ABM Lassa Virus Transmission
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; ABM - LASSA FEVER TRANSMISSION ; STUDENT NAME: VICTOR ODOH ; ID: C2397722 ; SCEDT, TEESSIDE UNIVERSITY ; Year: 2022 ; Two agentsets are involved in this Model (Humans and rats) ; Hence defining two breeds as follows breed [humans human] breed [rats rat] ; COLOUR CODES: ; Red rat (red - 2) - Multimammate Rat (All Assumed to be infectious) ; White Human - Healthy, not infected/infectious ; Yellow Human - Infected but not infectious (within virus incubation period) ; Orange Human (orange + 2) - Infectious with Mild Symptoms ; Red Human - Infectious with Severe Symptoms ; Cyan Human - Recovered, immune but still Infectious ; Lime Human (lime + 1) - Fully recovered and immune ; Gray Human - Dead ; Declaring humans owned variables humans-own [ hours ; each tick represents an hour human_speed ; to control human speed ] ; Declaring all global variables used... ; (excluding the sliders which do not need to be declared here) globals [ control_speed ; to regulate speed of model infected_not_infectious ; current count of infected humans within virus incubation period initial_mild_cases initial_severe_cases mild_cases_count ; current count of all mild cases severe_cases_count ; current count of all severe cases severe_cases ; counting variable for infected humans with severe symptoms mild_cases ; counting variable for infected humans with mild symptoms or asymptomatic total_mild_cases ; includes intial mild cases total_severe_cases ; includes initial severe cases fatalities ; counting variable for human deaths total_fatalities ; count of all deaths ever recorded immune_infectious ; current count of recovered and immune humans that are still carriers immune_not_infectious ; current count of immune humans who are no longer carriers %Mild_Cases %infected %uninfected %immune average_%CFR ; average case fatality rate in percentage immune_or_severe_%infectiousness ; virus spread chance of immune/recovered carriers ; or humans with severe symptoms assuming that they are hospitalized/isolated and pose little ; risk of infecting others current_cases ; number of cases at the curent time total_cases ; Count of all cases ever recorded : addition of counting variables (mild_cases + severe_cases) total_immune ; includes both immune carriers and immune with no virus total_infected ; all carrier humans total_infectious ; all carrier humans excluding infected_not_infectious ] ; Defining the "setup" command procedure: ; Assigning initial values to setup clear-all reset-ticks set %Mild_Cases (100 - %Severe_Cases) set initial_mild_cases (Initial_Number_Of_Cases * %Mild_Cases) / 100 set initial_severe_cases (Initial_Number_Of_Cases * %Severe_Cases) / 100 set immune_or_severe_%infectiousness %Infectiousness_Human_to_Human * (1 - Human_Behaviour_Factor) ; Declaring basic constant of the model set control_speed 1 ; creating the rat agents with their properties ; Distributing them randomly across the patches/world create-rats Multimammate_Rat_Population [ setxy random-xcor random-ycor set shape "mouse side" set color red - 2 set size 0.8 ] ; creating the human agents with initially infected humans ; Distributing them randomly across the patches/world create-humans Human_Population [ setxy random-xcor random-ycor set shape "person" set color white set size 1 set human_speed control_speed ] ; color coding to identify initial mild/severe cases ask n-of initial_mild_cases Humans [set color orange + 2] ask n-of initial_severe_cases Humans [ set color red ] end ; end of setup command procedure ; Defining the "go" command procedure: to go ; asking rats to move randomly across the world ask rats [ fd control_speed * -1 * ((1 / Human_Behaviour_Factor) * 0.01) rt random 100 lt random 100 ] ; asking humans to move randomly across the world ask humans [ fd human_speed * ((1 / Human_Behaviour_Factor) * 0.01) rt random 45 lt random 45 set hours hours + 1 ; advancing hours counting variables ] ; asking humans that are infectious and applying human to human infection probability.. ; ..to a nearby uninfected human, for possible infection ; color coding to identify each case ask humans [ ifelse (color = orange + 2) [ ask other humans-here [ if random 100 < %Infectiousness_Human_to_Human [ if color = white [ set color yellow