breed [persons person]
breed [viruses virus]


persons-own [infectious-period p-contagious susceptible infectious immunity vaccination]
viruses-own [infection infection-period]

Patches-own [ ]
Globals [max-daily-cases breakthrough]

;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;
;   Setup procedures
;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;


to setup
  clear-all
  set-default-shape viruses "c-virus-0"

  set-patches
  setup-people
  add-an-infectious
  color-code

  reset-ticks
end

to set-patches
  ask patches [set pcolor 9 + random-float 1]
end

to setup-people
  let masking (population * %-of-masking / 100)
  ask n-of masking  patches
  [ sprout-persons 1
    [set size 0.9
     set color 56
      set shape "person-1"
     set susceptible true
     set infectious false
     set immunity 0
     set infectious-period 0
     set vaccination false
     ]
  ]

    ask n-of (population - masking) patches
  [ sprout-persons 1
    [set size 0.9
     set color 56
     set shape "person-0"
     set susceptible true
     set infectious false
     set immunity 0
     set infectious-period 0
     set vaccination false
     ]
  ]

 let vaccinated (population * Vaccination-rate / 100)
  ask n-of vaccinated persons with [susceptible = true and infectious = false]
  [set susceptible false
   set infectious false
   set immunity Initial-Transmission-Rate
   set p-contagious Initial-Transmission-Rate
   set vaccination true
    set color 97]




end

to add-an-infectious
  ask one-of persons
  [set color 27
   set susceptible false
   set infectious true
   set p-contagious Initial-Transmission-Rate
   hatch-viruses 1 [
      set size 0.5
      set infection Initial-Transmission-Rate
      set-v-color
  ]]

end

;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;
;   Go procedures
;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;


to go

  if ticks > 0 and not any? persons with [susceptible = false and infectious = true] [stop]


  move
  produce-viruses
  infect
  virus-ability
  recover
  color-code
  find-max-daily-cases
  plot-levels
  tick
end

to move
  ask viruses
  [right random 360 forward 0.5]

end

to produce-viruses
  ask persons with [susceptible = false and infectious = true]                   ;ask infectious people
  [ifelse shape = "person-1"                      ;if masking
    [if random 100 < 50                             ;at a chance of 50%
      [hatch-viruses 1 [                              ;produce a new virus
        set size 0.5                                ;set the size of a virus
         ifelse random 100 < Virus-mutation-rate           ;set virus mutation rate
          [set infection 1 + random 100]            ;infection mutates to a rate between 1 to 100%
          [set infection [p-contagious] of myself]  ;not mutate
        set-v-color]                                ;set virus color based on infection rate
    ]]

    [hatch-viruses 1 [                              ;if no masking, always produce a new virus
        set size 0.5                                ;set the size of a virus
         ifelse random 100 < Virus-mutation-rate           ;set virus mutation rate
          [set infection 1 + random 100]            ;infection mutates to a rate between 1 to 100%
          [set infection [p-contagious] of myself]  ;not mutate
      set-v-color]]                                ;set virus color based on infection rate
  ]

end

to infect
  ask viruses
  [if any? persons with [infectious = false] in-radius 1.5
    [let infected-person one-of persons with [infectious = false] in-radius 1.5
     (ifelse
       [immunity] of infected-person > 0 and [shape] of infected-person = "person-1"  ;mutation lead to breakthough infection to a masked person,
           [if random 1000 < (0.05 * abs (infection - [immunity] of infected-person))     ;cut down 50% infection rate
               [move-to infected-person
                 ask infected-person
                  [set color 27
                   set susceptible false
                   set infectious true
                   set p-contagious [infection] of myself
                   set immunity [infection] of myself        ;update immunity
                  ]
             set breakthrough breakthrough + 1 die]]    ;ask virus to die after infecting a person

        [immunity] of infected-person > 0 and [shape] of infected-person = "person-0"  ;mutation lead to breakthough infection to an unmasked person,
            [if random 1000 < (0.1 * abs (infection - [immunity] of infected-person))     ;cut down 50% infection rate
              [move-to infected-person
               ask infected-person
                 [set color 27
                  set susceptible false
                  set infectious true
                  set p-contagious [infection] of myself
                  set immunity [infection] of myself        ;update immunity
                 ]
               set breakthrough breakthrough + 1 die]]    ;ask virus to die after infecting a person

