COVID-19 in the University
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globals [peopleShapes averageNumberLinksActual averagePContact averagePMask infectionRate networkSpaceColor roomColor ] breed [people person] people-own [infected infectedTime immune recoveredTime pContactPerLink pMask pCheck lastInfectionRate schedule testDate quarantined?] patches-own [load spaceID airTurnover physical? masked?] to setup clear-all reset-ticks set peopleShapes ["person business" "person doctor" "person farmer" "person graduate" "person lumberjack" "person police" "person service" "person soldier" "person student"] set networkSpaceColor 3 set roomColor 93 set classCap 10 ;;initialize patches ask patches [set load 0 set spaceID "N/A" set airTurnover 0 set physical? false] ;; set up the space ask patches with [pxcor < 0] [set spaceID "network" set pcolor networkSpaceColor] make-room 2 2 15 15 fracAirTurnover false "dining hall" make-room 18 2 5 10 fracAirTurnover true "class 1" make-room 24 2 5 10 fracAirTurnover true "class 2" make-room 18 20 5 10 fracAirTurnover true "class 3" make-room 24 20 5 10 fracAirTurnover true "class 4" make-room 2 20 5 10 fracAirTurnover true "class 5" make-room 8 20 5 10 fracAirTurnover true "class 6" ;;make default schedule (currently in 12 parts - 2h) let defaultSchedule (list "network" "network" "network" "network" "network" "network" "network" "network" "network" "network" "network" "network") create-people numberPeople [ go-to-space "network" set color green set infected false set immune false set quarantined? false set testDate 0 set pContactPerLink max list 0 random-normal pContactPerLinkPerDay_Mean pContactPerLink_SD set pCheck max list 0 random-normal pCheck_mean pCheck_SD set lastInfectionRate 0 set pMask max list 0 random-normal pMask_Initial_Mean pMask_Initial_SD set schedule defaultSchedule ;;add mealtime to schedule if groupLunch? [ let lunchDraw random-float 1 if-else lunchDraw < 0.3 [set schedule replace-item 5 schedule "dining hall"] [ if-else lunchDraw < 0.6 [set schedule replace-item 6 schedule "dining hall"] [ set schedule replace-item 7 schedule "dining hall"] ] ] ;;assign a shape randomly set shape one-of peopleShapes ] ;;make schedules ask n-of classCap people with [item 4 schedule = "network"] [set schedule replace-item 4 schedule "class 1"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 5 schedule "class 1"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 6 schedule "class 1"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 7 schedule "class 1"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 8 schedule "class 1"] ask n-of classCap people with [item 9 schedule = "network"] [set schedule replace-item 9 schedule "class 1"] ask n-of classCap people with [item 10 schedule = "network"] [set schedule replace-item 10 schedule "class 1"] ask n-of classCap people with [item 4 schedule = "network"] [set schedule replace-item 4 schedule "class 2"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 5 schedule "class 2"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 6 schedule "class 2"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 7 schedule "class 2"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 8 schedule "class 2"] ask n-of classCap people with [item 9 schedule = "network"] [set schedule replace-item 9 schedule "class 2"] ask n-of classCap people with [item 10 schedule = "network"] [set schedule replace-item 10 schedule "class 2"] ask n-of classCap people with [item 4 schedule = "network"] [set schedule replace-item 4 schedule "class 3"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 5 schedule "class 3"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 6 schedule "class 3"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 7 schedule "class 3"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 8 schedule "class 3"] ask n-of classCap people with [item 9 schedule = "network"] [set schedule replace-item 9 schedule "class 3"] ask n-of classCap people with [item 10 schedule = "network"] [set schedule replace-item 10 schedule "class 3"] ask n-of classCap people with [item 4 schedule = "network"] [set schedule replace-item 4 schedule "class 4"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 