ReportNodeDemographicsMalaria#

The malaria node demographics report is a CSV-formatted report that extends the ReportNodeDemographics report (see ReportNodeDemographics) by adding malaria-specific statistics. The report still contains population information stratified by node, but the data columns now also contain information about malaria parasite counts.

Configuration#

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

Parameter name

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.

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

boolean

0

1

1

Set to true (1) to stratify by gender; a value of 0 will 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": "ReportNodeDemographicsMalaria",
            "Age_Bins": [
                10,
                20,
                30,
                40,
                50,
                60,
                70,
                80,
                90,
                100,
                125
            ],
            "IP_Key_To_Collect": "",
            "Stratify_by_Gender": 1,
            "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 that meet the stratification values.

NumInfected

integer

The number of infected individuals that 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 NodeProperties, 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.

Example#

The following is an example of ReportNodeDemographicsMalaria.csv.

Time

NodeID

Gender

AgeYears

IndividualProp=StudyGroups

HasClinicalSymptoms

NumIndividuals

NumInfected

AvgInfectiousness

AvgParasiteDensity

AvgGametocyteDensity

AvgVariantFractionPfEMP1Major

AvgNumInfections

AvgInfectionClearedDuration

NumInfectionsCleared

NumHasFever

50

1

M

10

arm1

F

366

0

0

0

0

0

0

0

0

0

50

1

M

10

arm1

T

151

151

0.00593093

112435

1.06936

0.0165342

1

0

0

151

50

1

M

10

arm2

F

1256

0

0

0

0

0

0

0

0

0

50

1

M

10

arm2

T

292

292

0.00615811

111366

1.11031

0.0165525

1

0

0

292

50

1

M

10

arm3

F

2744

0

0

0

0

0

0

0

0

0

50

1

M

10

arm3

T

282

282

0.00600333

111783

1.08239

0.0165839

1

0

0

282

50

1

M

100

arm1

F

335

0

0

0

0

0

0

0

0

0

50

1

M

100

arm1

T

159

159

0.00205596

140531

0.371012

0.0166038

1

0

0

159

50

1

M

100

arm2

F

946

0

0

0

0

0

0

0

0

0

50

1

M

100

arm2

T

588

588

0.00205613

140583

0.371029

0.0165647

1

0

0

588

50

1

M

100

arm3

F

2645

0

0

0

0

0

0

0

0

0

50

1

M

100

arm3

T

297

297

0.00205629

140105

0.371017

0.0165545

1

0

0

297

50

1

F

10

arm1

F

379

0

0

0

0

0

0

0

0

0

50

1

F

10

arm1

T

164

164

0.00606003

110326

1.09222

0.0165447

1

0

0

164

50

1

F

10

arm2

F

1143

0

0

0

0

0

0

0

0

0

50

1

F

10

arm2

T

288

288

0.00595153

111696

1.07296

0.0165162

1

0

0

288

50

1

F

10

arm3

F

2809

0

0

0

0

0

0

0

0

0

50

1

F

10

arm3

T

302

302

0.00597365

111095

1.07672

0.0165011

1

0

0

302

50

1

F

100

arm1

F

355

0

0

0

0

0

0

0

0

0

50

1

F

100

arm1

T

144

144

0.00205568

141105

0.37102

0.0166435

1

0

0

144

50

1

F

100

arm2

F

887

0

0

0

0

0

0

0

0

0

50

1

F

100

arm2

T

579

579

0.00205593

140874

0.371017

0.0165688

1

0

0

579

50

1

F

100

arm3

F

2584

0

0

0

0

0

0

0

0

0

50

1

F

100

arm3

T

305

305

0.00205636

140043

0.371022

0.0165465

1

0

0

305

50

2

M

10

arm1

F

340

0

0

0

0

0

0

0

0

0

50

2

M

10

arm1

T

147

147

0.00608663

112032

1.09768

0.016644

1

0

0

147

50

2

M

10

arm2

F

1161

0

0

0

0

0

0

0

0

0

50

2

M

10

arm2

T

311

311

0.00599196

111639

1.08021

0.0165274

1

0

0

311

50

2

M

10

arm3

F

2742

0

0

0

0

0

0

0

0

0

50

2

M

10

arm3

T

285

285

0.00596162

112175

1.07493

0.0165731

1

0

0

285

50

2

M

100

arm1

F

327

0

0

0

0

0

0

0

0

0

50

2

M

100

arm1

T

160

160

0.0020567

139714

0.371016

0.0164792

1

0

0

160

50

2

M

100

arm2

F

899

0

0

0

0

0

0

0

0

0

50

2

M

100

arm2

T

583

583

0.00205599

140620

0.371006

0.0165638

1

0

0

583

50

2

M

100

arm3

F

2697

0

0

0

0

0

0

0

0

0

50

2

M

100

arm3

T

278

278

0.00205585

141016

0.371021

0.0165828

1

0

0

278

50

2

F

10

arm1

F

332

0

0

0

0

0

0

0

0

0

50

2

F

10

arm1

T

160

160

0.00600168

112563

1.08236

0.0166042

1

0

0

160

50

2

F

10

arm2

F

1184

0

0

0

0

0

0

0

0

0

50

2

F

10

arm2

T

333

333

0.00607677

111940

1.09565

0.0165566

1

0

0

333

50

2

F

10

arm3

F

2731

0

0

0

0

0

0

0

0

0

50

2

F

10

arm3

T

294

294

0.00601945

111251

1.08511

0.0165306

1

0

0

294

50

2

F

100

arm1

F

341

0

0

0

0

0

0

0

0

0

50

2

F

100

arm1

T

156

156

0.00205657

139663

0.371027

0.0165171

1

0

0

156

50

2

F

100

arm2

F

914

0

0

0

0

0

0

0

0

0

50

2

F

100

arm2

T

626

626

0.00205598

140771

0.371019

0.0165549

1

0

0

626

50

2

F

100

arm3

F

2728

0

0

0

0

0

0

0

0

0

50

2

F

100

arm3

T

271

271

0.00205597

140890

0.370996

0.0165068

1

0

0

271