [                                ;; ask normal non-sick agents to move randomly
    right (random-float 2 * 90 ) - 90
    fd 1
  ]
  ask turtles with [shape = "person" and color != red][                                    ;; non-sick helpers seek...
    ifelse any? turtles with [color = red and (helper-surrounding = 0)][
      let possible-targets turtles with [color = red]
      let targets possible-targets with [helper-surrounding = 0]
      let target min-one-of targets [distance myself]                                      ;; nearest sick agent without a helper (helper-surrounding = 0)
      face target
      fd 1
    ]
    [
      right (random-float 2 * 90 ) - 90                                                    ;; if all helpers busy or all are non-sick, move randomly
      fd 1
    ]
  ]
  ask turtles with [color = red] [                                                       ;; ask infected to seek nearest helper who isn't already helping someone else
    ifelse any? turtles with [shape = "person" and color != red and (infected-surrounding = 0)] [
      let possible-targets turtles with [shape = "person" and color != red]
      let targets possible-targets with [infected-surrounding = 0]
      let target min-one-of targets [distance myself]
      face target
      fd 1
    ]
    [
      right (random-float 2 * 90 ) - 90                                                 ;; if no non-sick helpers free, move randomly
      fd 1
    ]
  ]
]
end 

to infection-transmission
  ask turtles with [color = black and shape != "person"] [                                ;; normal suceptible agents calculate prob infection based on frac infected neighbors and infect-prob
    if (random-float 1) < infect-prob * count turtles with [color = red] in-radius infrad / count turtles in-radius infrad [
        set color red
        ask turtles with [color = red] in-radius infrad [
          set totalInfected totalInfected + 1                                             ;; infected how many agents across entire infective period
        ]
    ]
  ]
  ask turtles with [color = black and shape = "person"] [                                 ;; helpers get decreased chance of infection.
    if (random-float 1) < (1 - helper-immunity) * infect-prob * count turtles with [color = red] in-radius infrad / count turtles in-radius infrad [
        set color red
        ask turtles with [color = red] in-radius infrad [
          set totalInfected totalInfected + 1                                             ;; infected how many agents across entire infective period
        ]
    ]
  ]
end 

to help-calc
  ask turtles with [shape = "person" and color != red]
  [
    ifelse any? turtles with [color = red] in-radius hrad [
       set help maxhelp / count turtles with [color = red] in-radius hrad                 ;; ideal "maxhelp" from slider, helper splits effort between sick in radius
    ]
    [
       set help 0                                                                         ;; no one to help, set help 0
    ]
  ]
end 

to recover
  ask turtles with [color = red][
    ifelse any? turtles with [shape = "person" and color != red] in-radius hrad [        ;; ask helpers for help
      let totalhelp 0
      ask turtles with [shape = "person" and color != red] in-radius hrad [
        set totalhelp totalhelp + help
        if totalhelp > maxhelp [set totalhelp maxhelp]                                   ;; if aggregate help exceeds maxhelp, set total help back to max
      ]
      if (random-float 1) < recover-prob + totalhelp [                                   ;; increased probability of recovery with help
        set color blue
        if initial-infected? [set finish-infected ticks]
      ]
    ]
    [ if (random-float 1) < recover-prob [                                               ;; probability of recovery without help
        set color blue
        if initial-infected? [set finish-infected ticks]
      ]
      ]
  ]
end 

to calculate-r0
  set r0 mean [totalInfected] of turtles with [initial-infected?]                       ;; mean number infected by individual during entire infective state
  set length-infection mean [finish-infected] of turtles with [initial-infected?]       ;; average length of infection for initially infected agents
end 

to end-stats
  set end-time ticks
  set last-susceptible count turtles with [color = black]
  set final-epi-size (N - last-susceptible)
  set total-helper-infected count turtles with [color = blue and shape = "person"]
  set total-normal-infected count turtles with [color = blue and shape = "default"]
end