CystiAgent_Public
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;;;;;;CystiAgent Model;;;;;;; ;;;;PRIMING;;;; extensions [gis] globals [ ;;; PARAMETER VARIABLES;;; ;;Village characteristics;; prop-pig-owners ;P0.1: Proportion of households that raise pigs prop-corrals ;P0.2: Proportion of pig-owning households with corrals (or tie-up areas) prop-latrines ;P0.3: Proportion of households with a latrine or bathroom humans-per-household ;P0.4: POISSON mean for number of humans per household pigs-per-household ;P0.5: EXPONENTIAL mean for number of pigs per household baseline-tn-prev ;P0.6: Baseline prevalence of taeniasis baseline-light-infection ;P0.7: Baseline prevalence of light cyst infection baseline-heavy-infection ;P0.8: Baseline prevalence of heavy cyst infection ;;Pig slaughter age;; slaughter-age-mean ;P1.1: Log-mean of pig age at slaughter (in months) slaughter-age-sd ;P1.1: Log-SD of pig age at slaughter (in months) ;;Human travel;; traveler-prop ;P2.1: Proportion of households with a frequent traveler travel-freq ;P2.2: Frequency of trips among traveler households (departure for a trip every X weeks) travel-duration ;P2.3: Mean (ENTER DISTRIBUTION) duration of trips travel-incidence ;P2.4: Incidence of tapeworm infection for traveling humans (to other endemic areas) ;;Tapeworm lifespan;; tn-incubation ;P3.2: Tapeworm incubation time (weeks) tn-lifespan-mean ;P3.1: Tapeworm infection duration (mean) tn-lifespan-sd ;P3.1: Tapeworm infection duration (sd) ;;Environmental contamination;; latrine-use ;P4.1: Proportion of households with a latrine for which the latrine is in GOOD condition and ALWAYS used cont-radius-mean ;P4.2: Log-mean of the radius of contamination around tapeworm carrier house cont-radius-sd ;P4.2: Log-SD of the radius of contamination around tapeworm carrier house ;;Environmental egg decay;; decay-mean ;P5.1: Environmental egg decay rate parameter (probably of decay per week) ;;Pig roaming and corral use;; corral-always ;P6.1: Corral-use (proportion ALWAYS) among pig-owners with corrals corral-sometimes ;P6.1: Corral-use (proportion SOMETIMES) among pig-owners with corrals prop-corral-sometimes ;P6.2: Proportion of pigs that are corraled among households household that SOMETIMES use corral home-range-mean ;P6.3: Home range radius (mean) home-range-sd ;P6.3: Home range radius (sd) ;;Sale and distribution of pork;; pigs-sold ;P7.1: Proportion of pigs that are sold prior to slaughter pigs-exported ;P7.2: Proportion of sold pigs that are exported pig-import-rate ;P7.3: Rate of import of pigs from external communities import-prev ;P7.4: Prevalence of infection among pigs imported from external communities light-to-heavy-prop ;P7.5: Proportion of infected imported pigs that are lightly infected (compared to heavy) hh-only-pork ;P7.6-a: Proportion of pigs for which all meat consumed exclusively by pig-owner households sold-pork ;P7.6-b: Proportion of pigs for which all meat was sold within the village (none consumed at home) shared-pork-dist ;P7.7: (NOT ACTIVE) Number of households a pig is divided between when slaughtered for sale shared-pork-hh ;P7.8: Proportion of shared pork that is consumed by the pig-owner's household ;;;SPATIAL VARIABLES;;; household-dataset ;Shapefile specifying household coordinates in village data-location ;File-path of shapefile for households coordinates roads-dataset ;Shapefile of roads (if available) rivers-dataset ;Shapefile of rivers (if available) scale ;(Auto-generated variable) Transformation constant of meters to pixels in patch-environment hor ;Width (in patches) of environment ver ;Length (in patches) of environment ;;;MONITORS - ROUTINE;;; num-households ;(Auto-generated variables) number of households in the environment total-pig-owners ;(Auto-generated variables) number of pig-owning households ;;;MONITORS - SEROINCIDENCE (PIGS);;; week-counter ;(Auto-generated variable) counting weeks of exposure for 4-month incidence window in pigs seroconversions ;Counts the number of seronegative pigs that become seropositive during 4-month incidence window seroeligible ;Counts the number of pigs that are seronegative at the beginning of the 4-month incidence window and pigs born into the population seroincidence ;Calculation of seroconversions / seroeligible ;;;INTERVENTION SETTINGS;;; ;;General - human;; elisa-sens ;Sensitivity of the ELISA copro-antigen assay for taeniasis screening treat1-eff ;Efficacy of single-dose treatment for human taeniasis treat2-eff ;Efficacy of two-dose treatment for human taeniasis screen-trt-eff ;Efficacy of follow-to-cure treatment of human taeniasis after stool screening screen-trt-part ;Participation in treatment for human taeniasis AFTER a positive stool screening treat1-part ;Proportion of humans that receive 1 dose of treatment for taeniasis treat2-part ;Proportion of humans that receive 2 doses of treatment for taeniasis treat-mass-part ;Proportion of humans that participate in mass treatment screen-part ;Proportion of humans that participate in stool screening for taeniasis ;;General - pigs;; age-eligible ;Age at which pigs are eligible to participate in interventions treat-part-p ;Proportion of pigs that receive treatment for porcine cysticercosis oxf-protection ;Length of time infected pigs are protected from cyst infection after treatment with oxfendazole vacc-part ;Proportion of pigs that participation in vaccination with TSOL18 vacc-eff ;Efficacy of TSOL18 vaccine for porcine cysticercosis (after 2 doses) saca-part ;Proportion of pigs that are purchased and slaughtered in a community-wide necropsy ("saca") ;;Ring Strategy;; ring-size ;Radius (in meters) of intervention rings after screening a tongue-positive pig (RING STRATEGY ONLY) tongue-part ;Proportion of pigs screened with tongue inspection (RING STRATEGY ONLY) tongue-sens ;Sensitivity (probability) of detecting a heavily infected pig with tongue inspection (RING STRATEGY ONLY) tongue-fp ;False positive rate during tongue inspection (proportion on uninfected pigs with positive test) (RING STRATEGY ONLY) ; treat-final-part ;Proportion of humans that participate in a single round of mass treatment at the end of the study ] ;;;AGENTS;;; breed [ ;INACTIVE: only for visualization of corrals corral2s corral2] breed [ humans human] breed [ pigs pig] breed [ ;A slaughtered pig is divided into "carne" to be distributed within and between households carnes carne] breed [ ;Tapeworm carriers contaminate the environment with "eggs" (not intended to represent a single biological egg, but the presence of eggs) eggs egg] patches-own [ ;;ENVIRONMENTAL VARIABLES;; household ;FIXED, BINARY: Is the patch a household? pig-owner ;FIXED, BINARY: Does the household raise pigs? corral ;FIXED, BINARY: Does the pig-owning house have a pig corral? corraluse ;FIXED, ORDINAL: What is the frequency of corral-use at that household (always, sometimes, never)? latrine ;FIXED, BINARY: Does the household own a latrine? latrineusers ;FIXED, BINARY: Do the household members always use the latrine? light-infected-pork-meal ;DYNAMIC: Did the household consume a light-infected pork meal this week? heavy-infected-pork-meal ;DYNAMIC: Did the household consume a light-infected pork meal this week? travelerhh ;FIXED, BINARY: Does a member of the household regularly travel to other endemic areas? cont-radius-hh ;FIXED, CONTINUOUS: Distance from a household that environmental contamination is deposited (random angle) ] humans-own [ ;;HUMAN VARIABLES;; ;General; home-x ;FIXED: X-coordinate of household location on grid home-y ;FIXED: Y-coordinate of household location on grid latrine-user ;FIXED, BINARY: Does the person belong to a latrine-using household? ;Infection status; tapeworm ;DYNAMIC, BINARY: Is the person infected with a tapeworm? infection-duration ;DYNAMIC, DISCRETE: Pre-determined duration of tapeworm infection (new value randomly generated for every new infection) mature-tn ;DYNAMIC: If the person is a tapeworm carrier, is the tapeworm mature (producing eggs/proglottids)? tn-released ;DYNAMIC, BINARY: If the person has a mature tapeworm infection and does not use latrines, was the egg/proglottid released into the environment? time-since-infection ;DYNAMIC, DISCRETE: How many weeks since tapeworm infection occured (auto-generated counter) ;Travel-related; traveler ;FIXED: Is the person a regular traveler to other endemic areas? travel-ticker ;DYNAMIC: Automatic counter that determines time until the next trip to endemic areas (for travelers) traveling ;DYNAMIC: Is the person travel outside of the village this week? travel-time ;DYNAMIC: Amount of time this traveler will be out of the village on the current trip ;Interventions; screen-pos ;INTERVENTIONS: Was this person screened positive for taeniasis? eligible ;INTERVENTIONS: Is this person eligible for screening/treatment based on presence in a ring (RING STRATEGY ONLY) ] pigs-own [ ;;PIG VARIABLES;; ;Infection status; susceptible ;DYNAMIC, BINARY: Is the pig susceptible to infection (not infected or resistant)? light-exp ;DYNAMIC, BINARY: Was the pig exposed to eggs (light contamination) in the environment this week? heavy-exp ;DYNAMIC, BINARY: Was the pig exposed to proglottids (heavy contamination) in the environment this week? heavy-infected ;DYNAMIC, BINARY: Is the pig heavily infected with cysts (>100 cysts)? light-infected ;DYNAMIC, BINARY: Is the pig lightly infected with cysts (<100 cysts)? seropositive ;DYNAMIC, BINARY: Is the pig positive on a serological test (EITB)? ;General; home-x ;FIXED: X-coordinate of the pig's household on grid home-y ;FIXED: Y-coordinate of the pig's household on grid corraled ;FIXED, ORDINAL: How frequently is the pig corraled (ALWAYS, SOMETIMES, NEVER) home-range ;FIXED, CONTINUOUS: If the pig is free-roaming, what is the radius (in meters) of the pig's roaming area (home-range)? age ;DYNAMIC, DISCRETE: Current age of the pig (in weeks) slaughter-age ;FIXED, DISCRETE: Pre-determined age (in weeks) at which pig will be slaughtered marked-for-slaughter ;DYNAMIC, BINARY: Is the pig due for slaughter this week (reached slaughter-age)? ;Interventions; eligible ;INTERVENTIONS: Is the pig eligible for treatment based on precense in a ring (RING STRATEGY ONLY) protected ;INTERVENTIONS: Is the pig protected from future infection because it received vaccination and/or OFZ treatment while infected protected-time ;INTERVENTIONS: Amount of time remaining that pig is protected from infection (automatic counter) vacc-dose ;INTERVENTIONS: Number of vaccine doses received vaccinated ;INTERVENTIONS: Did the pig receive the full vaccine dose and full protection? ] carnes-own[ light-infected ;BINARY: Is pork meat lightly infected? heavy-infected ;BINARY: Is pork meat heavily infected? hh ;BINARY: Is pork meat consumed by the current household or sold/donated to a different household in the village? ] eggs-own[ id ;DISCRETE: Auto-generated index of the human that released the egg proglottid ;BINARY: Is this a proglottid (heavy contamination)? ova ;BINARY: Is this eggs (light contamination)? cont-radius-egg ;DISCRETE: Distance radius from the household that the contamination may appear within time-since-infection ;DISCRETE: Number of weeks since the human tapeworm carrier was infected (automatic counter, mirrors human counter) infection-duration ;DISCRETE: Total number of weeks the human tapeworm infection will last (mirrors human variable) traveling-human ;BINARY: Is the human that produced the egg currently traveling (mirrors human variable) ] ;;;;WORLD SETUP;;;; to setup clear-all setup-villages resize-world (- hor) hor (- ver) ver ;Changes the dimensions of the world if specified for a particular village setup-patches ifelse Households = "Random" ;ADDED option to allow for model processing without access to SHAPEFILES [ask n-of 100 patches [set household true] set calibrated? false] [draw-gis-layers] setup-globals setup-pigs setup-humans reset-ticks end to setup-villages set data-location "CystiAgentTestData.shp" set hor 180 set ver 200 end to setup-patches ask patches [ set household false set latrine false set latrineusers false set corral false set light-infected-pork-meal 0 set heavy-infected-pork-meal 0 set travelerhh false set cont-radius-hh false] end to draw-gis-layers set household-dataset gis:load-dataset data-location gis:set-transformation (gis:envelope-of household-dataset) (list (min-pxcor + 50) (max-pxcor - 50) (min-pycor + 50) (max-pycor - 50)) foreach gis:feature-list-of household-dataset [ vector-feature -> let location gis:location-of (first(first(gis:vertex-lists-of vector-feature))) if not empty? location [ ask patch item 0 location item 1 location [ set household true]]] ;;If roads or rivers layers are available, they can be drawn in with this, but are not converted into patch variables ;set roads-dataset gis:load-dataset "C:/Users/pray/Documents/PhD Dissertation/NetLogoShapefiles/TTEMP_Roads_proj.shp" ; foreach gis:feature-list-of roads-dataset [ vector-feature -> ; gis:set-drawing-color gray ; gis:draw vector-feature 2.0] ; ; set rivers-dataset gis:load-dataset "C:/Users/pray/Documents/PhD Dissertation/NetLogoShapefiles/TTEMP_Rivers_proj.shp" ; foreach gis:feature-list-of rivers-dataset [ vector-feature -> ; gis:set-drawing-color 96 ; gis:draw vector-feature 2.0] end to setup-globals ;;CALIBRATED TUNING VARIABLES;; if calibrated? = true [ set light-inf 0.0163 ;Tuning paramter (via calibration): Probability of light pig infection upon egg consumption set heavy-inf 0.0046 ;Tuning paramter (via calibration): Probability of heavy pig infection upon proglottid consumption set pl2h 0.0074 ;Tuning paramter (via calibration): Probability of human taeniasis upon lightly inf. pork consumption set ph2h 0.0059 ;Tuning paramter (via calibration): Probability of human taeniasis upon heavily inf. pork consumption set light-all 0.0141 ;Tuning paramter (via calibration): Probability of light pig infection for all pigs set heavy-all 0.0182 ;Tuning paramter (via calibration): Probability of heavy pig infection for all pigs set light-sero 0.15 ;Tuning paramter (via calibration): Probability of seropositivity after light exposure set heavy-sero 0.1] ;Tuning paramter (via calibration): Probability of seropositivity after heavy exposure ;;MODEL PARAMETERS;; set prop-pig-owners 0.39 ;(specified by village) P0.1: Proportion of households that raise pigs set prop-corrals 0.37 ;(specified by village) P0.2: Proportion of pig-owning households with corrals (or tie-up areas) set prop-latrines 0.78 ;(specified by village) P0.3: Proportion of households that have a latrine or bathroom set humans-per-household 3.86 ;(specified by village) P0.4: POISSON mean for number of humans per household set pigs-per-household 2.16 ;(specified by village) P0.5: EXPONENTIAL mean for number of pigs per household set baseline-tn-prev 0.0293 ;(specified by village) P0.6: Baseline prevalence of taeniasis set baseline-light-infection 0.1648 ;(specified by village) P0.7: Baseline