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GeneratedSchema8Doc
This page is automatically generated from the following schema file: scenario_8.xsd.
I recommend against editing it because edits will likely be lost later.
Key:
abc required (one)
[ def ] optional (zero or one)
( ghi )* any number (zero or more)
( jkl )+ at least one
( mno ){2,inf} two or more occurrences
→ scenario
<scenario
schemaVersion=int
analysisNo=int
maximumAgeYrs=double
name=string
popSize=int
simulationDuration=int
modelVersion=int
wuID=int
assimMode=("0" or "1")
mode=("2" or "3" or "4")
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="scenario_8.xsd"
>
IN THIS ORDER:
| <demography ... />
| <monitoring ... />
| <interventions ... />
| [ <caseManagements ... /> ]
| [ <healthSystem ... /> ]
| <entoData ... />
| <parameters ... />
</scenario>Description of scenario
schemaVersion=intVersion of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.
analysisNo=intUnits: Number Min: 1 Max: 100000000
Unique identifier of scenario
maximumAgeYrs=doubleUnits: Number Min: 0 Max: 100
Maximum age of simulated humans
name=stringUnits: string
Name of intervention
popSize=intUnits: Count Min: 1 Max: 100000
Population size
simulationDuration=intUnits: Time steps Min: 1 Max: 36500
Duration of main simulation
modelVersion=intUnits: Code Min: 0 Max: 100000000
Model Version
wuID=intUnits: Number Min: 1 Max: 100000000
Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.
assimMode=("0" or "1")Units: Code
Assimilator mode. Defines output of simulator as either complete (columns: time,agegroup,measure,value) or minimal (single column: value)
mode=("2" or "3" or "4")Units: Code
Transmission simulation mode
→ scenario → demography
<demography
name=string
[ growthRate=double ]
>
IN THIS ORDER:
| <ageGroup ... />
</demography>Description of demography
Description of demography
name=stringUnits: string
Name of demography data
growthRate=doubleUnits: Number Min: 0 Max: 0
Growth rate of human population.
→ scenario → demography → ageGroup
<ageGroup
lowerbound=double
>
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>List of age groups included in demography
List of age groups included in demography or surveys
lowerbound=doubleUnits: Years Min: 0 Max: 100
Lower bound of age group
→ scenario → demography → ageGroup → group
<group
poppercent=double
upperbound=double
/>poppercent=doubleupperbound=double→ scenario → monitoring
<monitoring
name=string
>
IN THIS ORDER:
| <surveys ... />
| <ageGroup ... />
</monitoring>Description of surveys
Description of surveys
name=stringUnits: string
Name of monitoring data
→ scenario → monitoring → surveys
<surveys
detectionLimit=double
summaryOption=int
>
IN THIS ORDER:
| <surveyTime ... />
</surveys>List of survey times
detectionLimit=doubleUnits: parasites/micolitre Min: 0 Max: 1000
Detection limit for parasitemia
summaryOption=intUnits: Code
Requested output variables
→ scenario → monitoring → surveys → surveyTime
<surveyTime>
int
</surveyTime>Survey time
→ scenario → monitoring → ageGroup
<ageGroup
lowerbound=double
>
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>List of age groups included in demography or surveys
List of age groups included in surveys
lowerbound=doubleUnits: Years Min: 0 Max: 100
Lower bound of age group
→ scenario → monitoring → ageGroup → group
<group
upperbound=double
/>upperbound=double<interventions
name=string
>
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>List of interventions
List of interventions
name=stringUnits: string
Name of age specific intervention
→ scenario → interventions → vaccineDescription
<vaccineDescription
vaccineType=int
>
IN THIS ORDER:
| <halfLifeYrs ... />
| <efficacyB ... />
| ( <initialEfficacy ... /> )+
</vaccineDescription>vaccineType=intUnits: Code
Type of vaccine
→ scenario → interventions → vaccineDescription → halfLifeYrs
<halfLifeYrs
value=double
/>Half life of drug effect
value=doubleTODO
→ scenario → interventions → vaccineDescription → efficacyB