        [immunity] of infected-person = 0 and [shape] of infected-person = "person-1"  ;first infection to a masked person,
            [if random 100 < infection * 0.5                       ;cut down 50% infection rate
               [move-to infected-person
                 ask infected-person
                  [set color 27
                   set susceptible false
                   set infectious true
                   set p-contagious [infection] of myself
                   set immunity [infection] of myself        ;update immunity
                  ]
                die]]    ;ask virus to die after infecting a person

        [immunity] of infected-person = 0 and [shape] of infected-person = "person-0"  ;first infection to an unmasked person,
            [if random 100 < infection
              [move-to infected-person
               ask infected-person
                [set color 27
                  set susceptible false
                  set infectious true
                  set p-contagious [infection] of myself
                  set immunity [infection] of myself        ;update immunity
                 ]
                die]])    ;ask virus to die after infecting a person
            ]]

end

to virus-ability
 ask viruses
  [ifelse infection-period >= 2 [die][set infection-period infection-period + 1]]
end

to recover
  ask persons with [susceptible = false and infectious = true]
  [ifelse infectious-period >= 7
    [ifelse random 100 < 10 [die] [set color 97 set susceptible false set infectious false set infectious-period 0]]   ;mortality equals 10%
    [set infectious-period infectious-period + 1]
  ]
end


;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;
;   supporting procedures
;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;


to set-v-color   ; set colors of viruses
  (ifelse
    infection >= 80  [set color 15]
    infection < 80 and infection >= 60 [set color 127]
    infection < 60 and infection >= 40 [set color 117]
    infection < 40 and infection >= 20 [set color 35]
    infection < 20  [set color 75])
end

to plot-levels ;; this creates creates the bar graph
    set-current-plot "People infected by variants with different transmissibilities"
    clear-plot
    plot-pen-down
    set-current-plot-pen "< 20%"
  plotxy 1 count persons with [p-contagious < 20 and p-contagious > 0]
    set-current-plot-pen "20%~39%"
  plotxy 2 count persons with [p-contagious < 40 and p-contagious >= 20]
    set-current-plot-pen "40%~59%"
  plotxy 3 count persons with [p-contagious < 60 and p-contagious >= 40]
    set-current-plot-pen "60%~79%"
  plotxy 4 count persons with [p-contagious < 80 and p-contagious >= 60]
    set-current-plot-pen ">= 80%"
  plotxy 5 count persons with [p-contagious >= 80]

end

to set-p-color  ; set colors of people
  ask persons
 [ (ifelse
    p-contagious >= 80 and vaccination = false [set color 15]
    p-contagious < 80 and p-contagious >= 60 and vaccination = false [set color 127.5]
    p-contagious < 60 and p-contagious >= 40 and vaccination = false [set color 117.5]
    p-contagious < 40 and p-contagious >= 20 and vaccination = false [set color 36]
    p-contagious < 20 and p-contagious > 0 and vaccination = false  [set color 75]
    p-contagious = 0 [set color 7]
    )]
end

to set-SIR-color
  ask persons
 [ (ifelse
    susceptible = true and infectious = false [set color 56]
    susceptible = false and infectious = true [set color 27]
    susceptible = false and infectious = false [set color 97]
    susceptible = true and infectious = true [set color 0])]
end

to color-code
 (ifelse
  Color-coding-modes = "Susceptible-infectious-recovered" [set-SIR-color]
  Color-coding-modes = "Variant transmission rates" [set-p-color])
end

to find-max-daily-cases
  if count persons with [susceptible = false and infectious = true] > max-daily-cases        ;Count the infectious.If it is greater than the current record of max daily cases
  [set max-daily-cases count persons with [susceptible = false and infectious = true]]       ;update the max daily case
end
@#$#@#$#@
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557
-1
-1
18.0
1
10
1
1
1
0
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-12
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ticks
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BUTTON
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821
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Start/Reset
setup
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T
OBSERVER
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NIL
1

BUTTON
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Run/Pause
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T
OBSERVER
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NIL
0

BUTTON
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852
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Run a day
go
NIL
1
T
OBSERVER
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NIL
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0

SLIDER
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Initial-Transmission-Rate
Initial-Transmission-Rate
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HORIZONTAL

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Virus-mutation-rate
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%
HORIZONTAL

SLIDER
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Population
Population
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600
350.0
50
1
People
HORIZONTAL

