Infectious disease

breed [healthies healthy] ;;Different breeds of turtles to show heatlh state.
breed [infecteds infected]
breed [sicks sick]
breed [immunes immune]
breed [deads dead]

globals [ ;; Global variables.
  total-healthy
  total-sick
  total-infected
  total-immune
  total-dead
]

turtles-own [  ;; Turtle variables.
  turn-check
  wall-turn-check
  incubate
  sickness
  terminal-check
  immune-check
]

to building-draw ;; Use the mouse to draw buildings.
  if mouse-down?
    [
      ask patch mouse-xcor mouse-ycor
        [ set pcolor brown ]]
end 

to setup  ;; Initialize the model.
  clear-turtles
  reset-ticks
  pop-check
  ask patches [set pcolor grey]
  setup-agents
  update-globals
  do-plots
end 

to go  ;; Run the model.
   disease-check
  tick
  repeat 5 [ ask healthies [ fd 0.2 ] display ]
   repeat 5 [ ask infecteds [ fd 0.2 ] display ]
   repeat 5 [ ask sicks [ fd 0.2 ] display ]
   repeat 5 [ ask immunes [ fd 0.2 ] display ]
   update-globals
   do-plots
end 

to setup-agents  ;;  Setup the begining number of agents and their initial states.
  set-default-shape healthies "person"
  set-default-shape infecteds "person"
  set-default-shape sicks "person"
  set-default-shape immunes "person"
  set-default-shape deads "person"

  ask n-of initial-healthy patches with [pcolor  = grey]
     [ sprout-healthies 1
      [ set color blue ] ]

  ask n-of initial-sick patches with [pcolor = grey]
    [ sprout-sicks 1
      [ set color yellow
        set sickness disease-period ] ]
end 

to disease-check ;;  Check to see if an infected or sick turtle occupies the same patch.
  ask healthies [
    if any? other turtles-here with [color = yellow]
    [infect]
    if any? other turtles-here with [color = pink]
    [infect]
    wander
  ]

  ask sicks [
    if any? other turtles-here with [color = blue]
    [infect]
    wander
    set sickness sickness - 1
    if sickness < 1
    [live-or-die]
  ]

  ask infecteds [
    if any? other turtles-here with [color = blue]
    [infect]
    wander
    set incubate incubate - 1
    if incubate = 0
    [get-sick]
  ]

  ask immunes [wander]
end 

to infect ;;  Infect a healthy turtle, test if it is immune and set the incubation timer if it isn't.
  set immune-check random 100
  ifelse immune-check < immune-chance-beforehand
  [recover]
  [ask healthies-on patch-here[
    set breed infecteds
    set incubate incubation-period]
  ask infecteds-on patch-here [set color pink]]
end 

to get-sick ;;  Change an infected turtle into an sick turtle and set the disease progression timer.
   set breed sicks
   set color yellow
   set sickness disease-period
end 

to terminate ;;  Kill a sick turtle who reaches the end of the disease progression and fails the terminal check.
  set breed deads
  set color black
end 

to live-or-die ;; Test if the turtle dies from the disease.
  set terminal-check random 100
  ifelse terminal-check < terminal-chance
  [terminate]
  [recover]
end 

to recover  ;;  Change turtle breed to immune.
  set immune-check random 100
  if immune-chance-after > immune-check
  [set breed immunes
  set color sky]
  if immune-chance-after < immune-check
  [set breed healthies set color blue]
end 

to wander ;; Random movement for agents.
    set turn-check random 20
    if turn-check > 15
    [right-turn]
    if turn-check < 5
    [left-turn]
     if [pcolor] of patch-ahead 1 != grey
     [wall]
end 

to wall ;;  Turn agent away from wall
    set wall-turn-check random 10
    if wall-turn-check >= 6
    [wall-right-turn]
    if wall-turn-check <= 5
    [wall-left-turn]
end 

to wall-right-turn ;;Generate a random degree of turn for the wall sub-routine.
  rt 170
end 

to wall-left-turn ;;Generate a random degree of turn for the wall sub-routine.
  lt 170
end 

to right-turn ;;Generate a random degree of turn for the wander sub-routine.
  rt random-float 10
end 

to left-turn   ;;Generate a random degree of turn for the wander sub-routine.
  lt random-float 10
end 

to update-globals ;;Set globals to current values for reporters.
  set total-healthy (count healthies)
  set total-infected (count infecteds)
  set total-sick (count sicks)
  set total-immune (count immunes)
  set total-dead (count deads)
end 

to do-plots ;; Update graph.
  set-current-plot "Population Totals"
  set-current-plot-pen "Healthy"
  plot total-healthy
  set-current-plot-pen "Infected"
  plot total-infected
  set-current-plot-pen "Sick"
  plot total-sick
  set-current-plot-pen "Immune"
  plot total-immune
  set-current-plot-pen "Dead"
  plot total-dead
end 

to pop-check  ;; Make sure total population does not exceed total number of patches.
  if initial-healthy + initial-sick > count patches
    [ user-message (word "This simulation only has room for " count patches " agents.")
      stop ]
end 

; *** NetLogo 4.1 Model Copyright Notice ***
;
; Copyright 2010 by Michael D. Ball.  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 Michael D. Ball.
; Contact Michael D. Ball for appropriate licenses for redistribution for
; profit.
;
; To refer to this model in academic publications, please use:
; Ball, M. (2010).  Infectious Disease Model ver. 1.
; http://www.personal.kent.edu/~mdball/netlogo_models.htm.
; The Center for Complexity in Health,
; Kent State University at Ashtabula, Ashtabula, OH.
;
; In other publications, please use:
; Copyright 2010 Michael D. Ball.  All rights reserved.
; See http://www.personal.kent.edu/~mdball/netlogo_models.htm
; for terms of use.
;
; *** End of NetLogo 4.1 Model Copyright Notice ***