Schema 16 documentation

Generated from: scenario_16.xsd.

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
    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>

Documentation (element)

Units: List of elements

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

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

→ scenario → demography

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

Documentation (element)

Units: List of elements

Description of demography

Documentation (type)

Units: List of elements

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

→ scenario → demography → ageGroup

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

Documentation (element)

Units: List of elements

List of age groups included in demography

Documentation (type)

Units: List of elements

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

→ scenario → demography → ageGroup → group

<group
    poppercent=double
    upperbound=double
  />

Attributes

poppercent

poppercent=double

upperbound

upperbound=double

monitoring

→ scenario → monitoring

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

Documentation (element)

Units: List of elements

Description of surveys

Documentation (type)

Units: List of elements

Description of surveys

Attributes

name

name=string

Units: string

Name of monitoring data

SurveyOptions

→ scenario → monitoring → SurveyOptions

<SurveyOptions>
IN THIS ORDER:
| ( <option ... /> )*
</SurveyOptions>

Documentation (element)

List of all active survey options. See include/Survey.h for a list of supported outputs. Should also be on the wiki.

option

→ scenario → monitoring → SurveyOptions → option

<option
    name=string
    value=boolean
  />

Attributes

name

name=string

Option name. Must be one of a strictly defined set. Options are not required to be listed if their default value is desired.

value

value=boolean

Option value (true/false). Each option has a default value (may be true or false) which is used if the option is not listed.

surveys

→ scenario → monitoring → surveys

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

Documentation (element)

Units: List of elements

List of survey times

Attributes

detectionLimit

detectionLimit=double

Units: parasites/micolitre Min: 0 Max: 1000

Detection limit for parasitemia

surveyTime

→ scenario → monitoring → surveys → surveyTime

<surveyTime>
    int
</surveyTime>

Documentation (element)

Units: Number Min: 0

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.

ageGroup

→ scenario → monitoring → ageGroup

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

Documentation (element)

Units: List of elements

List of age groups included in demography or surveys

Documentation (type)

Units: List of elements

List of age groups included in surveys

Attributes

lowerbound

lowerbound=double

Units: Years Min: 0 Max: 100

Lower bound of age group

group

→ scenario → monitoring → ageGroup → group

<group
    upperbound=double
  />

Attributes

upperbound

upperbound=double

interventions

→ scenario → interventions

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

Documentation (element)

Units: List of elements

List of interventions

Documentation (type)

Units: List of elements

List of interventions

Attributes

name

name=string

Units: string

Name of age specific intervention

MDADescription

→ scenario → interventions → MDADescription

<MDADescription>
IN THIS ORDER:
| ( <medicate ... /> )*
</MDADescription>

Documentation (element)

Units: List of medicate elements

Description of drug dose(s) used in a mass-drug-administration intervention.

medicate

→ scenario → interventions → MDADescription → medicate

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

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=double

Units: hours Min: 0

Number of hours past start of timestep the drug is medicated at (usually 0).

vaccineDescription

→ scenario → interventions → vaccineDescription

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

Attributes

vaccineType

vaccineType=int

Units: Code

Type of vaccine

halfLifeYrs

→ scenario → interventions → vaccineDescription → halfLifeYrs

<halfLifeYrs
    value=double
  />

Documentation (element)

Units: Years Min: 0 Max: 100

Half life of drug effect

Attributes

value

value=double

TODO

efficacyB

→ scenario → interventions → vaccineDescription → efficacyB

<efficacyB
    value=double
  />

Documentation (element)

Units: Positive real Min: 0.001 Max: 1.00E+06

Measure of variation in vaccine efficacy

Attributes

value

value=double

TODO

initialEfficacy

→ scenario → interventions → vaccineDescription → initialEfficacy

<initialEfficacy
    value=double
  />

Attributes

value

value=double

TODO

iptiDescription

→ scenario → interventions → iptiDescription

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

Attributes

iptiEffect

iptiEffect=int

infGenotype

→ scenario → interventions → iptiDescription → infGenotype

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

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=double

anopheles

→ scenario → interventions → anopheles

<anopheles
    mosquito=string
  >
IN THIS ORDER:
| [ <ITNDescription ... /> ]
| [ <IRSDescription ... /> ]
| [ <VADescription ... /> ]
</anopheles>

