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Diggory Hardy edited this page Jan 15, 2015 · 7 revisions

Generated schema 8 documentation

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

<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>

Documentation (element)

Description of scenario

Attributes

schemaVersion

schemaVersion=int

Version of xml schema. If not equal to the current version an error is thrown. Use SchemaTranslator to update xml files.

analysisNo

analysisNo=int

Units: Number Min: 1 Max: 100000000

Unique identifier of scenario

maximumAgeYrs

maximumAgeYrs=double

Units: Number Min: 0 Max: 100

Maximum age of simulated humans

name

name=string

Units: string

Name of intervention

popSize

popSize=int

Units: Count Min: 1 Max: 100000

Population size

simulationDuration

simulationDuration=int

Units: Time steps Min: 1 Max: 36500

Duration of main simulation

modelVersion

modelVersion=int

Units: Code Min: 0 Max: 100000000

Model Version

wuID

wuID=int

Units: Number Min: 1 Max: 100000000

Work unit ID. Only used to validate checkpointing, to prevent checkpoint cheats.

assimMode

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

mode=("2" or "3" or "4")

Units: Code

Transmission simulation mode

demography

scenariodemography

<demography
    name=string
  [ growthRate=double ]
  >
IN THIS ORDER:
|   <ageGroup ... /> 
</demography>

Documentation (element)

Description of demography

Documentation (type)

Description of demography

Attributes

name

name=string

Units: string

Name of demography data

growthRate

growthRate=double

Units: Number Min: 0 Max: 0

Growth rate of human population.

ageGroup

scenariodemographyageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

Documentation (element)

List of age groups included in demography

Documentation (type)

List of age groups included in demography or surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

scenariodemographyageGroupgroup

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

scenariomonitoring

<monitoring
    name=string
  >
IN THIS ORDER:
|   <surveys ... /> 
|   <ageGroup ... /> 
</monitoring>

Documentation (element)

Description of surveys

Documentation (type)

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

surveys

scenariomonitoringsurveys

<surveys
    detectionLimit=double
    summaryOption=int
  >
IN THIS ORDER:
|   <surveyTime ... /> 
</surveys>

Documentation (element)

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

summaryOption

summaryOption=int

Units: Code

Requested output variables

surveyTime

scenariomonitoringsurveyssurveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Survey time

ageGroup

scenariomonitoringageGroup

<ageGroup
    lowerbound=double
  >
IN THIS ORDER:
| ( <group ... /> )+
</ageGroup>

Documentation (element)

List of age groups included in demography or surveys

Documentation (type)

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

scenariomonitoringageGroupgroup

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

scenariointerventions

<interventions
    name=string
  >
IN THIS ORDER:
| ( <vaccineDescription ... /> ){0,3}
| [ <iptiDescription ... /> ]
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <continuous ... /> ]
| [ <timed ... /> ]
</interventions>

Documentation (element)

List of interventions

Documentation (type)

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

vaccineDescription

scenariointerventionsvaccineDescription

<vaccineDescription
    vaccineType=int
  >
IN THIS ORDER:
|   <halfLifeYrs ... /> 
|   <efficacyB ... /> 
| ( <initialEfficacy ... /> )+
</vaccineDescription>

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

scenariointerventionsvaccineDescriptionhalfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

scenariointerventionsvaccineDescriptionefficacyB

<efficacyB
    value=double
  />

Documentation (element)

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

scenariointerventionsvaccineDescriptioninitialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

scenariointerventionsiptiDescription

<iptiDescription
    iptiEffect=int
  >
IN THIS ORDER:
| ( <infGenotype ... /> )+
</iptiDescription>

Attributes

iptiEffect

iptiEffect=int

infGenotype

scenariointerventionsiptiDescriptioninfGenotype

<infGenotype
    name=string
    freq=double
    ACR=double
    proph=int
    tolPeriod=int
    atten=int
  />

Attributes

name

name=string

Units: string

Name of age specific intervention

freq

freq=double

ACR

ACR=double

proph

proph=int

tolPeriod

tolPeriod=int

atten

atten=int

ITNDescription

scenariointerventionsITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
| ( <anopheles ... /> )+
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

anopheles

scenariointerventionsITNDescriptionanopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</anopheles>

Attributes

mosquito

mosquito=string

deterrency

scenariointerventionsITNDescriptionanophelesdeterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

One minus this multiplies the host's availability (before decay).

