Inset chart output report

The inset chart output report is output with every simulation. It is a JSON-formatted file with the channel output results of the simulation, consisting of simulation-wide averages by time step. The channels in an inset chart are fully specified by the simulation type and cannot be altered without making changes to the EMOD source code. The file name is InsetChart.json. You can use the information contained in the file to create a chart, but EMOD does not automatically output a chart.

The file contains a header and a channels section.

Header

The header section contains the following parameters.

Parameter	Data type	Description
DateTime	string	The time stamp indicating when the report was generated.
DTK_Version	string	The version of EMOD used.
Report_Type	string	The type of output report.
Report_Version	string	The format version of the report.
Start_Time	integer	The time noted in days when the simulation begins.
Simulation_Timestep	integer	The number of days in each time step.
Timesteps	integer	The number of time steps in this simulation.
Channels	integer	The number of channels in the simulation.

Example

The following is a sample of an InsetChart.json file for a simulation with five time steps.

{
    "Header": {
        "DateTime": "Thu Dec 03 11:28:34 2015",
        "DTK_Version": "5738 HIV-Ongoing 2015/11/18 13:00:39",
        "Report_Type": "InsetChart",
        "Report_Version": "3.2",
        "Start_Time": 0,
        "Simulation_Timestep": 1,
        "Timesteps": 5,
        "Channels": 17
    },
    "Channels": {
        "Births": {
            "Units": "Births",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Campaign Cost": {
            "Units": "USD",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Cumulative Infections": {
            "Units": "",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Cumulative Reported Infections": {
            "Units": "",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Disease Deaths": {
            "Units": "",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Exposed Population": {
            "Units": "Exposed Fraction",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Human Infectious Reservoir": {
            "Units": "Total Infectivity",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Infected": {
            "Units": "Infected Fraction",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Infectious Population": {
            "Units": "Infectious Fraction",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Log Prevalence": {
            "Units": "Log Prevalence",
            "Data": [-10, -10, -10, -10, -10]
        },
        "New Infections": {
            "Units": "",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "New Reported Infections": {
            "Units": "",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Daily (Human) Infection Rate": {
            "Units": "Infection Rate",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Recovered Population": {
            "Units": "Recovered (Immune) Fraction",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        },
        "Statistical Population": {
            "Units": "Population",
            "Data": [
                900,
                900,
                900,
                900,
                900
            ]
        },
        "Susceptible Population": {
            "Units": "Susceptible Fraction",
            "Data": [
                1,
                1,
                1,
                1,
                1
            ]
        },
        "Waning Population": {
            "Units": "Waning Immunity Fraction",
            "Data": [
                0,
                0,
                0,
                0,
                0
            ]
        }
    }
}

Channels

The channels section contains the following parameters.

Parameter	Data type	Description
<Channel_Title>	string	The title of the particular channel.
Units	string	The units used for this channel.
Data	array	A list of the channel data at each time step.

When running TBHIV simulations, the following channels are included in the InsetChart.json file. Some of these may be irrelevant if you did not include HIV coinfection in your simulation.