Attributes

mosquito

mosquito=string

ITNDescription

→ scenario → interventions → anopheles → ITNDescription

<ITNDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <preprandialKillingEffect ... /> 
|   <postprandialKillingEffect ... /> 
</ITNDescription>

Attributes

name

name=string

Units: string

Name of Insecticide Treated Net intervention

deterrency

→ scenario → interventions → anopheles → ITNDescription → deterrency

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

Documentation (element)

Units: None Min: 0 Max: 1

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

→ scenario → interventions → anopheles → ITNDescription → preprandialKillingEffect

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

Documentation (element)

Units: None Min: 0 Max: 1

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

→ scenario → interventions → anopheles → ITNDescription → postprandialKillingEffect

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

Documentation (element)

Units: None Min: 0 Max: 1

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

→ scenario → interventions → anopheles → IRSDescription

<IRSDescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
|   <killingEffect ... /> 
</IRSDescription>

Attributes

name

name=string

Units: string

Name of Indoor Residual Spraying intervention

deterrency

→ scenario → interventions → anopheles → IRSDescription → deterrency

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

Documentation (element)

Units: None Min: 0 Max: 1

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

→ scenario → interventions → anopheles → IRSDescription → killingEffect

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

Documentation (element)

Units: None Min: 0 Max: 1

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).

VADescription

→ scenario → interventions → anopheles → VADescription

<VADescription
    name=string
  >
IN THIS ORDER:
|   <deterrency ... /> 
</VADescription>

Attributes

name

name=string

Units: string

Name of mosquito deterrency intervention

deterrency

→ scenario → interventions → anopheles → VADescription → deterrency

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

Documentation (element)

Units: None Min: 0 Max: 1

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).

continuous

→ scenario → interventions → continuous

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

vaccine

→ scenario → interventions → continuous → vaccine

<vaccine
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

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

→ scenario → interventions → continuous → ITN

<ITN
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

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

→ scenario → interventions → continuous → ipti

<ipti
    targetAgeYrs=double
    coverage=double
  />

Documentation (element)

Units: List of elements

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

→ scenario → interventions → timed

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

Documentation (element)

Units: List of elements

List of timed interventions

Documentation (type)

Units: List of elements

List of timed interventions

intervention

→ scenario → interventions → timed → intervention

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

Attributes

time

time=int

Units: Number Min: 1 Max: 10000

Time step of intervention

changeHS

→ scenario → interventions → timed → intervention → changeHS

<changeHS>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</changeHS>

Documentation (type)

Units: List of elements

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.

EventScheduler

→ scenario → healthSystem → EventScheduler

<EventScheduler>
IN THIS ORDER:
|   <CaseManagementTree ... /> 
|   <ClinicalOutcomes ... /> 
</EventScheduler>

CaseManagementTree

→ scenario → healthSystem → EventScheduler → CaseManagementTree

<CaseManagementTree
    mask=int
  >
IN THIS ORDER:
| ( <CM_pBranchSet ... /> )*
| ( <CM_leaf ... /> )+
</CaseManagementTree>

Documentation (element)

Units: List of elements

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).

Attributes

mask

mask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask decision ids before selecting a branch/leaf.

CM_pBranchSet

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_pBranchSet

<CM_pBranchSet
    ID=int
  >
IN THIS ORDER:
| ( <CM_pBranch ... /> )+
</CM_pBranchSet>

Documentation (element)

A probability branch node: contains a list of outcome nodes along with probabilities, which link to another probability/test branch or leaf node.

Attributes

ID

ID=int

Units: ID

Decision identifier.

