ReportHIVInfection#

The HIV disease progression report (ReportHIVInfection.csv) provides information on each individual’s disease state at each time step, including age, gender, CD4 count, survival prognosis, ART status, and factors impacting transmission and acquisition.

Configuration#

To generate the report, the following parameters must be configured in the config.json file:

Parameter

Data type

Min

Max

Default

Description

Report_HIV_Infection

boolean

NA

NA

0

Set this to 1 to generate the report.

Report_HIV_Infection_Start_Year

float

1900

2200

1900

Simulation time in years to start collecting data.

Report_HIV_Infection_Stop_Year

float

1900

2200

2200

Simulation time in years to start collecting data.

{
    "Report_HIV_Infection": 1,
    "Report_HIV_Infection_Start_Year": 1940,
    "Report_HIV_Infection_Stop_Year": 2000
}

Output file data#

The output report will contain the following information.

Data columns#

Data channel

Data type

Description

Year

float

Simulation time in years, including fractions of years.

Node_ID

integer

The identification number of the node.

Id

integer

The unique identification number of the individual.

MCWeight

integer

Not currently supported. This column will always show a Monte Carlo weight of 1.

Age

float

The age of the individual in years, including fractions of years.

Gender

boolean

Identifies the individual’s gender: 0 is assigned to males, 1 is assigned to females.

getProbMaternalTransmission

float

The hypothetical probability of mother-to-child transmission (MTCT), if the individual were to give birth at the present time and not receive any interventions such as PMTCT or AntiretroviralTherapy. Not applicable for males or for females of non-childbearing age.

TimeSinceHIV

float

The number of days since the individual became infected. Note: If the individual was infected by an OutbreakIndividual intervention with the Incubation_Period_Override parameter set to 0, the infected date will be randomly set in the past (uniformly selected from the amount of time until death). TimeSinceHIV will count accordingly from the ‘historic’ infection date.

CD4count

float

The current CD4 count, regardless of when CD4 testing was performed.

PrognosisCompletedFraction

float

The proportion of the total untreated HIV survival time that has already been lived; only relevant when the individual is not on ART.

Prognosis

float

The remaining untreated survival time until AIDS-related death; only relevant when the individual is not on ART.

Stage

integer

The individual’s disease stage. Possible values are:

  • 0 = Uninfected

  • 1 = Untreated acute HIV infection

  • 2 = Untreated latent HIV infection

  • 3 = Untreated late/AIDS stage

  • 4 = On ART

ViralLoad

float

Not currently supported.

WHOStage

float

The individual’s WHO stage, linearly interpolated between integer values. Round down to obtain the integer value for the WHO clinical stage. Uninfected individuals will be assigned a value of -1.

Infectiousness

float

Describes the individual’s infectiousness, which depends on the disease stage and ART status, and includes effects of heterogeneous infectiousness.

ModAcquire

float

Multiplicative modifier on disease acquisition; will be set to 1 by default for HIV, but can be impacted by the IndividualImmunityChanger intervention or by setting Enable_Maternal_Protection to 1 in the config.json file.

ModTransmit

float

Multiplicative modifier on disease transmission; will be set to 1 by default for HIV, but can be impacted by the IndividualImmunityChanger intervention.

ModMortality

float

Multiplicative modifier on disease mortality; will be set to 1 by default for HIV, but can be impacted by the IndividualImmunityChanger intervention.

ArtStatus

integer

Describes the individual’s ART status. Possible values are:

  • 1 = The individual is not currently receiving ART.

  • 5 = The individual is on ART, but their viral load is not yet suppressed.

  • 6 = The individual is on ART, and their viral load is suppressed.

  • 7 = The individual is on ART, but is experiencing virological failure.

  • 8 = The individual has had poor adherence to ART.

  • 9 = The individual has dropped out of ART.

InfectivitySuppression

float

The multiplier acting on Base_Infectivity to determine the per-act transmission probability of a virally suppressed HIV-positive individual. This can be reduced from ART_Viral_Suppression_Multiplier due to ARTBasic’s Days_To_Achieve_Viral_Suppression.

DurationOnArt

integer

The number of days since the individual most recently started ART. Set to -1 if they are not on ART.