<efficacyB
value=double
/>Measure of variation in vaccine efficacy
value=doubleTODO
→ scenario → interventions → vaccineDescription → initialEfficacy
<initialEfficacy
value=double
/>value=doubleTODO
→ scenario → interventions → iptiDescription
<iptiDescription
iptiEffect=int
>
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>iptiEffect=int→ scenario → interventions → iptiDescription → infGenotype
<infGenotype
name=string
freq=double
ACR=double
proph=int
tolPeriod=int
atten=int
/>name=stringUnits: string
Name of age specific intervention
freq=doubleACR=doubleproph=inttolPeriod=intatten=int→ scenario → interventions → ITNDescription
<ITNDescription
name=string
>
IN THIS ORDER:
| ( <anopheles ... /> )+
</ITNDescription>name=stringUnits: string
Name of Insecticide Treated Net intervention
→ scenario → interventions → ITNDescription → anopheles
<anopheles
mosquito=string
>
IN THIS ORDER:
| <deterrency ... />
| <preprandialKillingEffect ... />
| <postprandialKillingEffect ... />
</anopheles>mosquito=string→ scenario → interventions → ITNDescription → anopheles → deterrency
<deterrency
initial=double
halflife=double
[ Weibullk=double ]
/>One minus this multiplies the host's availability (before decay).
Specification of a proportion with Weibull or exponential decay.
initial=doubleUnits: None Min: 0 Max: 1
The value before any decay.
halflife=doubleUnits: Years Min: 0
Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).
Weibullk=doubleMin: 0
The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).
→ scenario → interventions → ITNDescription → anopheles → preprandialKillingEffect
<preprandialKillingEffect
initial=double
halflife=double
[ Weibullk=double ]
/>One minus this multiplies the survival rate of mosquitoes attempting to bite a host.
Specification of a proportion with Weibull or exponential decay.
initial=doubleUnits: None Min: 0 Max: 1
The value before any decay.
halflife=doubleUnits: Years Min: 0
Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).
Weibullk=doubleMin: 0
The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).
→ scenario → interventions → ITNDescription → anopheles → postprandialKillingEffect
<postprandialKillingEffect
initial=double
halflife=double
[ Weibullk=double ]
/>One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.
Specification of a proportion with Weibull or exponential decay.
initial=doubleUnits: None Min: 0 Max: 1
The value before any decay.
halflife=doubleUnits: Years Min: 0
Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).
Weibullk=doubleMin: 0
The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).
→ scenario → interventions → IRSDescription
<IRSDescription
name=string
>
IN THIS ORDER:
| ( <anopheles ... /> )+
</IRSDescription>name=stringUnits: string
Name of Indoor Residual Spraying intervention
→ scenario → interventions → IRSDescription → anopheles
<anopheles
mosquito=string
>
IN THIS ORDER:
| <deterrency ... />
| <killingEffect ... />
</anopheles>mosquito=string→ scenario → interventions → IRSDescription → anopheles → deterrency
<deterrency
initial=double
halflife=double
[ Weibullk=double ]
/>One minus this multiplies the host's availability.
Specification of a proportion with Weibull or exponential decay.
initial=doubleUnits: None Min: 0 Max: 1
The value before any decay.
halflife=doubleUnits: Years Min: 0
Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).
Weibullk=doubleMin: 0
The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).
→ scenario → interventions → IRSDescription → anopheles → killingEffect
<killingEffect
initial=double
halflife=double
[ Weibullk=double ]
/>One minus this multiplies the survival rate of resting mosquitoes.
Specification of a proportion with Weibull or exponential decay.
initial=doubleUnits: None Min: 0 Max: 1
The value before any decay.
halflife=doubleUnits: Years Min: 0
Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).
Weibullk=doubleMin: 0
The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).