PLOT
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298
872
559
People infected by variants with different transmissibilities
Transmission Rate Range
# of people
1.0
5.0
0.0
10.0
true
true
"" ""
PENS
"< 20%" 1.0 1 -14835848 true "" "plotxy 1 count persons with [p-contagious < 20 and p-contagious > 0]"
"20%~39%" 1.0 1 -6459832 true "" "plotxy 2 count persons with [p-contagious < 40 and p-contagious >= 20]"
"40%~59%" 1.0 1 -5204280 true "" "plotxy 3 count persons with [p-contagious < 60 and p-contagious >= 40]"
"60%~79%" 1.0 1 -3508570 true "" "plotxy 4 count persons with [p-contagious < 80 and p-contagious >= 60]"
">= 80%" 1.0 1 -2674135 true "" "plotxy 5 count persons with [p-contagious >= 80]"

PLOT
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98
872
295
Population over Time
Days
% of population
0.0
10.0
0.0
1.0
true
true
"" ""
PENS
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"Infectious" 1.0 0 -955883 true "" "plot count persons with [susceptible = false and infectious = true] / population"
"Recovered" 1.0 0 -13791810 true "" "plot count persons with [susceptible = false and infectious = false] / population"

CHOOSER
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10
667
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Color-coding-modes
Color-coding-modes
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1

BUTTON
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59
644
92
Switch color-coding mode
ifelse Color-coding-modes = \"Susceptible-infectious-recovered\"\n[set Color-coding-modes \"Variant transmission rates\" set-p-color]\n[set Color-coding-modes \"Susceptible-infectious-recovered\" set-SIR-color]
NIL
1
T
OBSERVER
NIL
NIL
NIL
NIL
0

SLIDER
171
10
307
43
%-of-masking
%-of-masking
0
100
0.0
1
1
%
HORIZONTAL

MONITOR
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576
655
Max daily cases
max-daily-cases
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11

MONITOR
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608
Susceptible
count persons with [susceptible = true and infectious = false]
0
1
11

MONITOR
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608
Recovered
count persons with [susceptible = false and infectious = false]
0
1
11

MONITOR
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670
608
Infectious
count persons with [susceptible = false and infectious = true]
0
1
11

MONITOR
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Outbreak Duration
ticks
0
1
11

MONITOR
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Death
population - count persons
0
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TEXTBOX
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74
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SIR colors:
9
0.0
1

TEXTBOX
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111
595
|Green:susceptible
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54.0
1

TEXTBOX
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|Orange:infectious
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25.0
1

TEXTBOX
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|Blue:recovered
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94.0
1

TEXTBOX
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330
583
Colors of variant transmission rates:
9
0.0
1

TEXTBOX
248
578
337
596
|Turquoise:<20%
9
74.0
1

TEXTBOX
329
577
414
595
|Brown:20-39%
9
35.0
1

TEXTBOX
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314
608
|Purple:40-59%
9
115.0
1

TEXTBOX
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392
607
|Magenta:60-79%
9
125.0
1

TEXTBOX
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588
396
606
|Red:>=80%
9
15.0
1

TEXTBOX
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|Gray:not infected
9
4.0
1

SLIDER
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10
471
43
Vaccination-rate
Vaccination-rate
0
100
0.0
1
1
%
HORIZONTAL

MONITOR
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610
724
655
Breakthrough infection
breakthrough
0
1
11

@#$#@#$#@
## WHAT IS IT?
This model allows students to examine the effects of mutation and masking on the max daily cases and epidemic duration in a population. Both human beings and viruses are represented in the model. 


## HOW IT WORKS

1. Susceptible-infectious-recovered (SIR) model is used to build the present model.

2. The model starts with a population of susceptible people (green) and one infectious person (orange). The infectious person carries the virus strain with the defined initial transmission rate. 

3. In each tick, each infectious person produces a new virus. The virus transmission rate either stays the same or mutates to become more or less transmissible at the defined mutation rate. 

4. The new virus may float 0.5 steps in a random direction and infect one of susceptible people within a radius of 1.5 at its transmission rate. The virus loses its ability to infect people if no susceptible people are within the infection radius.

5. Infectious people remain contagious for six days. They either recover (become blue) or die at a mortality rate of 10%. No new people join this model to maintain the population density. 