prevalence of light cyst infection set baseline-heavy-infection 0.0674 ;(specified by village) P0.8: Baseline prevalence of heavy cyst infection set slaughter-age-mean 2.279 ;P1.1: Log-mean pig age at slaughter (in months, will be later converted to weeks) set slaughter-age-sd 0.515 ;P1.1: Log-SD of pig age at slaughter (in months) set traveler-prop 0.423 ;P2.1: Proportion of households with a frequent traveler set travel-freq 8 ;P2.2: Frequency of trips among traveler households (departure for a trip every X weeks) set travel-duration 1.75 ;P2.3: Mean (ENTER DISTRIBUTION) duration of trips set travel-incidence 0.000231 ;P2.4: Incidence of taeniasis among humans traveling to other endemic areas set tn-lifespan-mean 104 ;P3.1: Tapeworm infection duration (mean) set tn-lifespan-sd 50 ;P3.1: Tapeworm infection duration (sd) set tn-incubation 8 ;P3.2: Tapeworm incubation time set latrine-use 0.25 ;P4.1: Proportion of households with a latrine in GOOD condition that they ALWAYS use set cont-radius-mean 3.27 ;P4.2: Log-mean of the radius of contamination around tapeworm carrier house set cont-radius-sd 0.547 ;P4.2: Log-SD of the radius of contamination around tapeworm carrier house set decay-mean 0.125 ;P5.1: Environmental egg decay rate parameter (probably of decay per week) set corral-always 0.05 ;P6.1: Corral-use (proportion ALWAYS) among pig-owners with corrals set corral-sometimes 0.57 ;P6.1: Corral-use (proportion SOMETIMES) among pig-owners with corrals set prop-corral-sometimes 0.32 ;P6.2: Proportion of pigs that are corraled among households household that SOMETIMES use corral set home-range-mean 3.79 ;P6.3: Home range radius (mean) set home-range-sd 0.552 ;P6.3: Home range radius (sd) set pigs-sold 0.514 ;P7.1: Proportion of pigs that are sold prior to slaughter set pigs-exported 0.731 ;P7.2: Proportion of sold pigs that are exported set pig-import-rate 0.00105 ;P7.3: Rate of import of pigs from external communities set import-prev 0.134 ;P7.4: Prevalence of infection among pigs imported from external communities set light-to-heavy-prop 0.755 ;P7.5: Proportion of infected imported pigs that are lightly infected (compared to heavy) set hh-only-pork 0.396 ;P7.6-a: Proportion of pigs for which all meat consumed exclusively by pig-owner households set sold-pork 0.115 ;P7.6-b: Proportion of pigs for which all meat was sold within the village (none consumed at home) set shared-pork-dist 0 ;P7.7: Number of households a pig is divided between when slaughtered for sale (NOT ACTIVE) set shared-pork-hh 0.80 ;P7.8: Proportion of shared pork that is consumed by the pig-owner's household set scale (item 1 gis:world-envelope - item 0 gis:world-envelope) / (max-pxcor * 2) ;Determines meters to cells conversion set num-households count patches with [household = true] ;Count number of households for future calculations set total-pig-owners round ((prop-pig-owners) * num-households) ;Calculate total pig-owning households ;;INTERVENTION SETTINGS;; ;General - human; set screen-part 0.75 set elisa-sens 0.964 set screen-trt-part 0.918 set screen-trt-eff 0.933 set treat1-part 0.15 set treat2-part 0.70 set treat1-eff 0.766 set treat2-eff 0.866 set treat-mass-part 0.78 set treat-final-part 0.736 ;General - pig; set age-eligible 10 set treat-part-p 0.60 set oxf-protection 17 set vacc-part 0.7 set vacc-eff 0.99 set saca-part 0.482 ;Ring Strategy; set ring-size 100 set tongue-part 0.72 set tongue-sens 0.909 set tongue-fp 0.021 end to setup-pigs ask n-of total-pig-owners patches with [household = true] ;Set pig-owning households [set pig-owner true] ask n-of (round((prop-corrals) * count patches with [pig-owner = true])) patches with [pig-owner = true] ;Set pig-owning households with corrals [set corral true] ask patches with [pig-owner = true] ;Set household corral-use (always, sometimes, never) among pig-owners with corrals [set corraluse "never"] ask n-of (round((corral-always) * count patches with [corral = true])) patches with [corral = true] [set corraluse "always"] ask n-of (round((corral-sometimes) * count patches with [corral = true])) patches with [corral = true and corraluse = "never"] [set corraluse "sometimes"] ask patches [ if pig-owner = true [ sprout-pigs ceiling random-exponential pigs-per-household [ ;Populate pig-owning households with pigs set shape "pig" set color pink set size 10]]] ;if corral = true [ ;Create object (turtle) to display corrals (INACTIVE) ; sprout-corral2s 1 [ ; set shape "square 2" ; set size 20 ;if corraluse = "always" [set color green] ;if corraluse = "sometimes" [set color yellow] ;if corraluse = "never" [set color red]]]] ask pigs [ ;Set initial variables for pigs set susceptible true set light-exp false set heavy-exp false set seropositive false set heavy-infected false set light-infected false set marked-for-slaughter false set eligible false set protected false set protected-time 0 set vacc-dose 0 set vaccinated false set corraled "never" set home-x xcor set home-y ycor if [corraluse] of patch-here = "always" ;Assign corral usage for pigs based on household corral practice [set corraled "always"] if [corraluse] of patch-here = "sometimes" [set corraled "sometimes"] set slaughter-age round(4.35 * (exp(random-normal slaughter-age-mean slaughter-age-sd))) ;Set age at which each pig will be slaughteed (in weeks, 4.35 weeks per month) set home-range (exp(random-normal home-range-mean home-range-sd)) ;Set the radius of each pigs home-range areae set age (slaughter-age - random slaughter-age) ;Randomly assign starting age for first batch of pigs if random-float 1 < baseline-heavy-infection [heavy-infect] ;Infect pigs at baseline (heavy) if (not heavy-infected) and (random-float 1 < baseline-light-infection) [light-infect]] ;Infect pigs at baseline (light) ;set total-pigs count pigs ;Count pigs at baseline (for INCIDENCE calculation - SENSITIVITY ANALYSIS) end to setup-humans ask patches [ if household [ let x random-poisson humans-per-household ;Assign humans to household (no zeros allowed) ifelse x > 0 [sprout-humans x [ set shape "house" set size 10 set color yellow move-to patch-here]] [sprout-humans 1 [ set shape "house" set size 10 set color yellow move-to patch-here]] set cont-radius-hh (exp(random-normal cont-radius-mean cont-radius-sd))]] ;Set radius of environmental contamination for each household ask n-of (prop-latrines * num-households) patches with [household = true] ;Assign latrines to households [set latrine true] ask n-of (latrine-use * count patches with [latrine = true]) patches with [latrine = true] ;Assign latrine use (BINARY) to households with latrines [set latrineusers true] ask n-of (traveler-prop * num-households) patches with [household = true] ;Assign households as travelers (BINARY) [set travelerhh true] ask humans [ ;Set initial variables for humans set latrine-user false set tapeworm false set traveling false set traveler false set time-since-infection 0 set infection-duration 0 set travel-time 0 set mature-tn false set tn-released false set screen-pos false set eligible false set home-x xcor set home-y ycor if latrineusers = true [ ;Assign latrine use of household to individuals set latrine-user true] if random-float 1 < baseline-tn-prev [ ;Infect humans with taeniasis at baseline infect-humans-baseline]] ask patches with [travelerhh = true][ ;Assign one person per traveling household to be a traveler ask one-of humans-here [ set traveler true set travel-ticker random (travel-freq + 1)]] ;Begin timer to countdown the weeks