Infectious Disease Outbreak-daily cases and daily new cases

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Screen_shot_2018-02-02_at_12.53.50_pm lin xiang (Author)

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WHAT IS IT?

This model simulates the epidemic dynamics in a human population based on a revised SEIR model, i.e., in this model the infectious (I) are fully isolated at home or in hospitals so that they do not transmit the disease. This model reveals the differences between the daily cases and daily new cases. Besides, this model allows students to label an individual person in the population and examine the chance at which the person is infected and follow the person through the epidemic.

HOW IT WORKS

The model starts with a human population consisting of susceptible (green color)people. Once a carrier (orange color) appears in the population, it will pass the disease to one of the susceptible people nearby (within a radius of 1.5) at the defined transmission rate. The carrier may become sick (infectious red color) after the defined incubation period. The sick people will be isolated, so they do not infect others. The sick people will remain ill for 14 days. By the 15th day of being sick, they die (disappear from the model) at the defined mortality or recover and become immune to the disease (blue color).

Buttons, Sliders, and Switches:

  • The population size slider is self-explanatory. So are the buttons of Set up/Reset, Run/Pause, and Run a day.

  • The Vaccination-rate slider determines the vaccination coverage of the population.

  • The Transmission-rate slider determines how likely a susceptible person is infected when exposed to the disease.

  • The Mortality slider determines how likely the infected people die on the 15th day.

  • The "Incubation-period" defines the number of days between a person is infected and becomes sick.

  • The "Illness-period" defines the number of days between a person becomes to show symptoms to recover.

  • The +1 Carrier button adds a carrier into the population.

  • The Select to watch a person button allows you to focus on an individual person. You may compare how often the person gets infected in different situations.

  • The Stop watching button allows you to stop watching the person.

HOW TO USE IT

  1. First, choose the factors, such as population size, transmission rate, etc.

  2. Click on Set up/Reset then Run/Pause. The model is set to stop when there are no infectious people.

  3. Observe the infection changes in the population in the plot and monitor.

  4. Use Run one day to run the model in a controlled way and collect day-by-day data.

THINGS TO TRY

There are so many things you can try in this model. Here are only very a few quick ideas:

  • How does the number of daily cases differ from the number of daily new cases?

  • How does the change in the number of daily cases related to the change in the number of daily new cases?

  • How can the daily cases and/or daily new cases be used to measure the severity of an epidemic? Why?

RELATED MODELS

Find this model series at http://3dsciencemodeling.com

  • Infectious Disease Outbreak-Basic Phenomenon
  • Infectious Disease Outbreak-Transmission and mortality
  • Infectious Disease Outbreak-Population Comparison
  • Infectious Disease Outbreak-HealthCare, Isolation and Quarantine
  • Infectious Disease Outbreak-Social distancing
  • Infectious Disease Outbreak-Vaccination
  • Infectious Disease Outbreak-SEIR model

CREDITS AND REFERENCES

Dr. Lin Xiang (lin.xiang@uky.edu) created this model at the University of Kentucky in 2021. If you mention this model in a publication, we ask that you include the citations below.

Xiang, L. (2021). Infectious Disease Outbreak-Daily cases and daily new cases. Department of STEM Education, University of Kentucky, Lexington, KY.

CC BY-NC-SA 4.0

This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/.

Comments and Questions

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turtles-own [ days-after-exposure  days-of-sick labeled]
Patches-own [ ]
Globals [ watching  max-daily-cases daily-new-cases max-daily-new-cases]

to setup
  ca
  setup-turtles

   set watching false

  reset-ticks
end 

to setup-turtles
  create-turtles population-size
  [set color 68
    set size 1.25
    set labeled 0
    set shape "person"
    setxy random-xcor random-ycor
  ]
end 

to go

if ticks > incubation-period and count turtles with [color = red] = 0 [stop]

  set daily-new-cases 0
  move
  transmission
  incubation
  sickness
  find-max-daily-cases
  tick
end 

to move
  ask turtles with [shape = "person"]
  [right random 360 forward mobility]
end 

to add-a-carrier
  ask one-of turtles                     ;choose a random person
  [set color orange                      ;set the color as orange (carrier color)
  ]
end 

to transmission
  ask turtles with [color = orange]                                              ;Hi, carriers
  [let susceptible-person one-of other turtles in-radius 1.5 with [color = 68]   ;Are there any susceptible people near you (within a radius of 1.5)?
    if susceptible-person != nobody                                              ;If there is at least one
    [ask susceptible-person                                                      ;ask the suscetiple person
      [ if random 100 < transmission-rate                                        ;at the defined transmission rate
        [set color orange]                                                       ;to become a carrier (orange color)
      ]
    ]
  ]
end 

to incubation
  ask turtles with [color = orange]                    ;Hi carriers
   [ifelse days-after-exposure < incubation-period     ;If the number of days after you get infected is smaller than the defined incubation period
    [set days-after-exposure days-after-exposure + 1]  ;increase the number of days after exposure by 1
    [set color red set shape "house"                   ;otherwise, become infectious (red color)
           set daily-new-cases daily-new-cases + 1     ;count daily neew cases
           if daily-new-cases > max-daily-new-cases    ;find the max daily new cases
            [set max-daily-new-cases daily-new-cases]  ]
   ]
end 

to sickness
  ask turtles with [color = red]          ;Hi sick people,
  [ifelse days-of-sick <= illness-period             ;if you have not been sick for 15 days
    [set days-of-sick days-of-sick + 1]   ;remain sick and increase the number of sick days by 1
    [ifelse random 100 < mortality        ;otherwise, at the define mortality rate
      [die]                               ;die
      [set color blue set shape "person"] ;or recover
    ]
   ]
end 

to vaccination
  let num-of-susceptible (count turtles with [color = 68])              ;find the number of susceptible people
  let num-of-vaccinated  (num-of-susceptible * vaccination-rate * 0.01) ;calculate number of susceptubel people to be vaccinated
  ask n-of num-of-vaccinated turtles with [color = 68]                  ;find these many susceptible people
     [set color blue]                                                   ;set as immune (blue)
end 

to find-max-daily-cases
  if count turtles with [color = red ] > max-daily-cases        ;Count the infectious.If it is greater than the current record of max daily cases
  [set max-daily-cases count turtles with [color = red ]]       ;update the max daily case
end 

to watch-an-infected-person
  watch one-of turtles with [color = red]
end 

to label-a-person

  if any? turtles = false [user-message "Nobody is here." stop]


  if mouse-inside? [
    if mouse-down? [
      let labeled-person min-one-of turtles [distancexy mouse-xcor mouse-ycor]
      if labeled-person != nobody [
        ask labeled-person [set label "me" set labeled 1]      ;label the 1st selected person as me
        watch labeled-person]
  ]]


 if count turtles with [labeled = 1] >= 1 [stop]   ;disable the button when one person is labelled.
end 

to unselect

  ask turtles
  [set labeled 0
    set label ""]
  rp
end 

There are 3 versions of this model.

Uploaded by When Description Download
lin xiang about 2 years ago adjust the interface Download this version
lin xiang almost 3 years ago update license Download this version
lin xiang almost 3 years ago Initial upload Download this version

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