6. Users may set up the percentage of masking in the population. The masked infectious people release 50% less viable viruses than unmasked infectious people. The transmission rate of a virus decreases by 50% when infecting a masked susceptible person (i.e., 70% become 35%, 50% become 25%, and so on).  

7. Users may set up the percentage of vaccinated people in the population. The present model assumes the vaccinated people will not be infected.  However, the vaccinated people may get a breakthrough infection at a low chance when viruses mutate. 


## 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.

5. The people in the model are color-coded in two ways: SIR coloring and transmission rate coloring. The mode of SIR coloring displays the population based on people's health status (i.e., susceptible, infectious, or recovered); the mode of transmission rate coloring displays the population based on the virus transmissibility when the people get infected (i.e., cyan and brown indicate the people who are infected by the less transmissible strains while red and purple indicate the people who are infected by the highly transmissible strains). Use the button **Switch color-coding mode** or the switch **Color-coding-modes** to switch between the two modes. 


## THINGS TO TRY

Collect the data of the max daily cases and epidemic duration to examine the effects of mutation rates and % of masking.


## 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
* Infectious Disease Outbreak-variants



## CREDITS AND REFERENCES

Dr. Lin Xiang (lin.xiang@uky.edu) created this model at the University of Kentucky in 2022. If you mention this model in a publication, we ask that you include the citations below.

Xiang, L. (2022). Infectious Disease Outbreak-mutation and masking. Department of STEM Education, University of Kentucky, Lexington, KY.

![CC BY-NC-SA 4.0](http://ccl.northwestern.edu/images/creativecommons/byncsa.png)

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/.

Science Brief: Community Use of Masks to Control the Spread of SARS-CoV-2  https://www.cdc.gov/coronavirus/2019-ncov/science/science-briefs/masking-science-sars-cov2.html
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Rectangle -16777216 true false 120 210 180 285
Polygon -7500403 true true 15 120 150 15 285 120
Line -16777216 false 30 120 270 120

humanbust
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leaf
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0
Polygon -7500403 true true 150 210 135 195 120 210 60 210 30 195 60 180 60 165 15 135 30 120 15 105 40 104 45 90 60 90 90 105 105 120 120 120 105 60 120 60 135 30 150 15 165 30 180 60 195 60 180 120 195 120 210 105 240 90 255 90 263 104 285 105 270 120 285 135 240 165 240 180 270 195 240 210 180 210 165 195
Polygon -7500403 true true 135 195 135 240 120 255 105 255 105 285 135 285 165 240 165 195

line
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Line -7500403 true 150 0 150 300

line half
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Line -7500403 true 150 0 150 150

pentagon
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Polygon -7500403 true true 150 15 15 120 60 285 240 285 285 120

person
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Circle -7500403 true true 110 5 80
Polygon -7500403 true true 105 90 120 195 90 285 105 300 135 300 150 225 165 300 195 300 210 285 180 195 195 90
Rectangle -7500403 true true 127 79 172 94
Polygon -7500403 true true 195 90 240 150 225 180 165 105
Polygon -7500403 true true 105 90 60 150 75 180 135 105

person-0
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0
Circle -7500403 true true 75 0 150
Polygon -7500403 true true 151 166 178 165 203 163 225 164 243 167 262 175 279 189 292 208 299 230 300 249 298 275 293 290 260 295 205 299 151 299 95 298 38 295 5 287 2 270 0 248 4 226 14 202 29 183 42 172 57 165 76 163 99 163 124 164 151 166

person-1
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Circle -7500403 true true 74 0 150
Polygon -7500403 true true 151 166 178 165 203 163 225 164 243 167 262 175 279 189 292 208 299 230 300 249 298 275 293 290 260 295 205 299 151 299 95 298 38 295 5 287 2 270 0 248 4 226 14 202 29 183 42 172 57 165 76 163 99 163 124 164 151 166
Polygon -1 true false 74 66 92 71 148 62 206 73 223 67 225 71 208 77 203 124 202 128 200 131 193 136 149 145 106 136 102 133 97 129 94 123 89 75 74 71

plant
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Rectangle -7500403 true true 135 90 165 300
Polygon -7500403 true true 135 255 90 210 45 195 75 255 135 285
Polygon -7500403 true true 165 255 210 210 255 195 225 255 165 285
Polygon -7500403 true true 135 180 90 135 45 120 75 180 135 210
Polygon -7500403 true true 165 180 165 210 225 180 255 120 210 135
Polygon -7500403 true true 135 105 90 60 45 45 75 105 135 135
Polygon -7500403 true true 165 105 165 135 225 105 255 45 210 60
Polygon -7500403 true true 135 90 120 45 150 15 180 45 165 90

