HIV disease progression report¶
The HIV disease progression report is a CSV-formatted output file which provides information on each individual’s state at every time step. The filename is ReportHIVInfection.csv.
To generate the report, set the configuration parameter Report_HIV_Infection to 1.
Report structure and data channel descriptions¶
The file contains the following data channels:
Data channel |
Data type |
Description |
|
|---|---|---|---|
Year |
float |
The time of the time step in units of calendar year including fractions of years up to two decimal places. |
|
Node_ID |
integer |
The identification number of the node. |
|
ID |
integer |
The individual’s unique identifier. |
|
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 MTCT, if the individual were to give birth at the present time and not receive any interventions such as PMTCT or ART. Not applicable for males or for females of non-childbearing age. |
|
TimeSinceHIV |
integer |
The number of days since the individual became infected. If the individual was infected by an Outbreak intervention with the Incubation_Period_Override parameter set to 0, the infection is ‘fast-forwarded.’ In this case, TimeSinceHIV is the effective time of infection and is in the past, and is adjusted accordingly. |
|
CD4count |
float |
The current CD4 count, regardless of when CD4 testing was performed. |
|
PognosisCompletedFraction |
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 not on ART. |
|
Stage |
integer |
The individual’s disease stage. 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 |
integer |
Describes the individual’s infectiousness, which depends on the disease stage and ART, and includes effects of heterogeneous infectiousness. |
|
ModAcquire |
float |
Multiplicative modifier on disease acquisition; will be set to 1 for HIV. Configured by Post_Infection_Acquisition_Multiplier. |
|
ModTransmit |
float |
Multiplicative modifier on disease transmission. Configured by Post_Infection_Transmission_Mulitplier. |
|
ModMortality |
float |
Multiplicative modifier on disease mortality. Configured by Post_Infection_Mortality_Mulitplier. |
|
ArtStatus |
integer |
Describes the individual’s ART status. Possible values are:
|
|
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; set to 0 if individual is not on ART, and 1 if the individual is on ART. |
|
CoInfectiveFactor |
float |
The per-act transmission multiplier for an individual with the co-infection flag. If the individual does not have the flag, the value will be 1. |
|
DebutAge |
integer |
The age of sexual debut in days. |
|
IsCircumcised |
boolean |
Only applicable to males; assigned to 0 if uncircumcised, 1 if 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 report:
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 |
2020.05481 |
1 |
3 |
1 |
20.1369863 |
0 |
0.75 |
0 |
530.5666504 |
0.01038052 |
2890.021973 |
1 |
10000 |
1.207343459 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6064.789551 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
4 |
1 |
20.1369863 |
1 |
0.75 |
0 |
535.9321289 |
0.004475715 |
6702.893066 |
1 |
10000 |
1.240228534 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6030.225098 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
8 |
1 |
20.1369863 |
0 |
0.75 |
0 |
536.4299316 |
0.004621493 |
6491.35791 |
1 |
10000 |
1.212454438 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5489.476074 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
10 |
1 |
20.1369863 |
0 |
0.75 |
0 |
527.9986572 |
0.012766905 |
2349.821045 |
1 |
10000 |
1.058985472 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6205.148926 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
11 |
1 |
20.1369863 |
0 |
0.75 |
0 |
527.1473389 |
0.013222025 |
2268.9375 |
1 |
10000 |
1.271012425 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6294.055176 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
12 |
1 |
20.1369863 |
0 |
0.75 |
0 |
534.3621216 |
0.006430737 |
4665.095215 |
1 |
10000 |
1.11394453 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6160.729004 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
13 |
1 |
20.1369863 |
1 |
0.75 |
0 |
538.0737305 |
0.002499918 |
12000.54785 |
1 |
10000 |
1.043146133 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5818.174316 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
14 |
1 |
20.1369863 |
0 |
0.75 |
0 |
534.4891357 |
0.006127219 |
4896.181641 |
1 |
10000 |
1.014352798 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5930.40332 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
15 |
1 |
20.1369863 |
0 |
0.75 |
0 |
537.1317749 |
0.003357016 |
8936.496094 |
1 |
10000 |