ProbMaternalTransmissionModifier

float

The better maternal transmission multiplier provided by PMTCT, or zero.

OnArtQuery

boolean

Describes whether the individual is on ART or not: 0 if individual is not on ART, and 1 if they are.

CoInfectiveTransmissionFactor

float

If the person has an STI co-infection (set by the ModifyStiCoInfectionStatus intervention), then this will be the value from the parameter STI_Coinfection_Transmission_Multiplier. Otherwise, the value will be 1.

CoInfectiveAcquisitionFactor

float

If the person has an STI co-infection (set by the ModifyStiCoInfectionStatus intervention), then this will be the value from the parameter STI_Coinfection_Acquisition_Multiplier. Otherwise, the value will be 1.

DebutAge

float

The age of sexual debut in days.

IsCircumcised

boolean

Indicates whether or not the individual is circumcised (only applicable to males): 0 for not circumcised (and females), 1 for circumcised.

InterventionReducedAcquire

float

The multiplier, based on interventions like SimpleVaccine, used to reduce the probability that an individual will acquire an infection.

InterventionReducedTransmit

float

The multiplier, based on interventions like SimpleVaccine, used to reduce the probability that an individual will transmit an infection.

InterventionReducedMortality

float

The multiplier, based on interventions like SimpleVaccine, used to reduce the probability that an individual will die due to an infection.

Example#

The following is an example of a ReportHIVInfection.csv file.