sheep
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15
Circle -1 true true 203 65 88
Circle -1 true true 70 65 162
Circle -1 true true 150 105 120
Polygon -7500403 true false 218 120 240 165 255 165 278 120
Circle -7500403 true false 214 72 67
Rectangle -1 true true 164 223 179 298
Polygon -1 true true 45 285 30 285 30 240 15 195 45 210
Circle -1 true true 3 83 150
Rectangle -1 true true 65 221 80 296
Polygon -1 true true 195 285 210 285 210 240 240 210 195 210
Polygon -7500403 true false 276 85 285 105 302 99 294 83
Polygon -7500403 true false 219 85 210 105 193 99 201 83

square
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Rectangle -7500403 true true 30 30 270 270

square 2
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Rectangle -7500403 true true 30 30 270 270
Rectangle -16777216 true false 60 60 240 240

star
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Polygon -7500403 true true 151 1 185 108 298 108 207 175 242 282 151 216 59 282 94 175 3 108 116 108

target
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Circle -7500403 true true 0 0 300
Circle -16777216 true false 30 30 240
Circle -7500403 true true 60 60 180
Circle -16777216 true false 90 90 120
Circle -7500403 true true 120 120 60

tree
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0
Circle -7500403 true true 118 3 94
Rectangle -6459832 true false 120 195 180 300
Circle -7500403 true true 65 21 108
Circle -7500403 true true 116 41 127
Circle -7500403 true true 45 90 120
Circle -7500403 true true 104 74 152

triangle
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0
Polygon -7500403 true true 150 30 15 255 285 255

triangle 2
false
0
Polygon -7500403 true true 150 30 15 255 285 255
Polygon -16777216 true false 151 99 225 223 75 224

truck
false
0
Rectangle -7500403 true true 4 45 195 187
Polygon -7500403 true true 296 193 296 150 259 134 244 104 208 104 207 194
Rectangle -1 true false 195 60 195 105
Polygon -16777216 true false 238 112 252 141 219 141 218 112
Circle -16777216 true false 234 174 42
Rectangle -7500403 true true 181 185 214 194
Circle -16777216 true false 144 174 42
Circle -16777216 true false 24 174 42
Circle -7500403 false true 24 174 42
Circle -7500403 false true 144 174 42
Circle -7500403 false true 234 174 42

turtle
true
0
Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210
Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105
Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105
Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87
Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210
Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99

wheel
false
0
Circle -7500403 true true 3 3 294
Circle -16777216 true false 30 30 240
Line -7500403 true 150 285 150 15
Line -7500403 true 15 150 285 150
Circle -7500403 true true 120 120 60
Line -7500403 true 216 40 79 269
Line -7500403 true 40 84 269 221
Line -7500403 true 40 216 269 79
Line -7500403 true 84 40 221 269

wolf
false
0
Polygon -16777216 true false 253 133 245 131 245 133
Polygon -7500403 true true 2 194 13 197 30 191 38 193 38 205 20 226 20 257 27 265 38 266 40 260 31 253 31 230 60 206 68 198 75 209 66 228 65 243 82 261 84 268 100 267 103 261 77 239 79 231 100 207 98 196 119 201 143 202 160 195 166 210 172 213 173 238 167 251 160 248 154 265 169 264 178 247 186 240 198 260 200 271 217 271 219 262 207 258 195 230 192 198 210 184 227 164 242 144 259 145 284 151 277 141 293 140 299 134 297 127 273 119 270 105
Polygon -7500403 true true -1 195 14 180 36 166 40 153 53 140 82 131 134 133 159 126 188 115 227 108 236 102 238 98 268 86 269 92 281 87 269 103 269 113

x
false
0
Polygon -7500403 true true 270 75 225 30 30 225 75 270
Polygon -7500403 true true 30 75 75 30 270 225 225 270
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NetLogo 6.3.0
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@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
@#$#@#$#@
default
0.0
-0.2 0 0.0 1.0
0.0 1 1.0 0.0
0.2 0 0.0 1.0
link direction
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Line -7500403 true 150 150 90 180
Line -7500403 true 150 150 210 180
@#$#@#$#@
0
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