CM_pBranch

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_pBranchSet → CM_pBranch

<CM_pBranch
    outcome=int
    p=double
  />

Attributes

outcome

outcome=int

ID of next probability/test branch or leaf node.

p

p=double

Units: Proportion Min: 0 Max: 1

Probability of this outcome

CM_leaf

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_leaf

<CM_leaf
    ID=int
  >
IN THIS ORDER:
| ( <medicate ... /> )*
</CM_leaf>

Documentation (element)

End points of the case management tree, listing treatments.

Attributes

ID

ID=int

Units: ID

Decision identifier.

medicate

→ scenario → healthSystem → EventScheduler → CaseManagementTree → CM_leaf → medicate

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

Attributes

name

name=string

Units: string

Abbreviated name of drug compound

qty

qty=double

Units: mg

Quantity of drug compound

time

time=double

Units: hours Min: 0

Number of hours past start of timestep the drug is medicated at (usually 0).

ClinicalOutcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes

<ClinicalOutcomes
    severeMask=int
  >
IN THIS ORDER:
| ( <outcomes ... /> )+
</ClinicalOutcomes>

Documentation (element)

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.

Attributes

severeMask

severeMask=int

Units: None Min: 0 Max: 0xFFFFFFFF

Value used to mask the final ID from the case-management tree before looking up values here.

outcomes

→ scenario → healthSystem → EventScheduler → ClinicalOutcomes → outcomes

<outcomes
    ID=int
    pDeath=double
    hospitalizationDaysDeath=int
    hospitalizationDaysRecover=int
  />

Documentation (element)

Parameters for a path through the case-management tree (i.e. table row).

Attributes

ID

ID=int

pDeath

pDeath=double

Units: 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

hospitalizationDaysDeath=int

Units: 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

hospitalizationDaysRecover=int

Units: 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.)

ImmediateOutcomes

→ scenario → healthSystem → ImmediateOutcomes

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

Documentation (type)

Units: List of elements

Description of "immediate outcomes" health system: Tediosi et al case management model (Case management as described in AJTMH 75 (suppl 2) pp90-103).

Attributes

name

name=string

Units: string

Name of health system

drugRegimen

→ scenario → healthSystem → ImmediateOutcomes → drugRegimen

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

Documentation (element)

Units: List of elements

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

→ scenario → healthSystem → ImmediateOutcomes → initialACR

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

Documentation (element)

Units: Proportion Min: 0 Max: 1

Initial cure rate

CQ

→ scenario → healthSystem → ImmediateOutcomes → initialACR → CQ

<CQ
    value=double
  />

Documentation (element)

Units: List of elements

Chloroquine

Attributes

value

value=double

TODO

SP

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SP

<SP
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine

Attributes

value

value=double

TODO

AQ

→ scenario → healthSystem → ImmediateOutcomes → initialACR → AQ

<AQ
    value=double
  />

Documentation (element)

Units: List of elements

Amodiaquine

Attributes

value

value=double

TODO

SPAQ

→ scenario → healthSystem → ImmediateOutcomes → initialACR → SPAQ

<SPAQ
    value=double
  />

Documentation (element)

Units: List of elements

Sulphadoxine-pyrimethamine/Amodiaquine

Attributes

value

value=double

TODO

ACT

→ scenario → healthSystem → ImmediateOutcomes → initialACR → ACT

<ACT
    value=double
  />

Documentation (element)

Units: List of elements

Artemisinine combination therapy

Attributes

value

value=double

TODO

QN

→ scenario → healthSystem → ImmediateOutcomes → initialACR → QN

<QN
    value=double
  />

Documentation (element)

Units: List of elements

Quinine

Attributes

value

value=double

TODO

selfTreatment

→ scenario → healthSystem → ImmediateOutcomes → initialACR → selfTreatment

<selfTreatment
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability of self-treatment

Attributes

value

value=double

TODO

compliance

→ scenario → healthSystem → ImmediateOutcomes → compliance

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

Documentation (element)

Units: Proportion Min: 0 Max: 1

Adherence to treatment

nonCompliersEffective

→ scenario → healthSystem → ImmediateOutcomes → nonCompliersEffective

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

Documentation (element)

Units: Proportion Min: 0 Max: 1

Effectiveness of treatment of non compliers

pSeekOfficialCareUncomplicated1

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated1

<pSeekOfficialCareUncomplicated1
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

