Covid Epidemic

breed [CITIZENS CITIZEN]

globals[

]
citizens-own [
  is_infected
  remaining_infection
  if_infected_die_prob
  dead
  quarantine
  remaining_infection
  random_infect
  is_infected
  infection_prob
  is_quarantined
  infection_immunity
  infected_neighbours
  is_immuned
  once_infected
  once_quarantined
  under_quarantine
  lim
  recovery_rate
  ]

to setup
  clear-all


  create-citizens 0.7 * count patches [
    set shape "person"
    set random_infect random 100
    set if_infected_die_prob random 100
    set dead 0
    set quarantine random 100
    set is_quarantined 0
    set infection_prob 0
    set infected_neighbours 0
    set infection_immunity random 100
    set is_immuned 0
    set once_infected 0
    set once_quarantined 0
    set under_quarantine 0
    set recovery_rate 1 / days_required_for_healing
    move-to one-of patches with [not any? turtles-here]
    ifelse(random_infect <= initial_infect)
    [set remaining_infection 1
    set is_infected 1
    set color red]
    [set remaining_infection 0
    set is_infected 0
    set color gray]
  ]
 reset-ticks
end 

to update_indection_probability
  set infected_neighbours sum [is_infected] of citizens with [dead = 0 and is_quarantined = 0 and 1 - contamination_period * recovery_rate <= remaining_infection ] in-radius 1
  if(infected_neighbours = 0)
  [set infection_prob  0]
  if(infected_neighbours = 1)
  [set infection_prob  infection_rate]
  if(infected_neighbours = 2)
  [set infection_prob  infection_rate + (1 - infection_rate) *  infection_rate ]
    if(infected_neighbours = 3)
  [set infection_prob  infection_rate + (1 - infection_rate) *  infection_rate + (1 - infection_rate) * (1 - infection_rate) * (infection_rate) ]
    if(infected_neighbours = 4)
  [set infection_prob  infection_rate + (1 - infection_rate) *  infection_rate + (1 - infection_rate) * (1 - infection_rate) * (infection_rate) +
 (1 - infection_rate) * (1 - infection_rate) * (1 - infection_rate) * (infection_rate) ]
   if(infected_neighbours > 4)
  [set infection_prob  1]
end 

to get_infected
  ifelse(infection_prob * 100 >= infection_immunity  and is_infected = 0 and dead = 0 and is_quarantined = 0 and is_immuned = 0)
  [set color red
  set is_infected 1
  set remaining_infection 1
  set once_infected 1]
  [set infection_prob 0
  set infected_neighbours 0]
end 

to get_cured
  if(is_infected = 1 and remaining_infection > recovery_rate and dead < 1)
  [set remaining_infection (remaining_infection - recovery_rate)]
  if(is_infected = 1 and remaining_infection <= recovery_rate and dead < 1)
  [set is_infected 0
  set color green
  set is_immuned 1]
end 

to get_quarantine
  set lim ticks * isolation_policy_toughness
  if(is_immuned = 0 and quarantine <= min list  lim quarantine_threshold and is_quarantined = 0 and ticks > isolation_start_date)
  [set color yellow
    set is_quarantined 1
  set once_quarantined 1]
end 

to get_die
  if(is_infected = 1 and remaining_infection < 1 - recovery_rate * 5 and  if_infected_die_prob <= death_rate)
  [set dead 1
    set is_infected  0
  set color pink]
end 

to move
  if count patches in-radius movement_rate with [not any? turtles-here] > 0
   [move-to one-of patches in-radius movement_rate with [not any? turtles-here]]
end 

to update_under_quarantine
  set under_quarantine under_quarantine + 1
end 

to end_quarantine
  if(under_quarantine >= isolation_duration)[
    set is_quarantined 0
    set under_quarantine 0
    if(is_infected = 1)[
      set color red]
    if(is_immuned = 1)[
      set color green]
    if(is_infected = 0 and is_immuned = 0)
    [set color gray]
  ]
end 

to go
  ask citizens[
    if(dead = 0 and is_quarantined = 0)[
    move
    update_indection_probability
    get_infected
    if(once_quarantined = 0)
      [get_quarantine]
    get_die
    get_cured
    ]
    if(dead = 0 and is_quarantined = 1)[
    get_die
    get_cured
    update_under_quarantine
    end_quarantine
    ]
  ]
  tick
end