Year

Node_ID

Id

MCWeight

Age

Gender

getProbMaternalTransmission

TimeSinceHIV

CD4count

PrognosisCompletedFraction

Prognosis

Stage

ViralLoad

WHOStage

Infectiousness

ModAcquire

ModTransmit

ModMortality

ArtStatus

InfectivitySuppression

DurationOnART

ProbMaternalTransmissionModifier

OnArtQuery

CoInfectiveTransmissionFactor

CoInfectiveAcquisitionFactor

DebutAge

IsCircumcised

InterventionReducedAcquire

InterventionReducedTransmit

InterventionReducedMortality

1960.502686

1

2

1

0.307482409

1

0.300000012

0

538.1308594

0.002955006

338.4078064

1

10000

1.012042642

0.026000001

1

1

1

1

1

-1

0

0

1

1

5090.935059

0

1

1

1

1960.502686

1

3

1

21.57338533

1

0.300000012

0

540.4145508

0.000165243

6050.577637

1

10000

1.00041461

0.026000001

1

1

1

1

1

-1

0

0

10

10

5013.489746

0

1

1

1

1960.502686

1

4

1

1.316084269

0

0.300000012

0

540.4000244

0.00018299

5463.524414

1

10000

1.000959992

0.026000001

1

1

1

1

1

-1

0

0

1

1

5758.322754

0

1

1

1

1960.502686

1

5

1

4.214282895

1

0.300000012

0

540.4743652

9.23E-05

10828.31738

1

10000

1.000107288

0.026000001

1

1

1

1

1

-1

0

0

1

1

5784.283203

0

1

1

1

1960.502686

1

6

1

35.359375

1

0.300000012

0

540.2758179

0.000334598

2988.656494

1

10000

1.004073143

0.026000001

1

1

1

1

1

-1

0

0

1

1

5227.504883

0

1

1

1

1960.502686

1

7

1

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0

0.300000012

0

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0.001268703

788.182312

1

10000

1.003529072

0.026000001

1

1

1

1

1

-1

0

0

1

1

5978.607422

0

1

1

1

1960.502686

1

8

1

44.97678189

0

0.300000012

0

540.0627441

0.000594637

1681.643921

1

10000

1.002447605

0.026000001

1

1

1

1

1

-1

0

0

1

1

6403.728516

0

1

1

1

1960.502686

1

9

1

8.954728302

1

0.300000012

0

538.0894775

0.003005542

332.7134705

1

10000

1.003447533

0.026000001

1

1

1

1

1

-1

0

0

1

1

5457.208496

0

1

1

1

1960.502686

1

10

1

61.55059396

1

0.300000012

0

540.2617798

0.000351696

2843.225098

1

10000

1.003378153

0.026000001

1

1

1

1

1

-1

0

0

1

1

5853.435547

0

1

1

1

1960.505493

1

2

1

0.310222135

1

0.300000012

1

535.7171021

0.005910011

338.4078064

1

10000

1.024085283

0.026000001

1

1

1

1

1

-1

0

0

1

1

5090.935059

0

1

1

1

1960.505493

1

3

1

21.57612505

1

0.300000012

1

540.2791748

0.000330486

6050.577637

1

10000

1.00082922

0.026000001

1

1

1

1

1

-1

0

0

10

10

5013.489746

0

1

1

1

1960.505493

1

4

1

1.318823995

0

0.300000012

1

540.250061

0.00036598

5463.524414

1

10000

1.001919866

0.026000001

1

1

1

1

1

-1

0

0

1

1

5758.322754

0

1

1

1

1960.505493

1

5

1

4.217022621

1

0.300000012

1

540.3986816

0.000184613

10828.31738

1

10000

1.000214458

0.026000001

1

1

1

1

1

-1

0

0

1

1

5784.283203

0

1

1

1

1960.505493

1

6

1

35.36211473

1

0.300000012

1

540.0016479

0.000669197

2988.656494

1

10000

1.008146405

0.026000001

1

1

1

1

1

-1

0

0

1

1

5227.504883

0

1

1

1

1960.505493

1

7

1

64.59389448

0

0.300000012

1

538.4723511

0.002537407

788.182312

1

10000

1.007058144

0.026000001

1

1

1

1

1

-1

0

0

1

1

5978.607422

0

1

1

1

1960.505493

1

8

1

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0

0.300000012

1

539.5757446

0.001189274

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1

10000

1.004895329

0.026000001

1

1

1

1

1

-1

0

0

1

1

6403.728516

0

1

1

1

1960.505493

1

9

1

8.957468028

1

0.300000012

1

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332.7134705

1

10000

1.006895065

0.026000001

1

1

1

1

1

-1

0

0

1

1

5457.208496

0

1

1

1

1960.505493

1

10

1

61.55333369

1

0.300000012

1

539.9736328

0.000703392

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1

10000

1.006756186

0.026000001

1

1

1

1

1

-1

0

0

1

1

5853.435547

0

1

1

1

1960.508179

1

2

1

0.312961861

1

0.300000012

2

533.3087769

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338.4078064

1

10000

1.036127925

0.026000001

1

1

1

1

1

-1

0

0

1

1

5090.935059

0

1

1

1

1960.508179

1

3

1

21.57886478

1

0.300000012

2

540.1437988

0.000495729

6050.577637

1

10000

1.001243949

0.026000001

1

1

1

1

1

-1

0

0

10

10

5013.489746

0

1

1

1

1960.508179

1

4

1

1.321563721

0

0.300000012

2

540.1001587

0.000548971

5463.524414

1

10000

1.002879858

0.026000001

1

1

1

1

1

-1

0

0

1

1

5758.322754

0

1

1

1

1960.508179

1

5

1

4.219762347

1

0.300000012

2

540.3230591

0.00027692

10828.31738

1

10000

1.000321746

0.026000001

1

1

1

1

1

-1

0

0

1

1

5784.283203

0

1

1

1

1960.508179

1

6

1

35.36485445

1

0.300000012

2

539.7276001

0.001003795

2988.656494

1

10000

1.012219548

0.026000001

1

1

1

1

1

-1

0

0

1

1

5227.504883

0

1

1

1

1960.508179

1

7

1

64.5966342

0

0.300000012

2

537.4350586

0.00380611

788.182312

1

10000

1.010587215

0.026000001

1

1

1

1

1

-1

0

0

1

1

5978.607422

0

1

1

1

1960.508179

1

8

1

44.98226134

0

0.300000012

2

539.0889282

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1681.643921

1

10000

1.007342935

0.026000001

1

1

1

1

1

-1

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0

1

1

6403.728516

0

1

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1

1960.508179

1

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1

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2

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332.7134705

1

10000

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1

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1

5457.208496

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1

1

1

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1

10

1

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1

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2

539.6856079

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2843.225098

1

10000

1.010134339

0.026000001

1

1

1

1

1

-1

0

0

1

1

5853.435547

0

1

1

1