COVID_19 spread with movement rules

COVID_19 spread with movement rules preview image

This model is seeking new collaborators — would you please help?

1 collaborator

Default-person Emiliano Alvarez (Author)

Tags

contagion 

Tagged by Emiliano Alvarez 6 months ago

covid-19 

Tagged by Emiliano Alvarez 6 months ago

movement 

Tagged by Emiliano Alvarez 6 months ago

Child of model COVID_19 Spread preview imageCOVID_19 Spread
Visible to everyone | Changeable by the author
Model was written in NetLogo 6.1.1 • Viewed 779 times • Downloaded 28 times • Run 0 times
Download the 'COVID_19 spread with movement rules' modelDownload this modelEmbed this model

Do you have questions or comments about this model? Ask them here! (You'll first need to log in.)


Info tab cannot be displayed because of an encoding error

Comments and Questions

File doesn't open. Either In Zip, 7zip or explorer.

It is possible a new file? or... there are some tip to decompress the file? thanks, Giovani - Brazil

Posted 6 months ago

Answer to Giovani

Hi, You can unzip the model via Terminal (using Linux), type: unzip \*.zip \\\ On Windows OS, Modeling Commons zip files have drawbacks. \\\ Search for a zip extractor online, like https://extract.me/ or others. \\\ Thanks, Emiliano.

Posted 6 months ago

Question Regarding the Modeling of Network Hubs (Question)

Hi I wanted to demonstrate how important network hubs (areas of high density) are in transmitting Covid. Namely, to show people why going camping in large groups of people, and then going to a local hub (grocery story, etc), completely defeats the point of social distancing.

Posted 6 months ago

response to Eric

Well, one possible modification is to increase the density of agents (for example, from 1500 to 5000 agents). It's similar to percolation models (one example to look is "fire model" in netlogo). Another improvement would be to set agents regarding xy (for example, more density when x&rt;0 and y&rt;0). Thanks, Emiliano

Posted 6 months ago

Click to Run Model

turtles-own
  [ sick?                ;; if true, the turtle is infectious
    remaining-immunity   ;; how many weeks of immunity the turtle has left
    sick-time            ;; how long, in days, the turtle has been infectious
    movement-turtles     ;; movement of each turtle
    sick-symptoms?       ;; if true, the turtle is infectouss and knows it
    days_sick
  age ]                  ;; how many weeks old the turtle is

globals
  [ %infected            ;; what % of the population is infectious
    %immune              ;; what % of the population is immune
    lifespan             ;; the lifespan of a turtle
    chance-reproduce     ;; the probability of a turtle generating an offspring each tick
    chance-recover       ;; the probability of recovery at each tick
;    carrying-capacity    ;; the number of turtles that can be in the world at one time
    immunity-duration    ;; how many weeks immunity lasts
;    sick-not-know-min    ;; how many days a person could be sick without notice
 ;   sick-not-know-max
number-people
    number-dead ]        ;; how many turtles die

;; The setup is divided into four procedures

to setup
  clear-all
  setup-constants
  setup-turtles
  update-global-variables
  update-display
  reset-ticks
end 

;; We create a variable number of turtles of which 1 are infectious,
;; and distribute them randomly

to setup-turtles
  create-turtles number-people
    [ setxy random-xcor random-ycor
      set age random lifespan
      set sick-time 0
      set remaining-immunity 0
      set size .7 ;; easier to see
      get-healthy ]
  ask n-of 1 turtles
    [ get-sick ]
end 

to get-sick ;; turtle procedure
  set sick? true
  set remaining-immunity 0
end 

to get-healthy ;; turtle procedure
  set sick? false
  set sick-symptoms? sick?
  set remaining-immunity 0
  set sick-time 0
end 

to become-immune ;; turtle procedure
  set sick? false
  set sick-symptoms? false
  set sick-time 0
  set remaining-immunity immunity-duration
  ask my-links [ die ] ;; remove link to turtle who infected us, if there was one
end 

;; This sets up basic constants of the model.

to setup-constants
  set lifespan 80 * 52 * 7     ;; 80 times 52 weeks times 7 days = 50 years = 2600 weeks old = 18200 days
;  set carrying-capacity 1000
  set chance-reproduce 0.34 ;; birth rate per 1000 people per week
  ifelse inmune [set immunity-duration 10000] [set immunity-duration 4 * 7] ;; 4 weeks for immunity duration
  if Weather = "Hot-Humid" [set infectiousness  .9 * infectiousness]
  if Weather = "Hot-Dry" [set infectiousness  .95 * infectiousness]
  if Weather = "Cold-Dry" [set infectiousness  .97 * infectiousness]
  if Weather = "Cold-Humid" [set infectiousness infectiousness]
  set number-people carrying-capacity
;  set sick-not-know-min  4
;  set sick-not-know-max 14
end 

to go
  visitor-infected

  ask turtles [
    get-older
    ifelse (age > 60 * 52 * 7) [set movement-turtles (movement * alpha)] [set movement-turtles movement]
    quarantine
    days-sick
    move
    if sick? [ recover-or-die ]
    ifelse sick? [ infect ] [ reproduce ]
  ]
  update-global-variables
  update-display
  tick
  if ticks = time-stop [stop]
end 

to days-sick
  ifelse sick? [set days_sick days_sick + 1] [set days_sick 0]
  if ( days_sick > ( sick-not-know-min + 1 + random sick-not-know-max ) ) [set sick-symptoms? true ]
end 