→ scenario → interventions → continuous
<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>→ scenario → interventions → continuous → vaccine
<vaccine
targetAgeYrs=double
coverage=double
/>List of age groups for vaccination
targetAgeYrs=doubleUnits: Years Min: 0 Max: 100
Target age of intervention
coverage=doubleUnits: Proportion Min: 0 Max: 1
Coverage of intervention
→ scenario → interventions → continuous → ITN
<ITN
targetAgeYrs=double
coverage=double
/>Description of ITN deployment in the community
targetAgeYrs=doubleUnits: Years Min: 0 Max: 100
Target age of intervention
coverage=doubleUnits: Proportion Min: 0 Max: 1
Coverage of intervention
→ scenario → interventions → continuous → ipti
<ipti
targetAgeYrs=double
coverage=double
/>List of age groups for IPTi distribution
targetAgeYrs=doubleUnits: Years Min: 0 Max: 100
Target age of intervention
coverage=doubleUnits: Proportion Min: 0 Max: 1
Coverage of intervention
→ scenario → interventions → timed
<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>List of timed interventions
List of timed interventions
→ scenario → interventions → timed → intervention
<intervention
time=int
>
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>time=intUnits: Number Min: 1 Max: 10000
Time step of intervention
→ scenario → interventions → timed → intervention → changeHS
<changeHS
name=string
healthSystemMemory=int
>
IN THIS ORDER:
| <drugRegimen ... />
| <initialACR ... />
| <compliance ... />
| <nonCompliersEffective ... />
| <pSeekOfficialCareUncomplicated1 ... />
| <pSelfTreatUncomplicated ... />
| <pSeekOfficialCareUncomplicated2 ... />
| <pSeekOfficialCareSevere ... />
| <pSequelaeInpatient ... />
| <CFR ... />
</changeHS>- drugRegimen
- initialACR
- compliance
- nonCompliersEffective
- pSeekOfficialCareUncomplicated1
- pSelfTreatUncomplicated
- pSeekOfficialCareUncomplicated2
- pSeekOfficialCareSevere
- pSequelaeInpatient
- CFR
Description of health system
name=stringUnits: string
Name of health system
healthSystemMemory=intUnits: Time steps Min: 1 Max: 100
Follow-up period during which a recurrence is considered to be a treatment failure
→ scenario → healthSystem → drugRegimen
<drugRegimen
firstLine=string
secondLine=string
inpatient=string
/>Description of drug regimen
firstLine=stringUnits: Drug code
Code for first line drug
secondLine=stringUnits: Drug code
Code for second line drug
inpatient=stringUnits: Drug code
Code for drug used for treating inpatients
→ scenario → healthSystem → initialACR
<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
| <selfTreatment ... />
</initialACR>Initial cure rate
→ scenario → healthSystem → initialACR → CQ
<CQ
value=double
/>Chloroquine
value=doubleTODO
→ scenario → healthSystem → initialACR → SP
<SP
value=double
/>Sulphadoxine-pyrimethamine
value=doubleTODO
→ scenario → healthSystem → initialACR → AQ
<AQ
value=double
/>Amodiaquine
value=doubleTODO
→ scenario → healthSystem → initialACR → SPAQ
<SPAQ
value=double
/>Sulphadoxine-pyrimethamine/Amodiaquine
value=doubleTODO
→ scenario → healthSystem → initialACR → ACT
<ACT
value=double
/>Artemisinine combination therapy
value=doubleTODO
→ scenario → healthSystem → initialACR → QN
<QN
value=double
/>Quinine
value=doubleTODO
→ scenario → healthSystem → initialACR → selfTreatment
<selfTreatment
value=double
/>Probability of self-treatment
value=doubleTODO
→ scenario → healthSystem → compliance
<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
| <selfTreatment ... />
</compliance>Adherence to treatment
→ scenario → healthSystem → nonCompliersEffective
<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
| <selfTreatment ... />
</nonCompliersEffective>Effectiveness of treatment of non compliers
→ scenario → healthSystem → pSeekOfficialCareUncomplicated1
<pSeekOfficialCareUncomplicated1
value=double
/>Probability that a patient with newly incident uncomplicated disease seeks official care
