# Covid-19 and Health System Capacity

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globals [ interaction-zone ;; The patches representing the area of social interactions in the world quarantine ;; The patches representing the humans are in quarantine hospital ;; The patches representing the hospital with severe cases of the disease upper-border ;; The borders of interaction-zone lower-border crowded-patch ;; The patch where the "CROWDED" label appears patients ;; Infected people being trated in the hospital count-infected ;; Cumulative number of infected people count-symptomatic ;; Cumulative number of infected and symptomatic people r0 ;; The number of secondary infections that arise due to a single infective introduced in a wholly susceptible population s0 ;; Initial population of susceptible people hospital-patch ;; The patch where the "HOSPITAL" label appears quarantine-patch ;; The patch where the "QUARANTINE" label appears ] breed [humans human] humans-own [susceptible? ;; If true, the human is susceptible. exposed? ;; If true, the human is infected but in latent period infected? ;; If true, the human is infected and infectious immune? ;; If true, the human is immune symptomatic? ;; If true, the infected human is symptomatic hospitalized? ;; If true, the infected and symptomatic human will be hospitalized protect? ;; If true, the human is protecting himself from infection need-hospital? ;; If true, an infected and symptomatic human will need a hospital isolated? ;; If true, an infected human will be isolated in quarantine risk-population? ;; The proportion of the population at risk of severe disease (i.e. old people, pre-existing chronic disease) latent-period ;; The latent period of the virus viremic-time ;; The time in days that individuals will be infectious and can transmit the virus to others ] ;;;;; ;;; SETUP PROCEDURES ;;;;; to setup clear-all setup-globals setup-host reset-ticks end to setup-globals ;; creating interaction-zone patches set interaction-zone patches with [(pxcor >= min-pxcor and pycor < int (max-pycor - (max-pycor / 2)) and pycor > min-pycor)] ask interaction-zone [ set pcolor gray ] ;; creating quarantine patches set quarantine patches with [(pxcor > (0.5 * min-pxcor) and pycor > int (max-pycor - (max-pycor / 2)) )] ask quarantine [set pcolor green ] ;; creating hospital patches set hospital patches with [(pxcor >= min-pxcor and pxcor <= (0.5 * min-pxcor) and pycor > int (max-pycor - (max-pycor / 2)))] ask hospital [set pcolor pink ] ;; creating border patches set upper-border patches with [(pycor = int (max-pycor - (max-pycor / 2)))] ask upper-border [ set pcolor gray ] set lower-border patches with [(pycor = min-pycor)] ask lower-border [ set pcolor gray ] ;; selecting patches where labels will appear ask patch (0.7 * min-pxcor) ( 0.8 * max-pycor) [ set crowded-patch self set plabel-color black] ask patch (0.7 * min-pxcor) ( 0.95 * max-pycor) [ set hospital-patch self set plabel "HOSPITAL" set plabel-color black] ask patch (0.3 * max-pxcor) ( 0.95 * max-pycor) [ set quarantine-patch self set plabel "QUARANTINE" set plabel-color black] end to setup-host ;; creating people and moving them to interaction-zone patches create-humans initial-people [ask humans [move-to one-of interaction-zone] set shape "person" set size 0.5 set infected? false set immune? false set susceptible? true set exposed? false set risk-population? false set symptomatic? false set hospitalized? false set protect? false set need-hospital? false set isolated? false ] ;; selecting initial number of infected people ask n-of initial-infected humans [ set susceptible? false set infected? true] ;; selecting people who will be less exposed to infection due to individual protection measures ask n-of (initial-people * proportion-of-population) humans [set protect? true] ;; selecting people who will belong to the risk group ask n-of (initial-people * risk-group) humans [set risk-population? true] ask humans [assign-color] end to assign-color ;; The colors for represent the virus circulation and individual status if susceptible? [ set color white ] if exposed? [ set color yellow ] if infected? [ set color red ] if immune? [ set color blue ] end ;;;;; ;;; GO PROCEDURES ;;;;; to go ask crowded-patch [ set plabel "" ] move-humans if all? humans [ not exposed? and not infected? ] [stop] ;; stopping the simulation ask humans with [exposed?] [become-viremic] ask humans with [infected?] [infect-others symptom] ask humans with [symptomatic?] [recovery-or-die] ask humans [if hospitalized? and immune? [move-to one-of interaction-zone]] ;; people who recovered at the hospital go back to interaction-zone ask humans with [symptomatic?] [check-for-hospital go-to-hospital] set patients count turtles-on hospital if patients > hospital-capacity [ask crowded-patch [ set plabel "CROWDED" ]] ;; If the hospital have more patients than it can handle, the label "CROWDED" will appear ;;Infected people who are detected will be quarantined (but only after the start of control measures). if isolate-infected? [ask humans with [infected? and not hospitalized?] [if ticks >= days-to-start-control-measures [ if random 100 < infected-detection [ move-to one-of quarantine set isolated? true]]]] ask humans-on quarantine [if immune? [move-to one-of interaction-zone set isolated? false]] ;; people who recovered in the quarantine go back to interaction-zone calculate-r0 tick end ;; People move around the world randomly, but they don't move around in the