5 schedule "class 4"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 6 schedule "class 4"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 7 schedule "class 4"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 8 schedule "class 4"] ask n-of classCap people with [item 9 schedule = "network"] [set schedule replace-item 9 schedule "class 4"] ask n-of classCap people with [item 10 schedule = "network"] [set schedule replace-item 10 schedule "class 4"] ask n-of classCap people with [item 4 schedule = "network"] [set schedule replace-item 4 schedule "class 5"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 5 schedule "class 5"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 6 schedule "class 5"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 7 schedule "class 5"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 8 schedule "class 5"] ask n-of classCap people with [item 9 schedule = "network"] [set schedule replace-item 9 schedule "class 5"] ask n-of classCap people with [item 10 schedule = "network"] [set schedule replace-item 10 schedule "class 5"] ask n-of classCap people with [item 4 schedule = "network"] [set schedule replace-item 4 schedule "class 6"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 5 schedule "class 6"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 6 schedule "class 6"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 7 schedule "class 6"] ask n-of classCap people with [item 8 schedule = "network"] [set schedule replace-item 8 schedule "class 6"] ask n-of classCap people with [item 9 schedule = "network"] [set schedule replace-item 9 schedule "class 6"] ask n-of classCap people with [item 10 schedule = "network"] [set schedule replace-item 10 schedule "class 6"] ;;inital infections ask n-of initialInfections people [ set infected true set infectedTime ticks ] ;;create social network links let numLinks averageLinksPerAgent * numberPeople / 2 while [numLinks > 0] [ ask one-of people [create-link-with one-of other people] set numLinks numLinks - 1 ] ;; update global variables update-globals end to go ask links [ if (any? both-ends with [infected = true]) and (count both-ends with [quarantined? = false] = 2) and (count both-ends with [physical? = false] = 2) [ let currentPContact [pContactPerLink] of one-of both-ends * (timeStep / 24) ;; let currentPMasks [pMask] of both-ends let currentPInfection pInfectionPerContact if random-float 1 < item 0 currentPMasks [set currentPInfection currentPInfection / riskReductionFactor_mask ] if random-float 1 < item 1 currentPMasks [set currentPInfection currentPInfection / riskReductionFactor_mask ] if random-float 1 < currentPInfection * currentPContact [ ask both-ends [ if not immune and not infected [set infected true set infectedTime ticks] ] ] ] ] let numContacts numberRandomContactsPerStep while [numContacts > 0] [ let currentPair n-of 2 people if any? currentPair with [infected = true] and (count currentPair with [quarantined? = false] = 2) and (count currentPair with [physical? = false] = 2) [ let currentPMasks [pMask] of currentPair let currentPInfection pInfectionPerContact if random-float 1 < item 0 currentPMasks [set currentPInfection currentPInfection / riskReductionFactor_mask ] if random-float 1 < item 1 currentPMasks [set currentPInfection currentPInfection / riskReductionFactor_mask ] if random-float 1 < currentPInfection [ ask currentPair [ if not immune and not infected [set infected true set infectedTime ticks] ] ] ] set numContacts numContacts - 1 ] ask people [ ;; move people if they are in the wrong place for this time let localTime ticks mod (24 / timeStep) set localTime floor localTime / (24 / timeStep / length schedule) if quarantined? = false and [spaceID] of patch-here != item localTime schedule [ go-to-space item localTime schedule ] if [physical?] of patch-here = true [ ;;let people move let currentRoom [spaceID] of patch-here if random-float 1 < probTurn [facexy [pxcor] of one-of patches with [spaceID = currentRoom] [pxcor] of one-of patches with [spaceID = currentRoom]] forward speed ;;drop viral load if infected] let factor 1 if infected [ ask patch-here [ if masked? = true [set factor factor / riskReductionFactor_mask] set