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

preprandialKillingEffect

scenariointerventionsITNDescriptionanophelespreprandialKillingEffect

<preprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

One minus this multiplies the survival rate of mosquitoes attempting to bite a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

postprandialKillingEffect

scenariointerventionsITNDescriptionanophelespostprandialKillingEffect

<postprandialKillingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

One minus this multiplies the survival rate of mosquitoes attempting to escape after biting a host.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

IRSDescription

scenariointerventionsIRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
| ( <anopheles ... /> )+
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

anopheles

scenariointerventionsIRSDescriptionanopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</anopheles>

Attributes

mosquito

mosquito=string

deterrency

scenariointerventionsIRSDescriptionanophelesdeterrency

<deterrency
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

One minus this multiplies the host's availability.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

killingEffect

scenariointerventionsIRSDescriptionanopheleskillingEffect

<killingEffect
    initial=double
    halflife=double
  [ Weibullk=double ]
  />

Documentation (element)

One minus this multiplies the survival rate of resting mosquitoes.

Documentation (type)

Specification of a proportion with Weibull or exponential decay.

Attributes

initial

initial=double

Units: None Min: 0 Max: 1

The value before any decay.

halflife

halflife=double

Units: Years Min: 0

Half-life in years (more generally, halflife/ln(2) is lambda from the Weibull distribution).

Weibullk

Weibullk=double

Min: 0

The parameter k of the Weibull distribution. If missing, 1.0 is used (equivalent to exponential decay).

continuous

scenariointerventionscontinuous

<continuous>
IN THIS ORDER:
| ( <vaccine ... /> )*
| ( <ITN ... /> )*
| ( <ipti ... /> )*
</continuous>

vaccine

scenariointerventionscontinuousvaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

List of age groups for vaccination

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

scenariointerventionscontinuousITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Description of ITN deployment in the community

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

scenariointerventionscontinuousipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

List of age groups for IPTi distribution

Attributes

targetAgeYrs

targetAgeYrs=double

Units: Years Min: 0 Max: 100

Target age of intervention

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

timed

scenariointerventionstimed

<timed>
IN THIS ORDER:
| ( <intervention ... /> )+
</timed>

Documentation (element)

List of timed interventions

Documentation (type)

List of timed interventions

intervention

scenariointerventionstimedintervention

<intervention
    time=int
  >
IN THIS ORDER:
| [ <changeHS ... /> ]
| [ <changeEIR ... /> ]
| [ <MDA ... /> ]
| [ <vaccinate ... /> ]
| [ <ITN ... /> ]
| [ <IRS ... /> ]
| [ <ipti ... /> ]
| [ <larviciding ... /> ]
</intervention>

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

scenariointerventionstimedinterventionchangeHS

<changeHS
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

drugRegimen

scenariohealthSystemdrugRegimen

<drugRegimen
    firstLine=string
    secondLine=string
    inpatient=string
  />

Documentation (element)

Description of drug regimen

Attributes

firstLine

firstLine=string

Units: Drug code

Code for first line drug

secondLine

secondLine=string

Units: Drug code

Code for second line drug

inpatient

inpatient=string

Units: Drug code

Code for drug used for treating inpatients

initialACR

scenariohealthSysteminitialACR

<initialACR>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</initialACR>

Documentation (element)

Initial cure rate

CQ

scenariohealthSysteminitialACRCQ

<CQ
    value=double
  />

Documentation (element)

Chloroquine

Attributes

value

value=double

TODO

SP

scenariohealthSysteminitialACRSP

<SP
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

scenariohealthSysteminitialACRAQ

<AQ
    value=double
  />

Documentation (element)

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

scenariohealthSysteminitialACRSPAQ

<SPAQ
    value=double
  />

Documentation (element)