1.068257928 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6662.154785 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
20 |
1 |
20.1369863 |
1 |
0.75 |
0 |
535.2338257 |
0.006401457 |
4686.419434 |
1 |
10000 |
1.014097095 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5784.049316 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
23 |
1 |
20.1369863 |
0 |
0.75 |
0 |
533.1539307 |
0.007178309 |
4179.232422 |
1 |
10000 |
1.029288888 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6150.652832 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
25 |
1 |
20.1369863 |
0 |
0.75 |
0 |
526.0744629 |
0.014117708 |
2124.995361 |
1 |
10000 |
1.27904582 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6399.663574 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
26 |
1 |
20.1369863 |
1 |
0.75 |
0 |
536.9612427 |
0.003690189 |
8129.62793 |
1 |
10000 |
1.002890825 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6241.647949 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
27 |
1 |
20.1369863 |
0 |
0.75 |
0 |
534.4625854 |
0.006498936 |
4616.147949 |
1 |
10000 |
1.075166821 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6768.329102 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
28 |
1 |
20.1369863 |
0 |
0.75 |
0 |
534.9790649 |
0.005618968 |
5339.072266 |
1 |
10000 |
1.005399466 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5545.100586 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
29 |
1 |
20.1369863 |
0 |
0.75 |
0 |
476.2661438 |
0.065596513 |
457.3411865 |
1 |
10000 |
1.823569179 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5776.763672 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
32 |
1 |
20.1369863 |
0 |
0.75 |
0 |
537.0706787 |
0.003729384 |
8044.229492 |
1 |
10000 |
1.004417181 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6488.079102 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
34 |
1 |
20.1369863 |
0 |
0.75 |
0 |
529.2407837 |
0.011370027 |
2638.506348 |
1 |
10000 |
1.159977674 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6070.652344 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
35 |
1 |
20.1369863 |
0 |
0.75 |
0 |
536.2340088 |
0.004250809 |
7057.412598 |
1 |
10000 |
1.011169076 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5910.400391 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
37 |
1 |
20.1369863 |
1 |
0.75 |
0 |
519.5267334 |
0.021527208 |
1393.587036 |
1 |
10000 |
2.384400606 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5745.703613 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
38 |
1 |
20.1369863 |
1 |
0.75 |
0 |
506.1029968 |
0.035287097 |
850.1690674 |
1 |
10000 |
1.280683398 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5542.922852 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
41 |
1 |
20.1369863 |
1 |
0.75 |
0 |
528.6607666 |
0.011833124 |
2535.262207 |
1 |
10000 |
1.022005677 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5273.448242 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
42 |
1 |
20.1369863 |
0 |
0.75 |
0 |
531.7854004 |
0.008749693 |
3428.706055 |
1 |
10000 |
1.008042812 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6543.255859 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
44 |
1 |
20.1369863 |
1 |
0.75 |
0 |
535.2116699 |
0.00504142 |
5950.734863 |
1 |
10000 |
1.045830607 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5682.976074 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
49 |
1 |
20.1369863 |
1 |
0.75 |
0 |
537.2387695 |
0.003326159 |
9019.432617 |
1 |
10000 |
1.014684558 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5502.225586 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
50 |
1 |
20.1369863 |
0 |
0.75 |
0 |
534.6325073 |
0.006939663 |
4322.953125 |
1 |
10000 |
1.024004698 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6212.691406 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
52 |
1 |
20.1369863 |
0 |
0.75 |
0 |
529.0888672 |
0.011367477 |
2639.111816 |
1 |
10000 |
1.147639751 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6085.556152 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
53 |
1 |
20.1369863 |
0 |
0.75 |
0 |
533.4486694 |
0.006862988 |
4371.291992 |
1 |
10000 |
1.028509378 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
6032.864258 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
56 |
1 |
20.1369863 |
1 |
0.75 |
0 |
535.7977905 |
0.004662102 |
6434.808594 |
1 |
10000 |
1.006386757 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
5913.200684 |
0 |
1 |
1 |
1 |
2020.05481 |
1 |
57 |
1 |
20.1369863 |
0 |
0.75 |
0 |
535.3372192 |
0.00590881 |
5077.156738 |
1 |
10000 |
1.030921698 |
0 |
1 |
1 |
1 |
1 |
1 |
-1 |
0 |
0 |
1 |
1 |
4827.637207 |
0 |
1 |
1 |
1 |