load load + viralLoad / factor]] ;;test if newly infected if (not immune and not infected and random-float 1 < pInfectionPerLoad / factor * load ) [ set infected true set infectedTime ticks ] ] ;;test if died if (infected and random-float 1 < caseMortalityRate / (recoveryTimeFromInfection_Days * (24 / timeStep)) ) [ let currentAgentSet self let currentDegrees degreesConsidered let currentBump pMaskBump_die while [currentDegrees > 0] [ ask currentAgentSet [ ask out-link-neighbors [set pMask pMask + currentBump] ] set currentBump currentBump * (1 - pMaskBumpDecay_degree) set currentAgentSet out-link-neighbors set currentDegrees currentDegrees - 1 ] die ] ;;check if recovered if (infected and ticks - infectedTime > recoveryTimeFromInfection_Days * (24 / timeStep) ) [ set infected false set immune true set recoveredTime ticks ] ;; test if immunity lost if (immune and ticks - recoveredTime > immunityTime_Days * (24 / timeStep) ) [ set immune false ] ;;update agent color based on infection if infected [set color red] if not infected [set color green] if immune [set color blue] ;;update other visualization parameters if seeNetwork? = true [ ask links [set hidden? false]] if seeNetwork? = false [ ask links [set hidden? true]] ;;update individual parameters set pMask pMask * (1 - pMask_decay) if random-float 1 < pCheck [ if infectionRate > lastInfectionRate [ set pMask pMask + pMaskBump_rise ] set lastInfectionRate infectionRate ] ] ;;run testing program once per day if ticks mod (24 / timeStep) = 0 [ ask up-to-n-of testingCapacityPerDay people with [testDate < ticks] [ ifelse infected = true [set quarantined? true go-to-space "network" ] [set quarantined? false] set testDate ticks + testingFrequency * (24 / timeStep) ] ] ;;update physical spaces ;;update patch color based on load ;;diffuse load diffuseShare ask patches with [physical? = false] [set load 0] ask patches with [physical? = true] [ ;;set load load * (1 - 1 / virusLifetime) update-virus-in-space if-else seeCovid? [ set pcolor scale-color yellow load 0 viralLoad ] [ set pcolor black ] ] ;; update global variables update-globals tick end to update-globals set averageNumberLinksActual count links / count people set averagePContact sum [pContactPerLink] of people / count people set averagePMask sum [pMask] of people / count people set infectionRate count people with [infected = true] / count people end to make-room [x y h w a m id] ask patches with [pxcor >= x and pxcor < x + h and pycor >= y and pycor < y + w] [ set spaceID id set airTurnover a set physical? true set masked? m ] draw-box x y h w end to draw-box [x y h w] ask patches with [pxcor = x and pycor >= y and pycor < y + w] [ sprout 1 [set shape "line" set color white set heading 0 set xcor xcor - 0.5 stamp die] ] ask patches with [pxcor = x + h - 1 and pycor >= y and pycor < y + w] [ sprout 1 [set shape "line" set color white set heading 0 set xcor xcor + 0.5 stamp die] ] ask patches with [pycor = y and pxcor >= x and pxcor < x + h] [ sprout 1 [set shape "line" set color white set heading 90 set ycor ycor - 0.5 stamp die] ] ask patches with [pycor = y + w - 1 and pxcor >= x and pxcor < x + h] [ sprout 1 [set shape "line" set color white set heading 90 set ycor ycor + 0.5 stamp die] ] end to go-to-space [id] let newPatch one-of patches with [spaceID = id] setxy [pxcor] of newPatch + (random 1 - 0.25) [pycor] of newPatch + (random 1 - 0.25) end to update-virus-in-space ;;let virus diffuse let roomNeighbors neighbors with [spaceID = [spaceID] of self] let loadOut load * diffuseShare ask roomNeighbors [set load load + loadOut / count roomNeighbors] set load max (list 0 (load - loadOut)) ;;let virus decay set load load * (1 - 1 / virusLifetime) ;;let air flow (flow is always from lower x to higher x, by default let movedLoad load * airTurnover set load load - movedLoad ask patch-at 1 0 [set load load + movedLoad] end
There is only one version of this model, created almost 3 years ago by Andrew Bell.
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COVID-19 in the University.png | preview | Preview for 'COVID-19 in the University' | almost 3 years ago, by Andrew Bell | Download |
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