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

scenariohealthSysteminitialACRACT

<ACT
    value=double
  />

Documentation (element)

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

scenariohealthSysteminitialACRQN

<QN
    value=double
  />

Documentation (element)

Quinine

Attributes

value

value=double

TODO

selfTreatment

scenariohealthSysteminitialACRselfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

scenariohealthSystemcompliance

<compliance>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</compliance>

Documentation (element)

Adherence to treatment

nonCompliersEffective

scenariohealthSystemnonCompliersEffective

<nonCompliersEffective>
IN THIS ORDER:
| [ <CQ ... /> ]
| [ <SP ... /> ]
| [ <AQ ... /> ]
| [ <SPAQ ... /> ]
| [ <ACT ... /> ]
| [ <QN ... /> ]
|   <selfTreatment ... /> 
</nonCompliersEffective>

Documentation (element)

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

scenariohealthSystempSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Probability that a patient with newly incident uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

scenariohealthSystempSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

scenariohealthSystempSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Probability that a patient with recurrence of uncomplicated disease seeks official care

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

scenariohealthSystempSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

scenariohealthSystempSequelaeInpatient

<pSequelaeInpatient>
IN THIS ORDER:
| ( <item ... /> )+
</pSequelaeInpatient>

Documentation (element)

List of age specific probabilities of sequelae in inpatients

item

scenariohealthSystempSequelaeInpatientitem

<item
    maxAgeYrs=double
  />

Attributes

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

scenariohealthSystemCFR

<CFR>
IN THIS ORDER:
| ( <group ... /> )+
</CFR>

group

scenariohealthSystemCFRgroup

<group
    cfr=double
    lowerbound=double
  />

Attributes

cfr

cfr=double

Units: Proportion Min: 0 Max: 1

Case fatality rate

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

changeEIR

scenariointerventionstimedinterventionchangeEIR

<changeEIR
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</changeEIR>

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

EIRDaily

scenarioentoDatanonVectorEIRDaily

<EIRDaily
  [ origin=string ]
  >
    double
</EIRDaily>

Documentation (type)

Value of daily EIR

Attributes

origin

origin=string

MDA

scenariointerventionstimedinterventionMDA

<MDA
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Description of mass drug deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

vaccinate

scenariointerventionstimedinterventionvaccinate

<vaccinate
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Description of vaccine deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ITN

scenariointerventionstimedinterventionITN

<ITN
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Description of ITN deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

IRS

scenariointerventionstimedinterventionIRS

<IRS
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

Description of IRS deployment in the community

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

ipti

scenariointerventionstimedinterventionipti

<ipti
  [ maxAge=double ]
  [ minAge=double ]
    coverage=double
  />

Documentation (element)

List of age groups for IPTi distribution

Attributes

maxAge

maxAge=double

Units: Years Min: 0 Max: 100

Maximum age of eligible individuals (defaults to 100)

minAge

minAge=double

Units: Years Min: 0 Max: 100

Minimum age of eligible individuals (defaults to 0)

coverage

coverage=double

Units: Proportion Min: 0 Max: 1

Coverage of intervention

larviciding

scenariointerventionstimedinterventionlarviciding

<larviciding>
IN THIS ORDER:
| ( <anopheles ... /> )+
</larviciding>

Documentation (element)

Simple larviciding intervention description.

anopheles

scenariointerventionstimedinterventionlarvicidinganopheles

<anopheles
    mosquito=string
    effectiveness=double
    duration=int
  />

Attributes

mosquito

mosquito=string

effectiveness

effectiveness=double

Units: none Min: 0 Max: 1

Proportion to reduce emergence rates by.

duration

duration=int

Units: days Min: 0 Max: inf

Number of days for which the intervention is active.

caseManagements

scenariocaseManagements

<caseManagements
    name=string
    reportingPeriodMemory=int
  >
IN THIS ORDER:
| ( <caseManagement ... /> )+
</caseManagements>

Documentation (element)

List of case managment interventions

Documentation (type)