until the next trip ;set num-humans count humans ;Count number of human at baseline (for INCIDENCE calculation - SENSITIVITY ANALYSIS) end to infect-humans-baseline ;Infect humans at baseline set tapeworm true let x random-normal tn-lifespan-mean tn-lifespan-sd ;Set predetermined duration of tapeworm infection (0-truncated) ifelse x < 0 [set infection-duration 0] [set infection-duration round x] let y random infection-duration ;Randomly assign time-since-infection to a starting value set time-since-infection (infection-duration - y) if time-since-infection >= tn-incubation [ ;Set tapeworm maturity set mature-tn true] ;set size 20 set color blue] ;OPTIONAL: change color for tapeworm carriers if tapeworm = true and mature-tn = true and latrine-user = false [ ;Contamination only occurs in households with mature tapeworm carriers not using latrines set tn-released true hatch-eggs 1 [ ;Set characteristics of environmental contamination set id [who] of myself ;Adopt index of human that produced egg/proglottid set proglottid true ;Both egg and proglottid (meaning it can cause heavy or light infection) set ova true set traveling-human false ;Human cannot be traveling yet (baseline infection) set cont-radius-egg cont-radius-hh move-to one-of patches in-radius (cont-radius-egg / scale) ;Place egg/proglottid on any patch within the contamination radius set size 10 set shape "circle" set color green ifelse x < 0 ;Set same infection duration and time-since infection as specified for human (mirror) [set infection-duration 0] [set infection-duration round x] set time-since-infection (infection-duration - y)]] end ;;;;RUN;;;; to go ask humans [advance-infection] ask eggs [eggs-advance] ask humans [return-home-humans] ask humans [travel] ask pigs [reset-exposure] ask pigs [mark-for-slaughter] ask pigs [birth-pigs] ask pigs [distribute-pigs] ask pigs [import-pigs] ask pigs [slaughter-pigs] ask carnes [distribute-pork] ask carnes [die] ask humans [eat-pork] ask humans [infect-travelers] ask pigs [slaughter] ask pigs [eat-eggs] ask pigs [seroconvert] ask pigs [infect-pigs] ask pigs [set age age + 1] ask humans [mature-infection] ask humans [tapeworm-die] ask eggs [environmental-decay] ask eggs [stop-contaminating] ask humans [clear-pork-meals] ask pigs [advance-protection] ;ask pigs [assign-color-pigs] ;OPTIONAL: if changing color for infection status ;set count-cyst count-heavy + count-light ;Add up incident pig infection (for INCIDENCE calculation - SENSITIVITY ANALYSIS) ;recorder ;Initiates script to record prevalence at given time-points (for CALIBRATION) track-incidence ;Initiates script to record pig sero-incidence tick end to advance-infection ;;Advance taeniasis infection by 1 week;; if tapeworm = true [set time-since-infection time-since-infection + 1] end to eggs-advance ;;Advance age of environmental contamination by 1 week;; set time-since-infection time-since-infection + 1 end to return-home-humans ;;Humans that are currently travel return home;; if traveling = true [ set travel-time travel-time - 1 if travel-time = 0 [ set xcor home-x set ycor home-y if tapeworm = true and latrine-user = false and mature-tn = true and tn-released = false [ ;Humans that have taeniasis and return home begin contaminating the environment (only if tapeworm is mature and contamination not already released) set tn-released true hatch-eggs 1 [ set id [who] of myself set proglottid true set ova true set traveling-human false set infection-duration infection-duration set time-since-infection tn-incubation set cont-radius-egg cont-radius-hh move-to one-of patches in-radius (cont-radius-egg / scale) set size 10 set shape "circle" set color green]] if tapeworm = true and latrine-user = false and mature-tn = true and tn-released = true [ ;When humans return from traveling, if taeniasis is active and environmental contamination already begun, resume heavy contamination ask eggs with [id = [who] of myself] [ set proglottid true set color green]] set traveling false ask eggs with [id = [who] of myself] [ set traveling-human false]]] end to travel ;;Initiate travel of humans;; if traveler = true and travel-ticker = 0 [ ;Begin travel when travel timer gets to 0 set traveling true ask eggs with [id = [who] of myself] [ ;When travel begins, associated environmental contamination turns to light (no active proglottids) set proglottid false set traveling-human true set color brown] set travel-time ceiling random-exponential travel-duration ;Assign duration of travel based on exponential distribution set travel-ticker travel-freq + 1 ;Reset travel timer back to constant interval until next trip set xcor max-pxcor set ycor max-pycor] ;Human that is traveling is placed in the top right corner of the world if traveler = true [ set travel-ticker travel-ticker - 1] end to reset-exposure ;Set all exposure to NULL to begin the week set light-exp false set heavy-exp false end to mark-for-slaughter ;If a pig reaches it pre-determined slaughter age, it is "marked" for slaughter if age = slaughter-age [set marked-for-slaughter true] end to birth-pigs ;For every pig that will be slaughtered, a new pig is born into the same household (to maintain constant population size) if marked-for-slaughter = true [ hatch 1 [ ;Set initial variables for new pigs (same as above for initial pig population) set shape "pig" set color pink set size 10 set susceptible true set light-exp false set heavy-exp false set seropositive false set heavy-infected false set light-infected false set marked-for-slaughter false set eligible false set protected false set protected-time 0 set vacc-dose 0 set vaccinated false set corraled "never" set age 0 set home-x xcor set home-y ycor if [corraluse] of patch-here = "always" [set corraled "always"] if [corraluse] of patch-here = "sometimes" [set corraled "sometimes"] set slaughter-age round(4.35 * (exp(random-normal slaughter-age-mean slaughter-age-sd))) set home-range (exp(random-normal home-range-mean home-range-sd))] ;set total-pigs total-pigs + 1 ;Add new pigs to population (for INCIDENCE calculation - SENSIVITY ANALYSIS) set seroeligible seroeligible + 1] ;Add new seronegative pigs to the population (to calculuate pig sero-incidence) end to distribute-pigs ;Sell and export pigs that will be slaughtered if marked-for-slaughter = true [ let x random-float 1 if x < pigs-sold [ ;Proportion of pigs that are sold prior to slaughter let y random-float 1 ifelse y < pigs-exported ;Proportion of sold pigs that are exported [die] ;If pigs are exported, they "die" and a not consumed [move-to one-of patches with [household = true]]]] ;If pigs are sold, they go to a random household within the village end to import-pigs ;Import infected pigs let x random-float 1 if x < (pig-import-rate * import-prev) [ ;Probability of a pig being imported and that pig being infected, per pig in the population hatch-pigs 1 [ set marked-for-slaughter true ;Imported pigs are immediately marked for slaughter (do not contribute to population size or prevalence) let y random-float 1 ifelse y < light-to-heavy-prop ;Infected imported pigs are either heavily or lightly infected [set light-infected true] [set heavy-infected true]]] end to slaughter-pigs ;Pigs are slaughtered and eithe sold, shared, or consumed (process separate for heavy and light infected pigs, but not differentiated (yet) by parameters if light-infected = true and marked-for-slaughter = true [ let x random-float 1 hatch-carnes 10 [ ;When slaughtered, pig is divided into 10 pieces, but