ReportNodeDemographicsMalariaGenetics

The malaria genetics node demographics report (ReportNodeDemographcsMalariaGenetics.csv) extends the data collected in the malaria node demographics report by adding data about the number of infections with specific gentic barcodes. The malaria node demographics genetics report does not include columns for Genome_Markers because this report assumes that the simulation setup parameter Malaria_Model is set to MALARIA_MECHANISTIC_MODEL_WITH_PARASITE_GENETICS.

Note

If you need detailed data on the infections with different barcodes, use the MalariaSQLReport. That report contains data on all barcodes, without specifying what they are.

Configuration

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

Parameter

Data type

Min

Max

Default

Description

Age_Bins

array of floats

-3.04E+38

3.04E+38

[ ]

The age bins (in years, in ascending order) to aggregate within and report. An empty array does not stratify by age.

Barcodes

array of strings

NA

NA

[ ]

A list of barcode strings. The report contains the number of human infections with each barcode. Use ‘*’ for a wild card at a loci to include all values at that loci. For example, ‘A*T’ includes AAT, ACT, AGT, and ATT. The report contains an OtherBarcodes column for barcodes that are not defined. Note: There is no validation that the barcode strings are valid barcodes for the scenario.

Drug_Resistant_Statistic_Type

enum

NA

NA

NUM_PEOPLE_WITH_RESISTANT_INFECTION

Indicates the statistic in the DrugResistant columns. Possible values are: NUM_PEOPLE_WITH_RESISTANT_INFECTION: A person is counted if they have one infection with that drug resistant marker; NUM_INFECTIONS: the total number of infections with that marker.

Drug_Resistant_Strings

array of strings

NA

NA

[ ]

A list of strings representing the set of drug resistant markers. A column will be created with the number of human infections with that barcode. One can use a ‘*’ for a wild card. An ‘OtherBarcodes’ column will be created for barcodes not defined.

IP_Key_To_Collect

string

NA

NA

(empty string)

The name of the IndividualProperties (IP) key by which to stratify the report. An empty string means the report is not stratified by IP.

Stratify_By_Gender

bool

NA

NA

1

Set to true (1) to stratify by gender. Set to false (0) to not stratify by gender.

Stratify_By_Has_Clinical_Symptoms

bool

NA

NA

1

If set to 1, the data will have an extra stratification for people who have clinical symptoms and those that do not. Default is 0 or no extra stratification.

 
{
    "Reports": [
        {
            "Class": "ReportNodeDemographicsMalariaGenetics",
            "Age_Bins": [
                10,
                100
            ],
            "Barcodes": [
                "TA",
                "AT",
                "TT"
            ],
            "Drug_Resistant_Stat_Type": "NUM_INFECTIONS",
            "Drug_Resistant_Strings": [
                "TA",
                "AT",
                "TT"
            ],
            "IP_Key_To_Collect": "",
            "Stratify_By_Gender": 0,
            "Stratify_By_Has_Clinical_Symptoms": 0
        }
    ],
    "Use_Defaults": 1
}

Output file data

The report will contain the following output data, divided between stratification columns and data columns.

Stratification columns

Parameter

Data type

Description

Time

float

The day of the simulation that the data was collected.

NodeID

integer

The External ID of the node for the data in the row in the report.

Gender

enum

Possible values are M or F; the gender of the individuals in the row in the report. This column only appears if Stratify_By_Gender = 1.

AgeYears

float

The max age in years of the bin for the individuals in the row in the report. If Age_Bins is empty, this column does not appear.

IndividualProp

string

The value of the IP for the individuals in the row in the report. If IP_Key_To_Collect is an empty string, then this column does not appear.

HasClinicalSymptoms

enum

T implies that the people in the row are having clinical symptoms. F implies they do not. This column only appears if Stratify_By_Has_Clinical_Symptoms = 1.

Data columns

Parameter

Data type

Description

NumIndividuals

integer

The number of individuals who meet the stratification values.

NumInfected

integer

The number of infected individuals who meet the stratification values.

NodeProp = <Node Property Keys>

string

For each possible Node Property, there is one column where the data in the column is the value of that particular property. If there are no Node Properties, then there are no columns.

AvgInfectiousness

float

The average infectiousness to mosquitos for the individuals of this row. Infectiousness is based on the number of mature gametocytes that the person has.

AvgParasiteDensity

float

The average true parasite density for the individuals of this row.

AvgGametocyteDensity

float

The average true gametocyte density for the individuals of this row.

AvgVariantFractionPfEMP1Major

float

For each individual, a count is made of the number of PfEMP1 Major antibodies the individual has and is divided by the total number of possible variants (Falciparum_PfEMP1_Variants). This is the average of this value for all the individuals represented in this row.

AvgNumInfections

float

The average number of infections for the people of this row.

AvgInfectionClearedDuration

float

The average duration to clear infections for the people of this row.

NumInfectionsCleared

integer

The number of cleared infections for the people of this row.