value=doubleTODO
→ scenario → healthSystem → pSelfTreatUncomplicated
<pSelfTreatUncomplicated
value=double
/>Probability that a patient with uncomplicated disease self-treats
value=doubleTODO
→ scenario → healthSystem → pSeekOfficialCareUncomplicated2
<pSeekOfficialCareUncomplicated2
value=double
/>Probability that a patient with recurrence of uncomplicated disease seeks official care
value=doubleTODO
→ scenario → healthSystem → pSeekOfficialCareSevere
<pSeekOfficialCareSevere
value=double
/>Probability that a patient with severe disease seeks official care
value=doubleTODO
→ scenario → healthSystem → pSequelaeInpatient
<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>List of age specific probabilities of sequelae in inpatients
→ scenario → healthSystem → pSequelaeInpatient → item
<item
maxAgeYrs=double
/>maxAgeYrs=doubleUnits: Years Min: 0 Max: 100
Upper bound of age group
→ scenario → healthSystem → CFR
<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>→ scenario → healthSystem → CFR → group
<group
cfr=double
lowerbound=double
/>cfr=doubleUnits: Proportion Min: 0 Max: 1
Case fatality rate
lowerbound=doubleUnits: Years Min: 0 Max: 100
Lower bound of age group
→ scenario → interventions → timed → intervention → changeEIR
<changeEIR
eipDuration=int
>
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>Parameters for the non-vector transmission model.
eipDuration=intThe duration of sporogony in days
→ scenario → entoData → nonVector → EIRDaily
<EIRDaily
[ origin=string ]
>
double
</EIRDaily>Value of daily EIR
origin=string→ scenario → interventions → timed → intervention → MDA
<MDA
[ maxAge=double ]
[ minAge=double ]
coverage=double
/>Description of mass drug deployment in the community
maxAge=doubleUnits: Years Min: 0 Max: 100
Maximum age of eligible individuals (defaults to 100)
minAge=doubleUnits: Years Min: 0 Max: 100
Minimum age of eligible individuals (defaults to 0)
coverage=doubleUnits: Proportion Min: 0 Max: 1
Coverage of intervention
→ scenario → interventions → timed → intervention → vaccinate
<vaccinate
[ maxAge=double ]
[ minAge=double ]
coverage=double
/>Description of vaccine deployment in the community
maxAge=doubleUnits: Years Min: 0 Max: 100
Maximum age of eligible individuals (defaults to 100)
minAge=doubleUnits: Years Min: 0 Max: 100
Minimum age of eligible individuals (defaults to 0)
coverage=doubleUnits: Proportion Min: 0 Max: 1
Coverage of intervention
→ scenario → interventions → timed → intervention → ITN
<ITN
[ maxAge=double ]
[ minAge=double ]
coverage=double
/>Description of ITN deployment in the community
maxAge=doubleUnits: Years Min: 0 Max: 100
Maximum age of eligible individuals (defaults to 100)
minAge=doubleUnits: Years Min: 0 Max: 100
Minimum age of eligible individuals (defaults to 0)
coverage=doubleUnits: Proportion Min: 0 Max: 1
Coverage of intervention
→ scenario → interventions → timed → intervention → IRS
<IRS
[ maxAge=double ]
[ minAge=double ]
coverage=double
/>Description of IRS deployment in the community
maxAge=doubleUnits: Years Min: 0 Max: 100
Maximum age of eligible individuals (defaults to 100)
minAge=doubleUnits: Years Min: 0 Max: 100
Minimum age of eligible individuals (defaults to 0)
coverage=doubleUnits: Proportion Min: 0 Max: 1
Coverage of intervention
→ scenario → interventions → timed → intervention → ipti
<ipti
[ maxAge=double ]
[ minAge=double ]
coverage=double
/>List of age groups for IPTi distribution
maxAge=doubleUnits: Years Min: 0 Max: 100
Maximum age of eligible individuals (defaults to 100)
minAge=doubleUnits: Years Min: 0 Max: 100
Minimum age of eligible individuals (defaults to 0)
coverage=doubleUnits: Proportion Min: 0 Max: 1
Coverage of intervention
→ scenario → interventions → timed → intervention → larviciding
<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>Simple larviciding intervention description.