this is artibrary set light-infected true set hh false ifelse x < hh-only-pork ;"x" is a random value generated for the whole pig to determine if the pig is consumed entirely by pig-owner households [set hh true] [ifelse x > (1 - sold-pork) ;"x" is a random value generated for the whole pig to determine if the pig is sold within the village (not consumed at home) [set hh false] [let y random-float 1 if y < shared-pork-hh [ ;"y" is a random value generated by each "carne" among pigs that are "shared" to determine if each piece is eaten at home or sold set hh true]]]]] if heavy-infected = true and marked-for-slaughter = true [ ;SAME as above for light-infected let x random-float 1 hatch-carnes 10 [ set heavy-infected true set hh false ifelse x < hh-only-pork [ set hh true] [ifelse x > (1 - sold-pork) [set hh false] [let y random-float 1 if y < shared-pork-hh [ set hh true]]]]] end to distribute-pork ;For pork that is not eaten at home, it is moved to a random household within the village if hh = false [ move-to one-of patches with [household = true]] if light-infected = true [ ;Count the number of light-infected pork meals consumed by each household this week set light-infected-pork-meal (count carnes-here with [light-infected = true])] if heavy-infected = true [ ;Count the number of heavy-infected pork meals consumed by each household this week set heavy-infected-pork-meal (count carnes-here with [heavy-infected = true])] end to eat-pork ;Each household eats infected pork if [light-infected-pork-meal] of patch-here > 0 [ ;If light-infected pork is consumed, ALL members of the household are exposed to a probability of tapeworm infection from each infected pork meal repeat (light-infected-pork-meal) [let x random-float 1 if x < pl2h [infect-humans]]] ;pl2h is the TUNING parameter determining probability of infection given exposure if [heavy-infected-pork-meal] of patch-here > 0 [ ;If heavy-infected pork is consumed, ALL members of the household are exposed to a probability of tapeworm infection from each infected pork meal repeat (heavy-infected-pork-meal) [let x random-float 1 if x < ph2h [infect-humans]]] ;ph2h is the TUNING parameter determining probability of infection given exposure end to infect-humans ;Human infection script ;if tapeworm = false [set count-tn count-tn + 1] ;Counts incident taeniasis infections (for INCIDENCE calculation - SENSITIVITY ANALYSIS) set tapeworm true let x random-normal tn-lifespan-mean tn-lifespan-sd ;Assign duration of taweworm infection (0-truncated) ifelse x < 0 [set infection-duration 0] [set infection-duration round x] set time-since-infection 0 end to infect-travelers ;Infect humans that are traveling if traveling = true [ if random-float 1 < travel-incidence [ ;Each traveler is exposued to possible infection based on endemic incidence rate ;if tapeworm = false [set count-tn count-tn + 1] ;Counts incident taeniasis infection (for INCIDENCE calculation - SENSITIVITY ANALYSIS) set tapeworm true let x random-normal tn-lifespan-mean tn-lifespan-sd ;Set lifespan of taweworm infection (0-truncated) ifelse x < 0 [set infection-duration 0] [set infection-duration round x] set time-since-infection 0 ]] end to slaughter ;Kill off pig that were slaughtered and already consumed if marked-for-slaughter = true [die] end to eat-eggs ;Expose pigs to environmental contamination if (corraled = "never") or (corraled = "sometimes" and random-float 1 > prop-corral-sometimes) [ ;Pigs that are "never" corraled may be exposed, and pigs that are "sometimes" corraled have a given probability of being free-roaming each week let egg-exp (count eggs in-radius (home-range / scale)) ;Count number of eggs/proglottids in each pigs home-range ;ask patches in-radius (home-range / scale) [set pcolor red] ;OPTIONAL (slows computation): display home-range areas for each pig if egg-exp > 0 [ ;If a pig is exposed to contamination... if (count eggs with [ova = true] in-radius (home-range / scale)) > 0 [ ;If contamination is light (ova), the pig is lightly exposed set light-exp true] if (count eggs with [proglottid = true] in-radius (home-range / scale)) > 0 [ ;If contamination is heavy (proglottid), the pig is heavy exposed set heavy-exp true]] let factor (count humans with [tapeworm = true]) ;Count the number of human tapeworm carriers in the village if random-float 1 < (1 - (1 - light-all) ^ factor) [ ;Expose all free-roaming pigs to a probability of light exposure based on number of human carriers in village (irrespective of location) set light-exp true] if random-float 1 < (1 - (1 - heavy-all) ^ factor) [ ;Expose all free-roaming pigs to a probability of heavy exposure based on number of human carriers in village (irrespective of location) set heavy-exp true]] end to seroconvert ;Pigs that are exposed may develop serological responses (EITB) if light-exp = true and seropositive = false [ ;The probability of seroconversion after light exposure is based on the "light-sero" tuning parameter if random-float 1 < light-sero [ set seropositive true set seroconversions seroconversions + 1]] ;Count new seroconversions for calculation of sero-incidence if heavy-exp = true and seropositive = false [ ;The probability of seroconversion after heavy exposure is based on the "heavy-sero" tuning parameter if random-float 1 < heavy-sero [ set seropositive true set seroconversions seroconversions + 1]] ;Count new seroconversions for calculation of sero-incidence end to infect-pigs ;If pigs are exposed, they may develop cyst infection if protected = false [ ;PROTECTION was added for INTERVENTIONS and may be caused by vaccination or treatment if heavy-exp = true [ if susceptible = true [ if random-float 1 < heavy-inf [ ;Probability of heavy infection after heavy exposure is determined by the "heavy-inf" tuning parameter ;set count-heavy count-heavy + 1 ;Count new heavy infection (for INCIDENCE calculuations - SENSITIVITY ANALYSIS) heavy-infect]] if light-infected = true [ if random-float 1 < heavy-inf [ ;Heavy infection can occur after heavy exposure if already lightly infected (here) or still susceptible (above) heavy-infect]]] if light-exp = true [ if susceptible = true [ ;Light infection can only occur if currently uninfected and lightly exposed if random-float 1 < light-inf [ ;set count-light count-light + 1 ;Count new light infections (for INCIDENCE calcuations - SENSITIVITY ANALYSIS) light-infect]]]] end to heavy-infect set heavy-infected true set light-infected false ;To prevent double-counting, pigs can only be heavy OR light infected set susceptible false end to light-infect set light-infected true set susceptible false end to mature-infection ;Initiate environmental contamination on tapeworm infections that reach maturity if tapeworm = true [ if time-since-infection = tn-incubation [ ;Initiate contamination when the infection duration reaches the incubation time set mature-tn true ;set color blue set size 20 ;OPTIONAL: turn mature tapeworm infections blue if latrine-user = false and not traveling [ ;Only release environmental contamination into environment for non-latrine users and people NOT traveling set tn-released true hatch-eggs 1 [ ;Release 1 "egg" per tapeworm carrier (this "egg" represent environmental contamination generally) set id [who] of myself ;Tag egg with the index number of parent human (for mirroring) set proglottid true ;All eggs begins as both light (ova) and heavy (proglottid) contamination, until tapeworm dies and only light contamination remains set ova