quarantine and in the hospital patches. to move-humans ask humans-on interaction-zone [rt random-float 360.0 forward random-float 1 assign-color] ask humans-on upper-border [ move-to patch-at-heading-and-distance 180 1 assign-color] ask humans-on lower-border [ move-to patch-at-heading-and-distance 180 -1 assign-color] ask humans-on hospital[ assign-color ] ask humans-on quarantine [ assign-color] end ;; Infected people can infect susceptible ones to infect-others ;; selecting a susceptible target in neighbor patches let target-h (humans-on neighbors) let hosth one-of (target-h with [susceptible?]) ;; The chance of a susceptible person becoming infected will depend on the transmission rate and whether or not he is protecting himself from the transmission. if hosth != nobody [ ifelse not protect? [ if random-float 1 < transmission-rate [ ask hosth [ set susceptible? false set exposed? true set count-infected count-infected + 1 ] ] ] [ if ticks < days-to-start-control-measures [ if random-float 1 < transmission-rate [ ask hosth [ set susceptible? false set exposed? true set count-infected count-infected + 1 ] ] ] if ticks >= days-to-start-control-measures [ if random-float 1 < (transmission-rate * (1 - protection-level)) [ ask hosth [ set susceptible? false set exposed? true set count-infected count-infected + 1 ] ] ] ] ] end ;; A human who has been infected with the virus will become infectious after the latency period to become-viremic set latent-period latent-period + 1 if latent-period > random-poisson 3 [ ;; An average latency period of 3 days was considered here set infected? true set exposed? false ] end ;; A given proportion of infected people will become symptomatic to symptom set viremic-time viremic-time + 1 ;;It was considered that the first symptoms may appear in 2 days after the virus latency period, which means an incubation period of 5 days on average. if viremic-time = 2 [ if random 100 < symptomatic-proportion [ set symptomatic? true set count-symptomatic count-symptomatic + 1 ]] ;; asymptomatic people become immune after recovery time if viremic-time = recovery-time and not symptomatic? [ set infected? false set immune? true ] end ;; Check if infected-symptomatic people need a hospital to check-for-hospital ifelse risk-population? [ if random 100 < 20 [ ;; For the people of the risk group, a 20% chance of needing a hospital was considered set need-hospital? true]] [if random 100 < 5 [ ;; For people who are not of risk group, a 5% chance of needing a hospital was considered set need-hospital? true ]] end ;; If the Hospital is not crowded, go to it. to go-to-hospital set patients count turtles-on hospital if need-hospital? [ if patients < hospital-capacity + 1 [ move-to one-of hospital set hospitalized? true]] end ;; After a few days, infected symptomatic people may recover from illness or die ;; This will depend on the severity of the case (need-hospital?), whether or not the person is hospitalized, and whether or not he belongs to the risk group. to recovery-or-die if need-hospital? [ ifelse not hospitalized? [ if viremic-time >= random-poisson recovery-time * 1.5 ;; severe cases will take 50% more time to recover [ if risk-population? [ ifelse random 100 < random-poisson 20 [ ;;people in the risk group who need a hospital and are not hospitalized have an average 20% chance of surviving set infected? false set symptomatic? false set immune? true set need-hospital? false] [ die ]] if not risk-population? [ ifelse random 100 < random-poisson 60 ;;people who are not in the risk group who need a hospital and are not hospitalized have an average 60% chance of surviving [ set infected? false set symptomatic? false set immune? true set need-hospital? false] [ die ]]]] [if viremic-time >= random-poisson recovery-time * 1.5 [ if risk-population? [ ifelse random 100 < (100 - random-poisson 7) ;; people who are the risk group and who are hospitalized have an average 93% chance of surviving [ set infected? false set symptomatic? false set immune? true set need-hospital? false] [ die ]] if not risk-population? [ ifelse random 100 < (100 - random-poisson 1) ;; people who are not in the risk group and who are hospitalized have an average 99% chance of surviving [ set infected? false set symptomatic? false set immune? true set need-hospital? false] [ die ]]]]] if not need-hospital? ;; Infected-symptomatic people who do not need a hospital will always recover from infection [ if viremic-time >= random-poisson recovery-time [ set infected? false set symptomatic? false set immune? true ]] end ;; This R0 is a numerical estimate of the basic reproduction number, as proposed by Uri Wilensky. ;; For more information on how this R0 equation was obtained, see the models 'epiDEM basic' and 'epiDEM travel and control'. to calculate-r0 set s0 initial-people - initial-infected if ((initial-people - count turtles with [ susceptible? ]) != 0 and (count turtles with [ susceptible? ] != 0)) ;; Prevent from dividing by 0 [ set r0 (ln (s0 / count turtles with [ susceptible? ]) / (initial-people - count turtles with [ susceptible? ])) set r0 r0 * s0 ] end

There is only one version of this model, created 2 months ago by Antônio Ralph Medeiros de Sousa.

## Attached files

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Covid-19 and Health System Capacity.png | preview | Preview for 'Covid-19 and Health System Capacity' | 2 months ago, by Antônio Ralph Medeiros de Sousa | Download |

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