→ scenario → interventions → timed → intervention → larviciding → anopheles
<anopheles
mosquito=string
effectiveness=double
duration=int
/>mosquito=stringeffectiveness=doubleUnits: none Min: 0 Max: 1
Proportion to reduce emergence rates by.
duration=intUnits: days Min: 0 Max: inf
Number of days for which the intervention is active.
<caseManagements
name=string
reportingPeriodMemory=int
>
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>List of case managment interventions
List of age-specific case managment descriptions
name=stringUnits: string
Name of age specific intervention
reportingPeriodMemory=intUnits: Time steps Min: 1 Max: 100
Follow-up period during which a recurrence is considered to be a treatment failure
→ scenario → caseManagements → caseManagement
<caseManagement
maxAgeYrs=decimal
>
IN THIS ORDER:
| <uc1 ... />
| <uc2 ... />
| <sev ... />
| <nmfP ... />
| <nmfNP ... />
| <decisions ... />
</caseManagement>Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities
maxAgeYrs=decimalUnits: Years Min: 0 Max: 100
Upper bound of age group
→ scenario → caseManagements → caseManagement → uc1
<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>→ scenario → caseManagements → caseManagement → uc1 → endPoint
<endPoint
decision=int
p=double
/>decision=intForeign key reference to outcome node
p=doubleUnits: Proportion Min: 0 Max: 1
Probability of outcome
→ scenario → caseManagements → caseManagement → uc2
<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>→ scenario → caseManagements → caseManagement → sev
<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>→ scenario → caseManagements → caseManagement → nmfP
<nmfP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfP>→ scenario → caseManagements → caseManagement → nmfNP
<nmfNP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfNP>→ scenario → caseManagements → caseManagement → decisions
<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>→ scenario → caseManagements → caseManagement → decisions → decision
<decision
id=int
>
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>describes treatment decisions, a list of medicate descisions.
id=intUnits: Number
Key of decision
→ scenario → caseManagements → caseManagement → decisions → decision → medicate
<medicate
name=string
qty=int
time=int
/>name=stringUnits: string
Name of drug compound
qty=intUnits: Number
Quantity of drug compound
time=intUnits: Number Min: 1 Max: 10000
Time step of intervention
→ scenario → healthSystem
<healthSystem
name=string
healthSystemMemory=int
>
IN THIS ORDER:
| <drugRegimen ... />
| <initialACR ... />
| <compliance ... />
| <nonCompliersEffective ... />
| <pSeekOfficialCareUncomplicated1 ... />
| <pSelfTreatUncomplicated ... />
| <pSeekOfficialCareUncomplicated2 ... />
| <pSeekOfficialCareSevere ... />
| <pSequelaeInpatient ... />
| <CFR ... />
</healthSystem>- drugRegimen
- initialACR
- compliance
- nonCompliersEffective
- pSeekOfficialCareUncomplicated1
- pSelfTreatUncomplicated
- pSeekOfficialCareUncomplicated2
- pSeekOfficialCareSevere
- pSequelaeInpatient
- CFR
Description of health system
Description of health system
name=stringUnits: string
Name of health system
healthSystemMemory=intUnits: Time steps Min: 1 Max: 100
Follow-up period during which a recurrence is considered to be a treatment failure
<entoData
name=string
>
IN THIS ORDER:
| EXACTLY ONE OF:
| | <nonVector ... />
| | <vector ... />
</entoData>Description of entomological data
Data for entomodel
name=stringUnits: string
Name of entomology data
→ scenario → entoData → nonVector
<nonVector
eipDuration=int
>
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>Parameters for the non-vector transmission model.
eipDuration=intThe duration of sporogony in days
→ scenario → entoData → vector
<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>Parameters for the vector transmission model.