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

Attributes

value

value=double

TODO

pSelfTreatUncomplicated

→ scenario → healthSystem → ImmediateOutcomes → pSelfTreatUncomplicated

<pSelfTreatUncomplicated
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with uncomplicated disease self-treats

Attributes

value

value=double

TODO

pSeekOfficialCareUncomplicated2

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareUncomplicated2

<pSeekOfficialCareUncomplicated2
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

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

Attributes

value

value=double

TODO

pSeekOfficialCareSevere

→ scenario → healthSystem → ImmediateOutcomes → pSeekOfficialCareSevere

<pSeekOfficialCareSevere
    value=double
  />

Documentation (element)

Units: Proportion Min: 0 Max: 1

Probability that a patient with severe disease seeks official care

Attributes

value

value=double

TODO

pSequelaeInpatient

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient

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

Documentation (element)

Units: List of elements

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.

item

→ scenario → healthSystem → ImmediateOutcomes → pSequelaeInpatient → item

<item
    value=double
    maxAgeYrs=double
  />

Attributes

value

value=double

TODO

maxAgeYrs

maxAgeYrs=double

Units: Years Min: 0 Max: 100

Upper bound of age group

CFR

→ scenario → healthSystem → CFR

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

group

→ scenario → healthSystem → CFR → group

<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

→ scenario → interventions → timed → intervention → changeEIR

<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

→ scenario → entoData → nonVector → EIRDaily

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

Documentation (type)

Units: Innoculations per person per day

Value of daily EIR; when multiple values are given for a single timestep they are averaged.

Attributes

origin

origin=string

MDA

→ scenario → interventions → timed → intervention → MDA

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

Documentation (element)

Units: List of elements

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

→ scenario → interventions → timed → intervention → vaccinate

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

Documentation (element)

Units: List of elements

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

→ scenario → interventions → timed → intervention → ITN

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

Documentation (element)

Units: List of elements

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

→ scenario → interventions → timed → intervention → IRS

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

Documentation (element)

Units: List of elements

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

VectorAvailability

→ scenario → interventions → timed → intervention → VectorAvailability

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

Documentation (element)

Units: List of elements

Description of a mosquito detterent 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

→ scenario → interventions → timed → intervention → ipti

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

Documentation (element)

Units: List of elements

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

→ scenario → interventions → timed → intervention → larviciding

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

Documentation (element)

Simple larviciding intervention description.

anopheles

→ scenario → interventions → timed → intervention → larviciding → anopheles

<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.

healthSystem

→ scenario → healthSystem

<healthSystem>
IN THIS ORDER:
| EXACTLY ONE OF:
| |   <EventScheduler ... /> 
| |   <ImmediateOutcomes ... /> 
|   <CFR ... /> 
</healthSystem>

Documentation (type)

Units: List of elements

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

→ scenario → entoData

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

Documentation (element)

Units: List of elements

Description of entomological data

Documentation (type)

Units: List of elements

Data for entomodel

Attributes

name

name=string

Units: string

Name of entomology data

nonVector

→ scenario → entoData → nonVector

<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

→ scenario → entoData → vector

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

Documentation (element)

Parameters for the vector transmission model.

anopheles

→ scenario → entoData → vector → anopheles

<anopheles
    mosquito=string
    propInfected=double
    propInfectious=double
  >
IN THIS ORDER:
|   <eir ... /> 
|   <mosq ... /> 
| ( <nonHumanHosts ... /> )*
</anopheles>

Attributes

mosquito

mosquito=string

propInfected

propInfected=double

Units: 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

propInfectious=double

Units: 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.

eir

→ scenario → entoData → vector → anopheles → eir

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

Documentation (element)

Units: Innoculations per person per day

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.