true set traveling-human false set infection-duration infection-duration ;Assign same duration for egg as parent tapeworm (mirror) set time-since-infection tn-incubation ;Assign time-since infection as the current time (incubation window has passed) set cont-radius-egg cont-radius-hh move-to one-of patches in-radius (cont-radius-egg / scale) ;Place egg in a random location within the pre-determined contamination radius set size 10 set shape "circle" set color green]]]] end to tapeworm-die ;Tapeworm infection reaches its predetermined time of death if tapeworm = true [ if time-since-infection = infection-duration [ set tapeworm false set time-since-infection 0 set infection-duration 0 set mature-tn false set tn-released false ;set color yellow set size 10 ]] end to environmental-decay ;For environmental contamination after tapeworm death, there is a constant probability of decay each week if traveling-human = false [ if ova = true and proglottid = false and (random-float 1 < decay-mean) [ die]] end to stop-contaminating ;When tapeworm infections clear, the environmental contamination goes from heavy (proglottid) to light (ova) and is sucsceptible to probablistic decay if time-since-infection = infection-duration [ set proglottid false set color brown] end to clear-pork-meals ;At the end of each week, all pork meals are cleared and the cycle begins again set light-infected-pork-meal 0 set heavy-infected-pork-meal 0 end to assign-color-pigs ;OPTIONAL - change color of infected pigs if heavy-infected = true [set color red] if light-infected = true [set color red] if not heavy-infected and not light-infected [set color pink] end to advance-protection ;for INTERVENTIONS - for protection due to treatment with OFZ, protection lasts a set amount of time (protected-time) and then fades (for vaccination, protection is life-long) if protected = true and vaccinated = false [ set protected-time protected-time - 1 if protected-time = 0 [ set protected false]] end ;to recorder ;for CALIBRATION - records the prevalence of TN, light and heavy pig infections, seroprevalence, seroincidence at set time-points ; if ticks = 500 [ ; set tn500 (count humans with [tapeworm = true] / count humans) ; set light500 (count pigs with [light-infected = true] / count pigs) ; set heavy500 (count pigs with [heavy-infected = true] / count pigs) ; set seroprev500 (count pigs with [seropositive = true] / count pigs) ; set sero500 seroincidence] ; if ticks = 600 [ ; set tn600 (count humans with [tapeworm = true] / count humans) ; set light600 (count pigs with [light-infected = true] / count pigs) ; set seroprev600 (count pigs with [seropositive = true] / count pigs) ; set heavy600 (count pigs with [heavy-infected = true] / count pigs) ; set sero600 seroincidence] ; if ticks = 700 [ ; set tn700 (count humans with [tapeworm = true] / count humans) ; set light700 (count pigs with [light-infected = true] / count pigs) ; set heavy700 (count pigs with [heavy-infected = true] / count pigs) ; set seroprev700 (count pigs with [seropositive = true] / count pigs) ; set sero700 seroincidence] ; if ticks = 800 [ ; set tn800 (count humans with [tapeworm = true] / count humans) ; set light800 (count pigs with [light-infected = true] / count pigs) ; set heavy800 (count pigs with [heavy-infected = true] / count pigs) ; set seroprev800 (count pigs with [seropositive = true] / count pigs) ; set sero800 seroincidence] ; if ticks = 900 [ ; set tn900 (count humans with [tapeworm = true] / count humans) ; set light900 (count pigs with [light-infected = true] / count pigs) ; set heavy900 (count pigs with [heavy-infected = true] / count pigs) ; set seroprev900 (count pigs with [seropositive = true] / count pigs) ; set sero900 seroincidence] ; if ticks = 1000 [ ; set tn1000 (count humans with [tapeworm = true] / count humans) ; set light1000 (count pigs with [light-infected = true] / count pigs) ; set heavy1000 (count pigs with [heavy-infected = true] / count pigs) ; set seroprev1000 (count pigs with [seropositive = true] / count pigs) ; set sero1000 seroincidence] ;end to track-incidence ;for calcuation of pig sero-incidence (need to activate other sero-incidence code chunks above) if week-counter = 0 [ ;At beginning of interval, calculate base population and set seroconversions to 0 set seroeligible count pigs with [seropositive = false] set seroconversions 0] set week-counter week-counter + 1 ;Count up to a pre-determined interval of weeks (here we used a 4-month incidence window (17 weeks)( if week-counter = 17 [ ;At the end of the window, calculate the incidence by dividing total seroconversions by total eligible population set seroincidence (seroconversions / seroeligible) set week-counter 0] end ;;;;;;;;INTERVENTIONS;;;;;;;;; ;;;Combined Functions;;; ;;RING STRATEGY;; to human-ring-screening ;RING SCREENING (HUMAN ONLY): Sequence of human ring screening (tongue-inspection, human screening, human treatment) reset-variables tongue-inspect-h repeat 1 [go] ring-screen-h repeat 4 [go] ring-screen-treat-h repeat ((Interval * 5) - 5) [go] end to combined-ring-screening ;RING SCREENING (HUMAN AND PIG): Sequence of combined ring screening (tongue-inspection, pig treatment, human screening, human treatment) reset-variables tongue-inspect-p repeat 1 [go] ring-screen-h ring-treat-p repeat 4 [go] ring-screen-treat-h repeat ((Interval * 5) - 5) [go] end to human-ring-treatment ;RING TREATMENT (HUMAN ONLY): Sequence of human ring treatment (tongue-inspection, human treatment) reset-variables tongue-inspect-h repeat 1 [go] ring-treat-h repeat ((Interval * 5) - 1) [go] end to combined-ring-treatment ;RING TREATMENT (HUMAN AND PIG): Sequence of combined ring treatment (tongue-inspection, pig treatment, human treatment) reset-variables tongue-inspect-h repeat 1 [go] ring-treat-h ring-treat-p repeat ((Interval * 5) - 1) [go] end ;;MASS APPLIED INTERVENTIONS;; to combined-mass-treatment ;MASS TREATMENT (HUMAN AND PIG) reset-variables mass-treat-h mass-treat-p repeat (Interval * 5) [go] end to human-mass-treatment ;MASS TREATMENT (HUMAN ONLY) reset-variables mass-treat-h repeat (Interval * 5) [go] end to combined-mass-screening ;MASS TREATMENT (HUMAN AND PIG) reset-variables mass-screen-h mass-treat-p repeat 4 [go] mass-screen-treat-h repeat (Interval * 5) [go] end to human-mass-screening ;MASS TREATMENT (HUMAN ONLY) reset-variables mass-screen-h repeat 4 [go] mass-screen-treat-h repeat (Interval * 5) [go] end to pig-vaccinate ;MASS PIG VACCINATION: Applied two rounds of pig vaccine two weeks apart reset-variables vaccinate repeat 2 [go] vaccinate repeat ((Interval * 5) - 2) [go] end to pig-vaccinate-treat reset-variables vaccinate-treat repeat 2 [go] vaccinate repeat ((Interval * 5) - 2) [go] end to pig-replacement ;MASS PIG REPLACEMENT reset-variables saca repeat (Interval * 5) [go] end ;;;Generic Functions;;; ;;;RING STRATEGY;;; to reset-variables ;Reset all visualizations ask humans [ set eligible false set screen-pos false set color yellow set size 10] ask pigs [ set eligible false set size 10 set color pink] ask patches [set pcolor black] end to tongue-inspect-h ;HUMAN-ONLY RING-STRATEGY: Screening pigs for heavy cyst infection using tongue inspection, and mark HUMANS ONLY as eligible for intervention if within ring ask pigs [ if age >= age-eligible [ ;Only tongue-inspect age-eligible pigs if random-float 1 < tongue-part [ ;Tongue inspection applied to a proportion of age-eligible pigs that participate ("tongue-part") if not heavy-infected and