→ scenario → entoData → vector → anopheles
<anopheles
mosquito=string
>
IN THIS ORDER:
| [ <eir ... /> ]
| [ <emergence ... /> ]
| <mosq ... />
| ( <nonHumanHosts ... /> )*
</anopheles>mosquito=string→ scenario → entoData → vector → anopheles → eir
<eir
a0=double
a1=double
a2=double
b1=double
b2=double
EIRRotateAngle=double
/>Description of entomological inoculation rate. Usually one of the eir and emergence elements are provided. If both are given, the emergence rate is validated against the eir. Providing an eir allows emergence rate calculations when emergence-rate data is not provided or not valid.
a0=doublea1=doublea2=doubleb1=doubleb2=doubleEIRRotateAngle=double→ scenario → entoData → vector → anopheles → emergence
<emergence>
IN THIS ORDER:
| <emergenceRate ... />
| <kappa ... />
| <N_v ... />
| <O_v ... />
| <S_v ... />
</emergence>Data to drive simulation from a pre-calculated emergence rate. Usually one of the eir and emergence elements are provided. If just emergence data is given the simulation is run from this; if both are given, the emergence rate is validated against the eir.
→ scenario → entoData → vector → anopheles → emergence → emergenceRate
<emergenceRate>
IN THIS ORDER:
| ( <item ... /> )+
</emergenceRate>Mosquitoes emerging per day of the year, per human.
→ scenario → entoData → vector → anopheles → emergence → emergenceRate → item
<item>
double
</item>→ scenario → entoData → vector → anopheles → emergence → kappa
<kappa>
IN THIS ORDER:
| ( <item ... /> )+
</kappa>Human infectivity (probability of infection of a mosquito biting a human) over last mosqRestDuration+extrinsicIncubationPeriod days.
→ scenario → entoData → vector → anopheles → emergence → N_v
<N_v>
IN THIS ORDER:
| ( <item ... /> )+
</N_v>Total population of mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.
→ scenario → entoData → vector → anopheles → emergence → O_v
<O_v>
IN THIS ORDER:
| ( <item ... /> )+
</O_v>Population of infected mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.
→ scenario → entoData → vector → anopheles → emergence → S_v
<S_v>
IN THIS ORDER:
| ( <item ... /> )+
</S_v>Population of infectious mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.
→ scenario → entoData → vector → anopheles → mosq
<mosq
mosqRestDuration=int
extrinsicIncubationPeriod=int
mosqSeekingDeathRate=double
mosqSeekingDuration=double
mosqEntoAvailability=double
mosqProbBiting=double
mosqProbFindRestSite=double
mosqProbResting=double
mosqProbOvipositing=double
/>Vector species
mosqRestDuration=intextrinsicIncubationPeriod=intmosqSeekingDeathRate=doublemosqSeekingDuration=doublemosqEntoAvailability=doublemosqProbBiting=doublemosqProbFindRestSite=doublemosqProbResting=doublemosqProbOvipositing=double→ scenario → entoData → vector → anopheles → nonHumanHosts
<nonHumanHosts
mosqEntoAvailability=double
mosqProbBiting=double
mosqProbFindRestSite=double
mosqProbResting=double
/>Non human host parameters, per type of host (must match up with non-species-specific parameters).
mosqEntoAvailability=doublemosqProbBiting=doublemosqProbFindRestSite=doublemosqProbResting=double→ scenario → entoData → vector → nonHumanHosts
<nonHumanHosts
[ name=string ]
populationSize=int
/>Populations of non-human hosts (must also have species-specific parameters).
name=stringpopulationSize=int→ scenario → parameters
<parameters
interval=int
iseed=int
delta=double
latentp=int
>
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>Parameters for mathematical model
Parameter vector
interval=intUnits: Days
Simulation step
iseed=intUnits: Number
Seed for RNG
delta=doubleUnits: ? Redundant
this no longer seems to be used
latentp=intUnits: Time steps Min: 0 Max: 20
pre-erythrocytic latent period, in time steps
→ scenario → parameters → parameter
<parameter
name=string
number=int
value=double
include=boolean
/>name=stringUnits: string
Name of parameter
number=intUnits: Number Min: 1 Max: 100
Reference number of input parameter
value=doubleUnits: Number Min: 0
Parameter value
include=booleanUnits: Number Min: 0 Max: 1
True if parameter is to be sampled in optimization runs. Not used in simulator app.