List of age-specific case managment descriptions

Attributes

name

name=string

Units: string

Name of age specific intervention

reportingPeriodMemory

reportingPeriodMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

caseManagement

scenariocaseManagementscaseManagement

<caseManagement
    maxAgeYrs=decimal
  >
IN THIS ORDER:
|   <uc1 ... /> 
|   <uc2 ... /> 
|   <sev ... /> 
|   <nmfP ... /> 
|   <nmfNP ... /> 
|   <decisions ... /> 
</caseManagement>

Documentation (element)

Age-specific case management description, describes entry-points and decisions, with entry-point-specific decision probabilities

Attributes

maxAgeYrs

maxAgeYrs=decimal

Units: Years Min: 0 Max: 100

Upper bound of age group

uc1

scenariocaseManagementscaseManagementuc1

<uc1>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc1>

endPoint

scenariocaseManagementscaseManagementuc1endPoint

<endPoint
    decision=int
    p=double
  />

Attributes

decision

decision=int

Foreign key reference to outcome node

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of outcome

uc2

scenariocaseManagementscaseManagementuc2

<uc2>
IN THIS ORDER:
| ( <endPoint ... /> )+
</uc2>

sev

scenariocaseManagementscaseManagementsev

<sev>
IN THIS ORDER:
| ( <endPoint ... /> )+
</sev>

nmfP

scenariocaseManagementscaseManagementnmfP

<nmfP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfP>

nmfNP

scenariocaseManagementscaseManagementnmfNP

<nmfNP>
IN THIS ORDER:
| ( <endPoint ... /> )+
</nmfNP>

decisions

scenariocaseManagementscaseManagementdecisions

<decisions>
IN THIS ORDER:
| ( <decision ... /> )+
</decisions>

decision

scenariocaseManagementscaseManagementdecisionsdecision

<decision
    id=int
  >
IN THIS ORDER:
| ( <medicate ... /> )+
</decision>

Documentation (element)

describes treatment decisions, a list of medicate descisions.

Attributes

id

id=int

Units: Number

Key of decision

medicate

scenariocaseManagementscaseManagementdecisionsdecisionmedicate

<medicate
    name=string
    qty=int
    time=int
  />

Attributes

name

name=string

Units: string

Name of drug compound

qty

qty=int

Units: Number

Quantity of drug compound

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

healthSystem

scenariohealthSystem

<healthSystem
    name=string
    healthSystemMemory=int
  >
IN THIS ORDER:
|   <drugRegimen ... /> 
|   <initialACR ... /> 
|   <compliance ... /> 
|   <nonCompliersEffective ... /> 
|   <pSeekOfficialCareUncomplicated1 ... /> 
|   <pSelfTreatUncomplicated ... /> 
|   <pSeekOfficialCareUncomplicated2 ... /> 
|   <pSeekOfficialCareSevere ... /> 
|   <pSequelaeInpatient ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (element)

Description of health system

Documentation (type)

Description of health system

Attributes

name

name=string

Units: string

Name of health system

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

Follow-up period during which a recurrence is considered to be a treatment failure

entoData

scenarioentoData

<entoData
    name=string
  >
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <nonVector ... /> 
| |   <vector ... /> 
</entoData>

Documentation (element)

Description of entomological data

Documentation (type)

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

scenarioentoDatanonVector

<nonVector
    eipDuration=int
  >
IN THIS ORDER:
| ( <EIRDaily ... /> )+
</nonVector>

Documentation (type)

Parameters for the non-vector transmission model.

Attributes

eipDuration

eipDuration=int

The duration of sporogony in days

vector

scenarioentoDatavector

<vector>
IN THIS ORDER:
| ( <anopheles ... /> )+
| ( <nonHumanHosts ... /> )*
</vector>

Documentation (element)

Parameters for the vector transmission model.

anopheles

scenarioentoDatavectoranopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <eir ... /> ]
| [ <emergence ... /> ]
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

eir

scenarioentoDatavectoranopheleseir

<eir
    a0=double
    a1=double
    a2=double
    b1=double
    b2=double
    EIRRotateAngle=double
  />

Documentation (element)

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.