random-float 1 < tongue-fp [ ;Uninfected pigs may be detected as tongue-positive based on a probability of false positivity ("tongue-fp") ask patches in-radius (ring-size / scale) [ ;OPTIONAL - visualize the intervention rings with BLUE set pcolor blue] ask humans in-radius (ring-size / scale) [ ;Humans currently present inside a ring are marked as eligible for intervention set eligible true] set marked-for-slaughter true] ;Pigs that are tongue-positive are marked for slaughter to be replaced if heavy-infected and random-float 1 < tongue-sens [ ;Heavily infected pigs are detected as tongue-positive based on the sensitivity of tongue-inspection for detecting heavy cyst infection ("tongue-sens") ask patches in-radius (ring-size / scale) [ ;OPTIONAL - visualize intervention rings with BLUE set pcolor blue] ask humans in-radius (ring-size / scale) [ ;Humans currently present inside a ring are marked as eligible for intervention set eligible true] set marked-for-slaughter true]] ;Pigs that are tongue-positive are marked for slaughter to be replaced birth-pigs ;Replace tongue-positive pigs with new uninfected pigs slaughter]] ;Slaughter (kill) tongue-positive pigs without consuming ;assign-color-pigs] ;OPTIONAL - refresh color for pigs ;ask humans with [eligible = true][set size 20] ;OPTIONAL - mark humans that are eligible for interventions end to ring-screen-h ;HUMAN RING SCREENING: Humans that are marked as eligible based on rings are screened for taeniasis ask humans [ ;set size 10 if eligible = true [ if random-float 1 < screen-part [ ;Apply screening to eligible humans that participate in stool screening ("screen-part") if tapeworm = true [ if random-float 1 < elisa-sens [ ;A proportion of screened humans that have taeniasis will actually test positive based on sensitivity of the ELISA assay ("elisa-sens") set screen-pos true ;Mark positively screened as "screen-pos" and eligible for treatment (false positives are not treated because it would be inconsequential) ;set color red set size 20 ;OPTIONAL - mark positive humans ]]]] set eligible false] ;Reset eligibility to NULL end to ring-screen-treat-h ;HUMAN RING SCREENING: Humans that screen positive for taeniasis are treated ask humans [ if screen-pos = true and random-float 1 < screen-trt-part [ ;A proportion of positively screened individuals will agree to participate in treatment based on ("screen-trt-part") if random-float 1 < screen-trt-eff [ ;A proportion of treated individuals will be cured (post-screening treatment assumed a specific efficacy for follow-to-cure therapy, "screen-trt-eff") set tapeworm false set time-since-infection 0 set infection-duration 0 set mature-tn false set tn-released false ;set color orange ask eggs with [id = [who] of myself][ ;When treatment is successful, heavy environmental contamination ceases, leaving only light contamination (ova) in the environment set proglottid false set color brown]]] set screen-pos false] ;Reset screening status to NULL end to ring-treat-h ;HUMAN RING TREATMENT: Humans that are marked as eligible based on rings are treated presumptively for taeniasis ask humans [ ;set size 10 if eligible = true [ let x random-float 1 if x < treat1-part [ ;A proportion of eligible humans receive only a SINGLE DOSE of treatment ("treat1-part") if tapeworm = true [ if random-float 1 < treat1-eff [ ;For people with taeniasis that are treated with one dose, SINGLE-DOSE treatment efficacy is defined by "treat1-eff" ;set size 20 set color red ;OPTIONAL - change color of cured humans set tapeworm false set time-since-infection 0 set infection-duration 0 set mature-tn false set tn-released false ask eggs with [id = [who] of myself][ ;When treatment is successful, heavy environmental contamination ceases, leaving only light contamination (ova) in the environment set proglottid false set color brown]]]] if x > (1 - treat2-part) [ ;A proportion of eligible humans receive TWO DOSES of treatment ("treat2-part") if tapeworm = true [ if random-float 1 < treat2-eff [ ;For people with taeniasis that are treated with two doses, TWO DOSE treatment efficacy is defined by "treat2-eff" ;set size 20 set color orange ;OPTIONAL - change color of cured humans set tapeworm false set time-since-infection 0 set infection-duration 0 set mature-tn false set tn-released false ask eggs with [id = [who] of myself][ ;When treatment is successful, heavy environmental contamination ceases, leaving only light contamination (ova) in the environment set proglottid false set color brown]]]]] set eligible false] ;Reset eligible status to NULL end to tongue-inspect-p ;COMBINED HUMAN AND PIG RING STRATEGY: Screening pigs for heavy cyst infection using tongue inspection, and mark HUMANS AND PIGS as eligible for intervention if within ring ask pigs [ if age >= age-eligible [ ;Only tongue-inspect age-eligible pigs if random-float 1 < tongue-part [ ;Tongue inspection applied to a proportion of age-eligible pigs that participate ("tongue-part") if not heavy-infected and random-float 1 < tongue-fp [ ;Uninfected pigs may be detected as tongue-positive based on a probability of false positivity ("tongue-fp") ask patches in-radius (ring-size / scale) [ ;OPTIONAL - visualize the intervention rings with BLUE set pcolor blue] ask humans in-radius (ring-size / scale) [ ;Humans currently present inside a ring are marked as eligible for intervention set eligible true] ask pigs in-radius (ring-size / scale) [ ;Pigs currently present inside a ring are marked as eligible for intervention set eligible true] set marked-for-slaughter true] ;Pigs that are tongue-positive are marked for slaughter to be replaced if heavy-infected and random-float 1 < tongue-sens [ ;Heavily infected pigs are detected as tongue-positive based on the sensitivity of tongue-inspection for detecting heavy cyst infection ("tongue-sens") ask patches in-radius (ring-size / scale) [ ;OPTIONAL - visualize intervention rings with BLUE set pcolor blue] ask humans in-radius (ring-size / scale) [ ;Humans currently present inside a ring are marked as eligible for intervention set eligible true] ask pigs in-radius (ring-size / scale) [ ;Pigs currently present inside a ring are marked as eligible for intervention set eligible true] set marked-for-slaughter true]] ;Pigs that are tongue-positive are marked for slaughter to be replaced birth-pigs ;Replace tongue-positive pigs with new uninfected pigs slaughter]] ;Slaughter (kill) tongue-positive pigs without consuming ;assign-color-pigs] ;OPTIONAL - refresh color for pigs ;ask humans with [eligible = true][set size 20] ;OPTIONAL - mark humans that are eligible for interventions ;ask pigs with [eligible = true][set size 40] ;OPTIONAL - mark pigs that are eligible for interventions end to ring-treat-p ;TREATMENT OF PIGS FOR RING STRATEGY: Pigs marked as eligible for ring treatment based on presence within ring are treated ask pigs [ if age >= age-eligible [ ;Only age-eligible pigs are treated if eligible = true and random-float 1 < treat-part-p [ ;A proportion of pigs that are age-eligible participate in the treatment ("treat-part-p") if heavy-infected = true or light-infected = true [ ;OFZ is expected to be ~100% efficacious against cyst infection, thus no efficacy variables is applied, all treated pigs assumed to be cured ;set color brown set size 40 ;OPTIONAL - change color of treated pigs set heavy-infected false set light-infected false set susceptible true set protected true ;Pigs that were infected and treated with OFZ confer