to update-global-variables
  if count turtles > 0
    [ set %infected (count turtles with [ sick? ] / count turtles) * 100
      set %immune (count turtles with [ immune? ] / count turtles) * 100 ]
end 

to update-display
  ask turtles
    [ if shape != turtle-shape [ set shape turtle-shape ]
      set label ifelse-value show-age? [ floor (age / 364) ] [ "" ]
      set color ifelse-value sick? [ red ] [ ifelse-value immune? [ grey ] [ green ] ]
      if age < 10 * 52 * 7 [set color blue]
      if age > 60 * 52 * 7 [set color yellow]
    ]
  stop-inspecting-dead-agents
  if watch-a-person? and subject = nobody
    [ watch one-of turtles with [ not hidden? ]
      clear-drawing
      ask subject [ pen-down ]
      inspect subject ]
  if not watch-a-person? and subject != nobody
    [ stop-inspecting subject
      ask subject
        [ pen-up
          ask my-links [ die ] ]
      clear-drawing
      reset-perspective ]
  ask patches [
  if Weather = "Hot-Humid" [set pcolor 68]
  if Weather = "Hot-Dry" [set pcolor 48]
  if Weather = "Cold-Dry" [set pcolor 38]
  if Weather = "Cold-Humid" [set pcolor 108]
  ]
end 

;;Turtle counting variables are advanced.

to get-older ;; turtle procedure
  ;; Turtles die of old age once their age exceeds the
  ;; lifespan (set at 80 years in this model).
  set age age + 1
  if age > lifespan [ die ]
  if age > 60 * 52 * 7 [ set chance-recover .95]
  if age < 60 * 52 * 7 [ set chance-recover .98]
  if immune? [ set remaining-immunity remaining-immunity - 1 ]
  if sick? [ set sick-time sick-time + 1 ]
end 

;; Turtles move about at random.

to move ;; turtle procedure
  rt random 100
  lt random 100
  move-infected
  fd movement-turtles    ; check if agents can be steady when they know that they're infected (1 period after)
end 

;; If a turtle is sick, it infects other turtles on the same patch.
;; Immune turtles don't get sick.

to infect ;; turtle procedure
  ask other turtles-here with [ not sick? and not immune? ]
    [ if random-float 1000 < infectiousness
      [ get-sick
        if self = subject             ;; if its the watched turtle getting sick
          [ create-link-with myself   ;; create a link with the one that infected it
            [ set color red
              set thickness .3 ] ] ] ]
end 

;; Once the turtle has been sick long enough, it
;; either recovers (and becomes immune) or it dies.

to recover-or-die ;; turtle procedure
  if age > 60 * 52 * 7 [ set chance-recover .90]
  if age < 60 * 52 * 7 [ set chance-recover .97]
  if sick-time > duration                        ;; If the turtle has survived past the virus' duration, then
    [ ifelse random-float 1 < chance-recover   ;; either recover or die
      [ become-immune ]
      [ set number-dead number-dead + 1
        die ]]
end 

;; If there are less turtles than the carrying-capacity
;; then turtles can reproduce.

to reproduce
  if count turtles < carrying-capacity and random-float 1 < chance-reproduce
    [ hatch 1
      [ set age 1
        lt 45 fd 1
        pen-up ;; in case we're hatched from the watched turtle
        get-healthy ] ]
end 

to-report immune?
  report remaining-immunity > 0
end 

to startup
  setup-constants ;; so that carrying-capacity can be used as upper bound of number-people slider
end 

to move-infected
   ifelse sick-symptoms? [set movement-turtles movement-turtles / 2] [set movement-turtles movement-turtles]
end 

to visitor-infected
if (random-float 1 < prob_infected) [crt 1
    [setxy random-xcor random-ycor
      set age random lifespan
      set sick-symptoms? false
      set sick-time 0
      set remaining-immunity 0
      set size .7 ;; easier to see
      get-sick]]
  if ( count turtles > number-people ) [ ask one-of turtles [die]]
end 

to quarantine
  if ( count turtles with [ sick-symptoms? ] > threshold-quarantine )
  [set movement-turtles movement / 10]
end 


; Copyright 1998 Uri Wilensky.
; See Info tab for full copyright and license.

There are 10 versions of this model.

Uploaded by When Description Download
Emiliano Alvarez 5 months ago some fixes - people with and without symptoms Download this version
Emiliano Alvarez 5 months ago bug fixes Download this version
Emiliano Alvarez 5 months ago bug fixes Download this version
Emiliano Alvarez 6 months ago plots corrected Download this version
Emiliano Alvarez 6 months ago bug fixes. quarantine rules and delays between infection and synthoms Download this version
Emiliano Alvarez 6 months ago fixes on elders' speed Download this version
Emiliano Alvarez 6 months ago Some fixes. Show mean movement. Prob of visitors (tourist) infected Download this version
Emiliano Alvarez 6 months ago switch to full-immunity. Alpha to regulate elders' movement Download this version
Emiliano Alvarez 6 months ago with changes in movement rules Download this version
Emiliano Alvarez 6 months ago changing carrying capacity, time, movement rules Download this version

Attached files

File Type Description Last updated
COVID_19 spread with movement rules.png preview preview 6 months ago, by Emiliano Alvarez Download

Parent: COVID_19 Spread

This model does not have any descendants.

Graph of models related to 'COVID_19 spread with movement rules'