Channel	Description
Active MDR TB Prevalence	The fraction of the population with active multidrug resistant tuberculosis.
Active Presymptomatic Prevalence	The fraction of the population with active tuberculosis that is presymptomatic.
Active Smear neg Prevalence	The fraction of the population with active smear-negative tuberculosis.
Active Sx Extrapulm Prevalence	The fraction of the population with active extrapulmonary tuberculosis.
Active Sx Smear neg Prevalence	The fraction of the population with active symptomatic smear-negative tuberculosis.
Active Sx Smear pos Prevalence	The fraction of the population with active symptomatic smear-positive tuberculosis.
Active Symptomatic Prevalence	The fraction of the population with active symptomatic tuberculosis.
Active TB in HIV+ Prevalence	The fraction of the population with active tuberculosis and HIV.
Births	The live births cumulative up to that day.
Campaign Cost	The cost of campaigns cumulative up to that day (set by the Cost_To_Consumer parameter).
Daily (Human) Infection Rate	The per-person daily rate of human infection (Human Infectious Reservoir divided by Statistical Population).
Disease Deaths	The number of individuals whose death is attributed to tuberculosis, cumulative up to that day.
Disease Deaths MDR	The number of individuals whose death is attributed to multidrug-resistant tuberculosis, cumulative up to that day.
Exposed Population	The fraction of the population that is currently infected but not contagious.
Fraction Smear pos that is MDR	The fraction of smear-positive tuberculosis cases that are multidrug resistant.
Fraction Sx MDR that is evolved	The fraction of multidrug-resistant tuberulosis cases that evolved resistance.
Fraction Sx that is MDR	The fraction of symptomatic tuberculosis cases that are multidrug resistant.
HIV prevalence	The fraction of the population that is HIV positive.
Human Infectious Reservoir	The total node infectivity, after modifications by the infectious reservoir, seasonality, climate, etc. (if present). The expected number of infections distributed, absent immunity or interventions.
Infected	The fraction of the population currently infected.
Infectious Population	The fraction of the population that is currently infected and contagious.
Infectiousness Fast Progressors	The total node infectivity (expected number of infections distributed) that are due to individuals with fast-progressing tuberculosis.
Latent Fast TB Prevalence	The fraction of the population with latent fast-progressing tuberculosis.”
Latent TB Prevalence	The fraction of the population that has latent tuberculosis.”
Latent TB in HIV+ Prevalence	The fraction of the population with latent tuberculosis and HIV.
Log Prevalence	The logarithm of the population prevalence.
MDR TB Prevalence	The fraction of the population with multidrug-resistant tuberculosis.
Mean CD4 count coinfected	The mean CD4 count of individuals coinfected with both tuberculosis and HIV.
New Active Fast TB Infections	The number of new active, fast-progressing tuberculosis infections on that day.
New Active Slow TB Infections	The number of new active, slow-progressing tuberculosis infections on that day.
New Active TB Infections	The number of new active tuberculosis infections on that day.
New Active TB with HIV	The number of new active tuberculosis infections in HIV+ individuals on that day.
New Active TB with HIV on ART	The number of new active tuberculosis infections in HIV+ individuals on ART on that day.
New Infections	The number of new tuberculosis infections on that day.
New MDR active infections	The number of new active, multidrug-resistant tuberculosis infections on that day.
New MDR evolved active infections	The number of tuberculosis infections that evolved new multidrug resistance on that day.
New MDR fast active infections	The number of new active, fast-progressing, multidrug-resistant tuberculosis infections on that day.
New Smear Positive Infections	The number of new smear-positive tuberculosis infections on that day.
New TB deaths with HIV	The number of deaths attributed to tuberculosis in HIV+ individuals on that day.
New TB deaths with HIV on ART	The number of deaths attributed to tuberculosis in HIV+ individuals on ART on that day.
Newly Cleared TB Infections	The number of tuberculosis infections cleared on that day.
Newly Symptomatic	The number of individuals with tuberculosis who developed symptoms on that day.
Number Active TB on Treatment	The number of individuals with active tuberculosis that are currently on treatment.
On TB Treatment	The number of individuals currently on tuberculosis treatment.
Prevalence Active TB CD4 < 350	The fraction of the population with active tuberculosis and HIV that has a CD4 count below 350.
Prevalence Active TB 350< CD4< 500	The fraction of the population with active tuberculosis and HIV that has a CD4 count between 350 and 500.
Prevalence Active TB CD4 > 500	The fraction of the population with active tuberculosis and HIV that has a CD4 count above 500.
Prevalence of ART in HIV+	The fraction of the HIV+ population that is on ART.
Recovered Population	The fraction of the population that is currently not infected and has zero susceptibility.
Statistical Population	The total number of individuals in the simulation on that day.
Susceptible Population	The fraction of the population that is currently not infected and is maximally susceptible.
Symptomatic Population	The total number of individuals with symptomatic tuberculosis on that day.
TB HIV+ Prevalence	The fraction of HIV+ individuals that have tuberculosis.
TB Immune Fraction	The fraction of the population that is immune to tuberculosis.
Waning Population	The fraction of the population that is currently not infected, has non-zero susceptibility, but is less than maximally susceptible.