BinnedReport#
The binned output report (BinnedReport.json) is a JSON-formatted file where the channel data has been sorted into age bins. It is very similar to an inset chart, however, with the binned report all channels are broken down into sub-channels (bins) based on age. For example, instead of having a single prevalence channel, you might have prevalence in the “0-3 years old bin” and the “4-6 years old bin, and so forth.
To generate the binned report, set the Enable_Demographics_Reporting configuration parameter to 1. The demographics summary output report will also be generated.
The file contains a header and a channels section.
Header#
The header section contains the following parameters.
Parameter |
Data type |
Description |
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
DateTime |
string |
The time stamp indicating when the report was generated. |
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DTK_Version |
string |
The version of EMOD used. |
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Report_Type |
string |
The type of output report. |
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Report_Version |
string |
The format version of the report. |
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Timesteps |
integer |
The number of time steps in this simulation. |
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Channels |
integer |
The number of channels in the simulation. |
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Subchannel_Metadata |
nested JSON object |
Metadata that describes the bins and axis information. The metadata includes the following parameters:
|
Channels#
Malaria binned reports have the following channel data:
Parameter |
Description |
|---|---|
Blood Smear Gametocyte Positive |
The number of individuals who are detectable with the BLOOD_SMEAR_GAMETOCYTES version of MalariaDiagnostic intervention. The detectability of the diagnostic is controlled by parameters Report_Gametocyte_Smear_Sensitivity and Report_Detection_Threshold_Blood_Smear_Gametocytes. |
Blood Smear Parasite Positive |
The number of individuals who are detectable with the BLOOD_SMEAR_PARASITES version of MalariaDiagnostic intervention. The detectability of the diagnostic is controlled by parameters Report_Parasites_Smear_Sensitivity and Report_Detection_Threshold_Blood_Smear_Parasites. |
Fever Positive |
The number of individuals currently with a fever. Detectable fever is determined by the parameter Report_Detection_Threshold_Fever. which is the level of temperature above normal (Celsius) for an individual to be considered to have a fever. |
Infected |
The number of individuals who are infected on that day in that age bin. |
Mean Parasitemia |
The geometric mean number of parasites per microliter of blood. [Exponential of (Sum of log(BLOOD_SMEAR_PARASITES diagnostic ) for all individuals divided by the number of individuals detected using BLOOD_SMEAR_PARASITES) diagnostic - geometric mean]. |
New Clinical Cases |
The number of new clinical cases on that day. This channel is controlled by the Clinical_Fever_Threshold_Low and Clinical_Fever_Threshold_High parameters. The amount that an individual’s fever is above normal must be greater than both of these values to be considered clinical. |
New Infections |
The number of individuals who got infected on that day. This is not the number of new infections on that day. An individual could receive multiple infections in a single day depending on the value of the Malaria_Model parameter in your configuration setup. |
New Severe Cases |
The number of new severe cases of malaria on that day. An individual is considered to be a severe case if the combined probability of anemia, parasite density, and fever is greater than a uniform random number. This combined probability is the combination of sigmoid using the following parameters: Anemia_Severe_Threshold and Anemia_Severe_Inverse_Width, Parasite_Severe_Threshold and Parasite_Severe_Inverse_Width , and Fever_Severe_Threshold and Fever_Severe_Inverse_Width. |
PCR Gametocytes Positive |
The number of individuals who are detectable with the PCR_GAMETOCYTES version of MalariaDiagnostic. The detectability of the diagnostic is controlled by parameter Report_Detection_Threshold_PCR_Gametocytes. |
PCR Parasites Positive |
The number of individuals who are detectable with the PCR_PARASITES version of MalariaDiagnostic. The detectability of the diagnostic is controlled by parameter Report_Detection_Threshold_PCR_Parasites. |
PfHRP2 Positive |
The number of individuals who are detectable with the PF_HRP2 version of MalariaDiagnostic. The detectability of the diagnostic is controlled by parameter Report_Detection_Threshold_PCR_PfHRP2. |
Population |
The total number of individuals in this age range on this day. |
Sum MSP Variant Fractions |
This the sum of each individual’s fraction of MSP variants that an individual has had. The parameter Falciparum_MSP_Variants defines the total number of possible variants. This channel indicates the average fraction that an individual has seen of this total number. The greater the fraction the more that the population has developed antibodies to the parasite. |
Sum Non-Specific Variant Fractions |
This the sum of each individual’s fraction of Non-Specific variants that an individual has had. The parameter Falciparum_Nonspecific_Types defines the total number of possible variants. This channel indicates the average fraction that an individual has seen of this total number. The greater the fraction the more that the population has developed antibodies to the parasite. |
Sum of Squared MSP Variant Fractions |
This is the sum of the squares of the values used in calculating Sum MSP Variant Fractions. |
Sum of Squared Non-Specific Variant Fractions |
This is the sum of the squares of the values used in calculating Sum Non-Specific Variant Fractions. |
Sum of Squared PfEMP1 Variant Fractions |
This is the sum of the squares of the values used in calculating Sum PfEMP1 Variant Fractions. |
Sum PfEMP1 Variant Fractions |
This the sum of each individual’s fraction of variants of the PfEMP1 var genes that an individual has had. The parameter Falciparum_PfEMP1_Variants defines the total number of possible variants. This channel indicates the average fraction that an individual has seen of this total number. The greater the fraction the more that the population has developed antibodies to the parasite. |
True Positive |
The number of individuals who are detectable with the TRUE_PARASITE_DENSITY version of MalariaDiagnostic. The detectability of the diagnostic is controlled by parameter Report_Detection_Threshold_True_Parasite_Density. |
Example#
The following is a sample of a BinnedReport.json file for malaria.
{
"Header": {
"DateTime": "Mon Dec 21 11:33:27 2020",
"DTK_Version": " Malaria-Ongoing (bb265ad) Dec 21 2020 11:15:31",
"Report_Version": "2.1",
"Timesteps": 730,
"Subchannel_Metadata": {
"AxisLabels": [
[
"Age"
]
],
"NumBinsPerAxis": [
[
21
]
],
"ValuesPerAxis": [
[
[
1825,
3650,
5475
]
]
],
"MeaningPerAxis": [
[
[
"<5",
"55-59",
"95-99"
]
]
]
},
"Channels": 19
},
"Channels": {
"Blood Smear Gametocyte Positive": {
"Units": "",
"Data": [
[
380,
300,
1670
]
]
},
"Blood Smear Parasite Positive": {
"Units": "",
"Data": [
[
90,
80,
90
]
]
},
"Fever Positive": {
"Units": "",
"Data": [
[
1700,
1760,
1660
]
]
},
"Infected": {
"Units": "",
"Data": [
[
1790,
1090,
1723
]
]
}
}
}