Attributes

a0

a0=double

a1

a1=double

b1

b1=double

a2

a2=double

b2

b2=double

EIRRotateAngle

EIRRotateAngle=double

mosq

→ scenario → entoData → vector → anopheles → mosq

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

Documentation (element)

Units: List of elements

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

→ scenario → entoData → vector → anopheles → nonHumanHosts

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

Documentation (element)

Units: List of elements

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

Attributes

name

name=string

mosqEntoAvailability

mosqEntoAvailability=double

mosqProbBiting

mosqProbBiting=double

mosqProbFindRestSite

mosqProbFindRestSite=double

mosqProbResting

mosqProbResting=double

drugDescription

→ scenario → drugDescription

<drugDescription>
IN THIS ORDER:
| ( <drug ... /> )+
</drugDescription>

Documentation (element)

Units: List of elements

Drug model parameters

drug

→ scenario → drugDescription → drug

<drug
    abbrev=string
  >
IN THIS ORDER:
|   <PD ... /> 
|   <PK ... /> 
</drug>

Documentation (element)

Sequence of drug descriptions forming a library of drug parameters.

Attributes

abbrev

abbrev=string

PD

→ scenario → drugDescription → drug → PD

<PD>
IN THIS ORDER:
| ( <allele ... /> )+
</PD>

allele

→ scenario → drugDescription → drug → PD → allele

<allele
    name=string
  >
IN THIS ORDER:
|   <initial_frequency ... /> 
|   <max_killing_rate ... /> 
|   <IC50 ... /> 
|   <slope ... /> 
</allele>

Documentation (element)

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.

Attributes

name

name=string

initial_frequency

→ scenario → drugDescription → drug → PD → allele → initial_frequency

<initial_frequency>
    double
</initial_frequency>

Documentation (element)

Units: relative frequency Min: 0

Frequency, relative to the total frequency of all alleles for this drug/locus.

max_killing_rate

→ scenario → drugDescription → drug → PD → allele → max_killing_rate

<max_killing_rate>
    double
</max_killing_rate>

Documentation (element)

Units: 1/days Min: 0

k1 — Maximal parasite killing rate.

IC50

→ scenario → drugDescription → drug → PD → allele → IC50

<IC50>
    double
</IC50>

Documentation (element)

Units: mg/l Min: 0

Half maximal effect concentration.

slope

→ scenario → drugDescription → drug → PD → allele → slope

<slope>
    double
</slope>

Documentation (element)

Units: no units

n — Slope of the concentration effect curve

PK

→ scenario → drugDescription → drug → PK

<PK>
IN THIS ORDER:
|   <negligible_concentration ... /> 
|   <half_life ... /> 
|   <vol_dist ... /> 
</PK>

negligible_concentration

→ scenario → drugDescription → drug → PK → negligible_concentration

<negligible_concentration>
    double
</negligible_concentration>

Documentation (element)

Units: mg/l Min: 0

Concentration below which drug's effects are deemed negligible and can be removed from simulation.

half_life

→ scenario → drugDescription → drug → PK → half_life

<half_life>
    double
</half_life>

Documentation (element)

Units: days Min: 0

Used to calculate elimintation rate (which is: ln(2) / half_life).

vol_dist

→ scenario → drugDescription → drug → PK → vol_dist

<vol_dist>
    double
</vol_dist>

Documentation (element)

Units: l/kg Min: 0

Volume of Distribution

model

→ scenario → model

<model>
IN THIS ORDER:
|   <ModelOptions ... /> 
|   <clinical ... /> 
|   <parameters ... /> 
</model>

Documentation (element)

Encapsulation of all parameters which describe the model according to which fitting is done.

ModelOptions

→ scenario → model → ModelOptions

<ModelOptions>
IN THIS ORDER:
| ( <option ... /> )*
</ModelOptions>

Documentation (element)

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

→ scenario → model → clinical

<clinical
    healthSystemMemory=int
  />

Documentation (type)

Units: List of elements

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.

Attributes

healthSystemMemory

healthSystemMemory=int

Units: Time steps Min: 1 Max: 100

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

parameters

→ scenario → model → parameters

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

Documentation (element)

Units: List of elements

Parameters for mathematical model

Documentation (type)

Units: List of elements

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

→ scenario → model → parameters → parameter

<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.