protection against future infections that persists a set amount of time ("oxf-protection") set protected-time oxf-protection]]] set eligible false] ;Reset eligible status to NULL end to mass-treat-final ;FINAL-ROUND MASS TREATMENT OF HUMANS: At conclusion of trial, all humans are screened with follow-up treatment offered to all ask humans [ if not traveling [ ;Only individuals NOT traveling are eligible to participate if random-float 1 < treat-final-part [ ;Among eligible individuals, a proportion will participate based on "treat-final-part" if tapeworm = true [ if random-float 1 < screen-trt-eff [ ;A proportion of treated individuals will be cured (post-screening treatment assumed a specific efficacy for follow-to-cure therapy, "screen-trt-eff") ;set size 20 set color red ;OPTIONAL - mark humans that are cured set tapeworm false set time-since-infection 0 set infection-duration 0 set mature-tn false set tn-released false ask eggs with [id = [who] of myself][ ;When treatment is successful, heavy environmental contamination ceases, leaving only light contamination (ova) in the environment set proglottid false set color brown]]]]]] end ;;MASS APPLIED INTERVENTIONS;; to mass-treat-h ;MASS TREATMENT for humans to treat taeniasis ask humans [ if not traveling [ ;Only humans not currently traveling are eligible to participate if random-float 1 < treat-mass-part [ ;Among eligible individuals, a proportion will participate based on "treat-mass-part" if tapeworm = true [ if random-float 1 < treat1-eff [ ;All participating individuals recieve a SINGLE-DOSE of treatment with an efficacy of "treat1-eff" set tapeworm false set time-since-infection 0 set infection-duration 0 set mature-tn false set tn-released false ask eggs with [id = [who] of myself][ ;When treatment is successful, heavy environmental contamination ceases, leaving only light contamination (ova) in the environment set proglottid false set color brown]]]]]] end to mass-treat-p ;MASS TREATMENT for pigs to treat cyst infection ask pigs [ if age >= age-eligible [ ;Only age-eligible pigs may receive treatment if random-float 1 < treat-part-p [ ;Among eligible pigs, a proportion will participate based on "treat-part-p" if heavy-infected = true or light-infected = true [ set heavy-infected false set light-infected false set susceptible true set protected true ;Pigs that were infected and treated with OFZ confer protection against future infections that persists a set amount of time ("oxf-protection") set protected-time oxf-protection]]]] end to mass-screen-h ;MASS SCREENING of humans for taeniasis ask humans [ if not traveling [ ;Only humans not currently traveling are eligible to participate if random-float 1 < screen-part [ ;Among eligible individuals, a proportion will participate based on "screen-part" if tapeworm = true [ if random-float 1 < treat1-eff [ ;Despite being a screening program, all eligible individuals received a SINGLE dose of treatment with an efficacy of "treat1-eff" set tapeworm false set time-since-infection 0 set infection-duration 0 set mature-tn false set tn-released false ask eggs with [id = [who] of myself][ ;When treatment is successful, heavy environmental contamination ceases, leaving only light contamination (ova) in the environment set proglottid false set color brown]] if random-float 1 < elisa-sens [ ;A proportion of screened humans that have taeniasis will actually test positive based on sensitivity of the ELISA assay ("elisa-sens") set screen-pos true]]]]] end to mass-screen-treat-h ;MASS SCREENING: Humans that are screened positively for taeniasis receive follow-up treatment ask humans [ if screen-pos = true and random-float 1 < screen-trt-part [ ;A proportion of positively screened individuals will agree to participate in treatment based on ("screen-trt-part") if random-float 1 < screen-trt-eff [ ;A proportion of treated individuals will be cured (post-screening treatment assumed a specific efficacy for follow-to-cure therapy, "screen-trt-eff") set tapeworm false set time-since-infection 0 set infection-duration 0 set mature-tn false set tn-released false ask eggs with [id = [who] of myself][ ;When treatment is successful, heavy environmental contamination ceases, leaving only light contamination (ova) in the environment set proglottid false set color brown]]] set screen-pos false] end to vaccinate ;PIG VACCINATION: Pigs receive two independent doses of vaccine that may confer protection against future infection ask pigs [ if age >= age-eligible [ ;Only age-eligible pigs receive vaccine if random-float 1 < vacc-part [ ;A proportion of eligible pigs participate in vaccination set vacc-dose vacc-dose + 1]] ;Counts the number of doses each pig has received if vacc-dose = 2 [ ;If a pig receives a second dose... ;set vacc-dose 0 if random-float 1 < vacc-eff [ ;Protection/immunity is acheived based on the vaccine efficacy ("vacc-eff") set vaccinated true ;Pig is marked as vaccinated, and its protection will not wane over time set protected-time 0 set protected true]]] ;Pig is protected from future infections end to vaccinate-treat ;PIG VACCINATION AND TREATMENT: Pigs receive two independent doses of vaccine that may confer protection against future infection ask pigs [ if age >= age-eligible [ ;Only age-eligible pigs receive vaccine if random-float 1 < vacc-part [ ;A proportion of eligible pigs participate in vaccination set vacc-dose vacc-dose + 1 ;Counts the number of doses each pig has received if heavy-infected = true or light-infected = true [ set heavy-infected false set light-infected false set susceptible true set protected true ;Pigs that were infected and treated with OFZ confer protection against future infections that persists a set amount of time ("oxf-protection") set protected-time oxf-protection] if vacc-dose = 2 [ ;If a pig receives a second dose... ;set vacc-dose 0 if random-float 1 < vacc-eff [ ;Protection/immunity is acheived based on the vaccine efficacy ("vacc-eff") set vaccinated true ;Pig is marked as vaccinated, and its protection will not wane over time set protected-time 0 set protected true]]]]] ;Pig is protected from future infections end to saca ;MASS SALE AND PIG NECROSPY: A proportion of pigs are purchased and slaughtered ask pigs [ if age >= age-eligible [ ;Only age-eligible pigs are included if seropositive = true [ ;In this SACA, only seropositive pigs were eligible to be purchased if random-float 1 < saca-part [ ;A proportion of eligible seropositive pigs participated in the saca set marked-for-slaughter true]]] ;Participating pigs are marked for slaughter, replaced with new pigs, and then killed birth-pigs slaughter] end
There is only one version of this model, created over 4 years ago by Ian Pray.
Attached files
| File | Type | Description | Last updated | |
|---|---|---|---|---|
| CystiAgent_Public.png | preview | Preview | over 4 years ago, by Ian Pray | Download |
| CystiAgentTestData.cpg | data | Coordinates | over 4 years ago, by Ian Pray | Download |
| CystiAgentTestData.dbf | data | Coordinates | over 4 years ago, by Ian Pray | Download |
| CystiAgentTestData.prj | data | Coordinates | over 4 years ago, by Ian Pray | Download |
| CystiAgentTestData.qpj | data | Coordinates | over 4 years ago, by Ian Pray | Download |
| CystiAgentTestData.shp | data | Coordinates | over 4 years ago, by Ian Pray | Download |
| CystiAgentTestData.shx | data | Coordinates | over 4 years ago, by Ian Pray | Download |
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