set infected_not_infectious infected_not_infectious + 1 set hours 0 ] ] ] ] ; asking rats and applying rat to human infection probability ; to nearby uninfected human in contact, for possible infection [ ask rats [ ask other humans-here [ if random-float 100 < %Infectiousness_rat_to_Human [ if color = white [ set color yellow set hours 0 ] ] ] ] ] ; If hospitalized or immune carrier, applying infection probability for possible infection... ; ... of other uninfected humans nearby if (color = cyan) or (color = red) [ ask other humans-here [ if random-float 100 < immune_or_severe_%infectiousness [ if (color = white) [ set color yellow set hours 0 ] ] ] ] ; converting incubation period in days to hours ; what should happen if infection has exceded incubation period? ; applying %Severe_Cases probabilty to determine if an infected human... ; ... falls under the mild or severe case if (color = yellow) and (hours > (incubation_Period * 24)) [ ifelse random-float 100 < %Severe_Cases [ set color red set severe_cases severe_cases + 1 ; advancing severe_cases counting variable set hours 0 set human_speed 0 ; if severe, assumes human is hospitalized and stops moving ] [ set color orange + 2 set mild_cases mild_cases + 1 ; advancing mild_cases counting variable set hours 0 set human_speed 0.5 ; value assigned to variable to make speed a bit slower than that of other agents ] ] ; converting "days before recovery or death" in days to hours ; what should happen if infection has lingered for this period? ; applying case fatality probabilty of both type of cases to determine... ; ... if an infected human dies or survives ; "orange + 2" for mild case, red for severe case if (color = orange + 2) and (hours = (Sick_Days * 24)) [ ifelse random-float 100 < CFR_Mild_Case [ set color gray set fatalities fatalities + 1 ; advancing fatalities counting variable set hours 0 set human_speed 0 ; if dead, human stops moving ] [ set color cyan ; if they survived, they become immune but still carriers (cyan from color coding) set hours 0 set human_speed 0.5 ] ] if (color = red) and (hours = (Sick_Days * 24)) [ ifelse random-float 100 < CFR_Severe_Case [ set color gray set fatalities fatalities + 1 set hours 0 set human_speed 0 ] [ set color cyan set hours 0 set human_speed control_speed ] ] ; what should happen if immune carriers have exceeded the Infectious days after recovery? ; mark them as immune and no longer infectious (Lime) if (color = cyan) and (hours = (Infectious_Days_After_Recovery * 24)) [ set color lime + 1 ; lime human is immune and no longer infectious set hours 0 set human_speed control_speed ] ] ; Updating global variables for plotting purposes and for output display on monitor set infected_not_infectious count humans with [color = yellow] set mild_cases_count count humans with [color = orange + 2] set severe_cases_count count humans with [color = red] set immune_infectious count humans with [color = cyan] set immune_not_infectious count humans with [color = lime + 1] set total_immune (immune_infectious + immune_not_infectious) set current_cases (mild_cases_count + severe_cases_count) set total_mild_cases (mild_cases + initial_mild_cases) set total_severe_cases (severe_cases + initial_severe_cases) set total_cases (total_mild_cases + total_severe_cases) set total_infectious (current_cases + immune_infectious) set total_infected (infected_not_infectious + total_infectious + total_fatalities) set total_fatalities count humans with [color = gray] set average_%CFR (fatalities / total_cases) * 100 set %infected (total_infected / Human_Population) * 100 set %uninfected ((count humans with [color = white]) / Human_Population) * 100 set %immune (total_immune / Human_Population) * 100 if infected_not_infectious + current_cases + count humans with [color = white] = 0 [stop] ; condition (if true) to halt simulation tick ; advancing the tick counter by 1 end
There is only one version of this model, created almost 2 years ago by Victor Odoh.
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File | Type | Description | Last updated | |
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ABM Lassa Virus Transmission.png | preview | Preview for 'ABM Lassa Virus Transmission' | almost 2 years ago, by Victor Odoh | Download |
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