Attributes

a0

a0=double

a1

a1=double

a2

a2=double

b1

b1=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

emergence

scenarioentoDatavectoranophelesemergence

<emergence>
IN THIS ORDER:
|   <emergenceRate ... /> 
|   <kappa ... /> 
|   <N_v ... /> 
|   <O_v ... /> 
|   <S_v ... /> 
</emergence>

Documentation (element)

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.

emergenceRate

scenarioentoDatavectoranophelesemergenceemergenceRate

<emergenceRate>
IN THIS ORDER:
| ( <item ... /> )+
</emergenceRate>

Documentation (element)

Mosquitoes emerging per day of the year, per human.

item

scenarioentoDatavectoranophelesemergenceemergenceRateitem

<item>
    double
</item>

kappa

scenarioentoDatavectoranophelesemergencekappa

<kappa>
IN THIS ORDER:
| ( <item ... /> )+
</kappa>

Documentation (element)

Human infectivity (probability of infection of a mosquito biting a human) over last mosqRestDuration+extrinsicIncubationPeriod days.

N_v

scenarioentoDatavectoranophelesemergenceN_v

<N_v>
IN THIS ORDER:
| ( <item ... /> )+
</N_v>

Documentation (element)

Total population of mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

O_v

scenarioentoDatavectoranophelesemergenceO_v

<O_v>
IN THIS ORDER:
| ( <item ... /> )+
</O_v>

Documentation (element)

Population of infected mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

S_v

scenarioentoDatavectoranophelesemergenceS_v

<S_v>
IN THIS ORDER:
| ( <item ... /> )+
</S_v>

Documentation (element)

Population of infectious mosquitoes over the last mosqRestDuration+extrinsicIncubationPeriod days, per human.

mosq

scenarioentoDatavectoranophelesmosq

<mosq
    mosqRestDuration=int
    extrinsicIncubationPeriod=int
    mosqSeekingDeathRate=double
    mosqSeekingDuration=double
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
    mosqProbOvipositing=double
  />

Documentation (element)

Vector species

Attributes

mosqRestDuration

mosqRestDuration=int

extrinsicIncubationPeriod

extrinsicIncubationPeriod=int

mosqSeekingDeathRate

mosqSeekingDeathRate=double

mosqSeekingDuration

mosqSeekingDuration=double

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

mosqProbOvipositing

mosqProbOvipositing=double

nonHumanHosts

scenarioentoDatavectoranophelesnonHumanHosts

<nonHumanHosts
    mosqEntoAvailability=double
    mosqProbBiting=double
    mosqProbFindRestSite=double
    mosqProbResting=double
  />

Documentation (element)

Non human host parameters, per type of host (must match up with non-species-specific parameters).

Attributes

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

nonHumanHosts

scenarioentoDatavectornonHumanHosts

<nonHumanHosts
  [ name=string ]
    populationSize=int
  />

Documentation (element)

Populations of non-human hosts (must also have species-specific parameters).

Attributes

name

name=string

populationSize

populationSize=int

parameters

scenarioparameters

<parameters
    interval=int
    iseed=int
    delta=double
    latentp=int
  >
IN THIS ORDER:
| ( <parameter ... /> )+
</parameters>

Documentation (element)

Parameters for mathematical model

Documentation (type)

Parameter vector

Attributes

interval

interval=int

Units: Days

Simulation step

iseed

iseed=int

Units: Number

Seed for RNG

delta

delta=double

Units: ? Redundant

this no longer seems to be used

latentp

latentp=int

Units: Time steps Min: 0 Max: 20

pre-erythrocytic latent period, in time steps

parameter

scenarioparametersparameter

<parameter
    name=string
    number=int
    value=double
    include=boolean
  />

Attributes

name

name=string

Units: string

Name of parameter

number

number=int

Units: Number Min: 1 Max: 100

Reference number of input parameter

value

value=double

Units: Number Min: 0

Parameter value

include

include=boolean

Units: Number Min: 0 Max: 1

True if parameter is to be sampled in optimization runs. Not used in simulator app.

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