NumHasFever

integer

The number of people in the row that have a fever according to the diagnostic using the Report_Detection_Threshold_Fever parameter.

NumHasClinicalSymptoms

integer

If Stratify_By_Has_Clinical_Symptoms = 0, then this column is present with the number of people in the row that are considered to have ‘clinical’ symptoms.

[barcodes]

integer

The number of human infections with the barcode that is the column header. If you used a wild card at a loci, it includes all the barcodes that match the other loci exactly but ignores differences at this loci. For example, A*T includes AAT, ACT, AGT, and ATT. There will be one column for each barcode.

OtherBarcodes

integer

The number of human infections whose barcode is not counted by the other columns.

Example

The following is an example of a ReportNodeDemographicsMalariaGenetics.csv

Time

NodeID

AgeYears

NumIndividuals

NumInfected

AvgInfectiousness

AvgParasiteDensity

AvgGametocyteDensity

AvgVariantFractionPfEMP1Major

AvgNumInfections

AvgInfectionClearedDuration

NumInfectionsCleared

NumHasFever

NumHasClinicalSymptoms

TA

AT

TT

OtherBarcodes

TA

AT

TT

NoDrugResistance

200

4

10

339

339

0.61637

12162.5

1038.6

0.180659

8.50443

61.6944

72

153

199

1491

1094

163

135

1491

1094

163

135

200

4

100

661

661

0.627337

12805.6

1084.05

0.174226

8.72315

64.2336

107

275

374

2989

2206

276

295

2989

2206

276

295

200

3

10

343

343

0.610594

10458.5

1086.55

0.180894

8.43149

61.4211

57

123

172

0

2892

0

0

0

2892

0

0

200

3

100

657

657

0.639379

14241.1

1074.46

0.175525

8.78691

64.4853

136

260

359

0

5773

0

0

0

5773

0

0

200

2

10

330

330

0.62785

15945.3

1107.33

0.173889

8.56364

61.6377

69

134

179

2826

0

0

0

2826

0

0

0

200

2

100

670

670

0.649023

13305.3

1150.4

0.175338

8.68806

64.8

115

268

361

5821

0

0

0

5821

0

0

0

200

1

10

321

321

0.650348

12543.2

1097.84

0.173842

8.64486

61.678

59

134

191

0

0

0

2775

0

0

0

2775

200

1

100

679

679

0.65758

14437.5

1330.21

0.170324

8.72607

65.3988

100

295

408

0

0

0

5925

0

0

0

5925

201

4

10

339

339

0.605389

11346.4

995.784

0.183186

8.39233

61.7711

83

145

202

1465

1075

163

142

1465

1075

163

142

201

4

100

661

661

0.625909

13623.3

1074.37

0.175986

8.66566

63.8224

133

286

376

2960

2191

277

300

2960

2191

277

300

201

3

10

342

342

0.616016

10373.4

1081.56

0.183762

8.43275

62.6765

68

142

176

0

2884

0

0

0

2884

0

0

201

3

100

658

658

0.631187

12559.5

1054.92

0.177351

8.71125

65.0115

141

259

350

0

5732

0

0

0

5732

0

0

201

2

10

330

330

0.618134

13675.8

1121.95

0.176455

8.52424

61.2059

68

137

184

2813

0

0

0

2813

0

0

0

201

2

100

670

670

0.648521

13363.5

1191.18

0.177448

8.68507

64.4876

121

269

359

5819

0

0

0

5819

0

0

0

201

1

10

321

321

0.655716

12432.2

1214.83

0.175867

8.65732

62.1475

61

134

180

0

0

0

2779

0

0

0

2779

201

1

100

679

679

0.644713

13488.7

1274.26

0.172356

8.67894

65.386

114

283

400

0

0

0

5893

0

0

0

5893

202

4

10

339

339

0.598077

10570.8

975.812

0.185811

8.38053

62.5556

72

149

204

1454

1076

165

146

1454

1076

165

146

202

4

100

661

661

0.613423

12068.9

1060.33

0.178084

8.65053

64.641

117

270

372

2950

2183

281

304

2950

2183

281

304

202

3

10

342

342

0.593883

10130.2

1061.35

0.185741

8.41521

62.3333

63

132

186

0

2878

0

0

0

2878

0

0

202

3

100

658

658

0.625583

12888.2

1052.63

0.179271

8.68541

64.9604

139

256

347

0

5715

0

0

0

5715

0

0

202

2

10

330

330

0.606342

14340

1131.78

0.17805

8.44545

61.1493

67

137

182

2787

0

0

0

2787

0

0

0

202

2

100

670

670

0.637783

12996.4

1159.33

0.179343

8.67015

64.4728

115

260

362

5809

0

0

0

5809

0

0

0

202

1

10

321

321

0.646784

12130

1165.26

0.177684

8.64486

61.4776

67

131

179

0

0

0

2775

0

0

0

2775

202

1

100

679

679

0.641917

13286.9

1271.64

0.174335

8.69072

65.7283

115

280

399

0

0

0

5901

0

0

0

5901