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GeneratedSchema16Doc
This page is automatically generated from the following schema file: scenario_16.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
wuID=int
assimMode=("0" or "1")
mode=("2" or "3" or "4")
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="scenario_16.xsd"
>
IN THIS ORDER:
| <demography ... />
| <monitoring ... />
| <interventions ... />
| <healthSystem ... />
| <entoData ... />
| [ <drugDescription ... /> ]
| <model ... />
</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
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:
| <SurveyOptions ... />
| <surveys ... />
| <ageGroup ... />
</monitoring>Description of surveys
Description of surveys
name=stringUnits: string
Name of monitoring data
→ scenario → monitoring → SurveyOptions
<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.
→ scenario → monitoring → SurveyOptions → option
<option
name=string
value=boolean
/>name=stringOption name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.
value=booleanOption value (true/false). Each option has a default value (may be true or false) which is used if the option is not listed.
→ scenario → monitoring → surveys
<surveys
detectionLimit=double
>
IN THIS ORDER:
| <surveyTime ... />
</surveys>List of survey times
detectionLimit=doubleUnits: parasites/micolitre Min: 0 Max: 1000
Detection limit for parasitemia
→ scenario → monitoring → surveys → surveyTime
<surveyTime>
int
</surveyTime>Survey time; 0 means just before start of main sim and is a valid survey-point. Reported data is either from a point-time survey (immediate data) or is collected over the previous year (data from previous timesteps-per-year period). Simulation will end immediately after last survey is taken.
→ 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:
| [ <MDADescription ... /> ]
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| ( <anopheles ... /> )*
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>List of interventions
List of interventions
name=stringUnits: string
Name of age specific intervention
→ scenario → interventions → MDADescription
<MDADescription>
IN THIS ORDER:
| ( <medicate ... /> )*
</MDADescription>Description of drug dose(s) used in a mass-drug-administration intervention.
→ scenario → interventions → MDADescription → medicate
<medicate
name=string
qty=double
time=double
/>name=stringUnits: string
Abbreviated name of drug compound
qty=doubleUnits: mg
Quantity of drug compound
time=doubleUnits: hours Min: 0
Number of hours past start of timestep the drug is medicated at (usually 0).
→ 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=double
/>name=stringUnits: string
Name of age specific intervention
freq=doubleACR=doubleproph=inttolPeriod=intatten=double→ scenario → interventions → anopheles
<anopheles
mosquito=string
>
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>mosquito=string→ scenario → interventions → anopheles → ITNDescription
<ITNDescription
name=string
>
IN THIS ORDER:
| <deterrency ... />
| <preprandialKillingEffect ... />
| <postprandialKillingEffect ... />
</ITNDescription>name=stringUnits: string
Name of Insecticide Treated Net intervention
→ scenario → interventions → anopheles → ITNDescription → 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 → anopheles → ITNDescription → 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 → anopheles → ITNDescription → 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 → anopheles → IRSDescription
<IRSDescription
name=string
>
IN THIS ORDER:
| <deterrency ... />
| <killingEffect ... />
</IRSDescription>name=stringUnits: string
Name of Indoor Residual Spraying intervention
→ scenario → interventions → anopheles → IRSDescription → 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 → anopheles → IRSDescription → 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 → anopheles → VADescription
<VADescription
name=string
>
IN THIS ORDER:
| <deterrency ... />
</VADescription>name=stringUnits: string
Name of mosquito deterrency intervention
→ scenario → interventions → anopheles → VADescription → 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 → 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 ... /> ]
| [ <VectorAvailability ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>time=intUnits: Number Min: 1 Max: 10000
Time step of intervention
→ scenario → interventions → timed → intervention → changeHS
<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| | <EventScheduler ... />
| | <ImmediateOutcomes ... />
| <CFR ... />
</changeHS>Generic description of health system, used to specify the default or a replacement-as-intervention.
Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.
→ scenario → healthSystem → EventScheduler
<EventScheduler>
IN THIS ORDER:
| <CaseManagementTree ... />
| <ClinicalOutcomes ... />
</EventScheduler>→ scenario → healthSystem → EventScheduler → CaseManagementTree
<CaseManagementTree
mask=int
>
IN THIS ORDER:
| ( <CM_pBranchSet ... /> )*
| ( <CM_leaf ... /> )+
</CaseManagementTree>Partial description of the case management tree. The tree consists of: Probability branches: map an ID to another ID (the outcome) stochastically. Test branches: map an ID with a special flag to another ID; these are hard-coded. Leaf nodes: these map an ID to a list of drug medications.
Test branches are used if a flag requests a test (currently only RESULT_DETERMINE for parasite tests). Otherwise a probability or leaf branch is used by masking the current ID with mask (attribute for this element).
mask=intUnits: None Min: 0 Max: 0xFFFFFFFF
Value used to mask decision ids before selecting a branch/leaf.
→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_pBranchSet
<CM_pBranchSet
ID=int
>
IN THIS ORDER:
| ( <CM_pBranch ... /> )+
</CM_pBranchSet>A probability branch node: contains a list of outcome nodes along with probabilities, which link to another probability/test branch or leaf node.
ID=intUnits: ID
Decision identifier.
→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_pBranchSet → CM_pBranch
<CM_pBranch
outcome=int
p=double
/>outcome=intID of next probability/test branch or leaf node.
p=doubleUnits: Proportion Min: 0 Max: 1
Probability of this outcome
→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_leaf
<CM_leaf
ID=int
>
IN THIS ORDER:
| ( <medicate ... /> )*
</CM_leaf>End points of the case management tree, listing treatments.
ID=intUnits: ID
Decision identifier.
→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_leaf → medicate
<medicate
name=string
qty=double
time=double
/>name=stringUnits: string
Abbreviated name of drug compound
qty=doubleUnits: mg
Quantity of drug compound
time=doubleUnits: hours Min: 0
Number of hours past start of timestep the drug is medicated at (usually 0).
→ scenario → healthSystem → EventScheduler → ClinicalOutcomes
<ClinicalOutcomes
severeMask=int
>
IN THIS ORDER:
| ( <outcomes ... /> )+
</ClinicalOutcomes>Tables describing the probability of death and the expected length of hospital stay.
The ID looked up in each table is the final outcome ID of the case-management tree binary or-ed with the mask given here.
severeMask=intUnits: None Min: 0 Max: 0xFFFFFFFF
Value used to mask the final ID from the case-management tree before looking up values here.
→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → outcomes
<outcomes
ID=int
pDeath=double
hospitalizationDaysDeath=int
hospitalizationDaysRecover=int
/>Parameters for a path through the case-management tree (i.e. table row).
ID=intpDeath=doubleUnits: None Min: 0 Max: 1
The probability of death. This probability is applied once-only for each case, irrespective of the branch (thus entries with p=0 for UC cases are probably needed).
hospitalizationDaysDeath=intUnits: Days Min: 0
The median length of stay in hospital, given the patient dies directly from this event. (Use median rather than a distribution because data should be more reliable and the effect of heterogeneity should be small.)
hospitalizationDaysRecover=intUnits: Days Min: 0
The median length of stay in hospital, given the patient recovers from this event. (Use median rather than a distribution because data should be more reliable and the effect of heterogeneity should be small.)
→ scenario → healthSystem → ImmediateOutcomes
<ImmediateOutcomes
name=string
>
IN THIS ORDER:
| <drugRegimen ... />
| <initialACR ... />
| <compliance ... />
| <nonCompliersEffective ... />
| <pSeekOfficialCareUncomplicated1 ... />
| <pSelfTreatUncomplicated ... />
| <pSeekOfficialCareUncomplicated2 ... />
| <pSeekOfficialCareSevere ... />
| <pSequelaeInpatient ... />
</ImmediateOutcomes>- drugRegimen
- initialACR
- compliance
- nonCompliersEffective
- pSeekOfficialCareUncomplicated1
- pSelfTreatUncomplicated
- pSeekOfficialCareUncomplicated2
- pSeekOfficialCareSevere
- pSequelaeInpatient
Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).
name=stringUnits: string
Name of health system
→ scenario → healthSystem → ImmediateOutcomes → 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 → ImmediateOutcomes → initialACR
<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
| <selfTreatment ... />
</initialACR>Initial cure rate
→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ
<CQ
value=double
/>Chloroquine
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP
<SP
value=double
/>Sulphadoxine-pyrimethamine
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ
<AQ
value=double
/>Amodiaquine
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ
<SPAQ
value=double
/>Sulphadoxine-pyrimethamine/Amodiaquine
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT
<ACT
value=double
/>Artemisinine combination therapy
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN
<QN
value=double
/>Quinine
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment
<selfTreatment
value=double
/>Probability of self-treatment
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → compliance
<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
| <selfTreatment ... />
</compliance>Adherence to treatment
→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective
<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
| <selfTreatment ... />
</nonCompliersEffective>Effectiveness of treatment of non compliers
→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1
<pSeekOfficialCareUncomplicated1
value=double
/>Probability that a patient with newly incident uncomplicated disease seeks official care
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated
<pSelfTreatUncomplicated
value=double
/>Probability that a patient with uncomplicated disease self-treats
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2
<pSeekOfficialCareUncomplicated2
value=double
/>Probability that a patient with recurrence of uncomplicated disease seeks official care
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere
<pSeekOfficialCareSevere
value=double
/>Probability that a patient with severe disease seeks official care
value=doubleTODO
→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient
<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>List of age specific probabilities of sequelae in inpatients.
Note: previously these ranges were silently remapped. To prevent unexpected differences, there must be two groups, with maxAgeYrs bounds 5 and 99 respectively.
→ scenario → healthSystem → ImmediateOutcomes → 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; when multiple values are given for a single timestep they are averaged.
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 → VectorAvailability
<VectorAvailability
[ maxAge=double ]
[ minAge=double ]
coverage=double
/>Description of a mosquito detterent 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.
→ scenario → healthSystem
<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| | <EventScheduler ... />
| | <ImmediateOutcomes ... />
| <CFR ... />
</healthSystem>Generic description of health system, used to specify the default or a replacement-as-intervention.
Contains a sub-element describing the particular health-system in use. Health system data is here defined as data used to decide on a treatment strategy, given a case requiring treatment.
<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 ... /> )+
</vector>Parameters for the vector transmission model.
→ scenario → entoData → vector → anopheles
<anopheles
mosquito=string
propInfected=double
propInfectious=double
>
IN THIS ORDER:
| <eir ... />
| <mosq ... />
| ( <nonHumanHosts ... /> )*
</anopheles>mosquito=stringpropInfected=doubleUnits: Proportion Min: 0 Max: 1
Initial guess of the proportion of mosquitoes which are infected, o: O_v(t) = o*N_v(t). Only used as a starting value.
propInfectious=doubleUnits: Proportion Min: 0 Max: 1
Initial guess of the proportion of mosquitoes which are infectious, s: S_v(t) = s*N_v(t). Used as a starting value and then fit.
→ scenario → entoData → vector → anopheles → eir
<eir
a0=double
a1=double
b1=double
a2=double
b2=double
EIRRotateAngle=double
/>Description of target entomological inoculation rate, used to calculate the vector emergence rate. An EIR array is generated from the exponent of the inverse discrete fourier transform of these parameters.
a0=doublea1=doubleb1=doublea2=doubleb2=doubleEIRRotateAngle=double→ 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
name=string
mosqEntoAvailability=double
mosqProbBiting=double
mosqProbFindRestSite=double
mosqProbResting=double
/>Non human host parameters, per type of host (must match up with non-species-specific parameters).
name=stringmosqEntoAvailability=doublemosqProbBiting=doublemosqProbFindRestSite=doublemosqProbResting=double<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>Drug model parameters
→ scenario → drugDescription → drug
<drug
abbrev=string
>
IN THIS ORDER:
| <PD ... />
| <PK ... />
</drug>Sequence of drug descriptions forming a library of drug parameters.
abbrev=string→ scenario → drugDescription → drug → PD
<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>→ scenario → drugDescription → drug → PD → allele
<allele
name=string
>
IN THIS ORDER:
| <initial_frequency ... />
| <max_killing_rate ... />
| <IC50 ... />
| <slope ... />
</allele>PD parameters per allele, plus initial frequency of each allele.
Note: we assume a one-to-one correspondance of drugs to loci, hence each drug has an independent set of alleles here.
name=string→ scenario → drugDescription → drug → PD → allele → initial_frequency
<initial_frequency>
double
</initial_frequency>Frequency, relative to the total frequency of all alleles for this drug/locus.
→ scenario → drugDescription → drug → PD → allele → max_killing_rate
<max_killing_rate>
double
</max_killing_rate>k1 — Maximal parasite killing rate.
→ scenario → drugDescription → drug → PD → allele → IC50
<IC50>
double
</IC50>Half maximal effect concentration.
→ scenario → drugDescription → drug → PD → allele → slope
<slope>
double
</slope>n — Slope of the concentration effect curve
→ scenario → drugDescription → drug → PK
<PK>
IN THIS ORDER:
| <negligible_concentration ... />
| <half_life ... />
| <vol_dist ... />
</PK>→ scenario → drugDescription → drug → PK → negligible_concentration
<negligible_concentration>
double
</negligible_concentration>Concentration below which drug's effects are deemed negligible and can be removed from simulation.
→ scenario → drugDescription → drug → PK → half_life
<half_life>
double
</half_life>Used to calculate elimintation rate (which is: ln(2) / half_life).
→ scenario → drugDescription → drug → PK → vol_dist
<vol_dist>
double
</vol_dist>Volume of Distribution
<model>
IN THIS ORDER:
| <ModelOptions ... />
| <clinical ... />
| <parameters ... />
</model>Encapsulation of all parameters which describe the model according to which fitting is done.
→ scenario → model → ModelOptions
<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>All model options (bug fixes, choices between models, etc.).
The list of recognised options can be found in the code at: include/util/ModelOptions.hpp and should also be in the wiki.
<clinical
healthSystemMemory=int
/>Description of clinical parameters.
This is related to the health-system description, but contains data which can't be changed as part of an intervention and is not restricted to treatment.
healthSystemMemory=intUnits: Time steps Min: 1 Max: 100
Follow-up period during which a recurrence is considered to be a treatment failure
→ scenario → model → 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 → model → 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.