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	NumHasFever
50	1	M	10	arm1	F	366	0	0	0	0	0	0	0
50	1	M	10	arm1	T	151	151	0.00593093	112435	1.06936	0.0165342	1	151
50	1	M	10	arm2	F	1256	0	0	0	0	0	0	0
50	1	M	10	arm2	T	292	292	0.00615811	111366	1.11031	0.0165525	1	292
50	1	M	10	arm3	F	2744	0	0	0	0	0	0	0
50	1	M	10	arm3	T	282	282	0.00600333	111783	1.08239	0.0165839	1	282
50	1	M	100	arm1	F	335	0	0	0	0	0	0	0
50	1	M	100	arm1	T	159	159	0.00205596	140531	0.371012	0.0166038	1	159
50	1	M	100	arm2	F	946	0	0	0	0	0	0	0
50	1	M	100	arm2	T	588	588	0.00205613	140583	0.371029	0.0165647	1	588
50	1	M	100	arm3	F	2645	0	0	0	0	0	0	0
50	1	M	100	arm3	T	297	297	0.00205629	140105	0.371017	0.0165545	1	297
50	1	F	10	arm1	F	379	0	0	0	0	0	0	0
50	1	F	10	arm1	T	164	164	0.00606003	110326	1.09222	0.0165447	1	164
50	1	F	10	arm2	F	1143	0	0	0	0	0	0	0
50	1	F	10	arm2	T	288	288	0.00595153	111696	1.07296	0.0165162	1	288
50	1	F	10	arm3	F	2809	0	0	0	0	0	0	0
50	1	F	10	arm3	T	302	302	0.00597365	111095	1.07672	0.0165011	1	302
50	1	F	100	arm1	F	355	0	0	0	0	0	0	0
50	1	F	100	arm1	T	144	144	0.00205568	141105	0.37102	0.0166435	1	144
50	1	F	100	arm2	F	887	0	0	0	0	0	0	0
50	1	F	100	arm2	T	579	579	0.00205593	140874	0.371017	0.0165688	1	579
50	1	F	100	arm3	F	2584	0	0	0	0	0	0	0
50	1	F	100	arm3	T	305	305	0.00205636	140043	0.371022	0.0165465	1	305
50	2	M	10	arm1	F	340	0	0	0	0	0	0	0
50	2	M	10	arm1	T	147	147	0.00608663	112032	1.09768	0.016644	1	147
50	2	M	10	arm2	F	1161	0	0	0	0	0	0	0
50	2	M	10	arm2	T	311	311	0.00599196	111639	1.08021	0.0165274	1	311
50	2	M	10	arm3	F	2742	0	0	0	0	0	0	0
50	2	M	10	arm3	T	285	285	0.00596162	112175	1.07493	0.0165731	1	285
50	2	M	100	arm1	F	327	0	0	0	0	0	0	0
50	2	M	100	arm1	T	160	160	0.0020567	139714	0.371016	0.0164792	1	160
50	2	M	100	arm2	F	899	0	0	0	0	0	0	0
50	2	M	100	arm2	T	583	583	0.00205599	140620	0.371006	0.0165638	1	583
50	2	M	100	arm3	F	2697	0	0	0	0	0	0	0
50	2	M	100	arm3	T	278	278	0.00205585	141016	0.371021	0.0165828	1	278
50	2	F	10	arm1	F	332	0	0	0	0	0	0	0
50	2	F	10	arm1	T	160	160	0.00600168	112563	1.08236	0.0166042	1	160
50	2	F	10	arm2	F	1184	0	0	0	0	0	0	0
50	2	F	10	arm2	T	333	333	0.00607677	111940	1.09565	0.0165566	1	333
50	2	F	10	arm3	F	2731	0	0	0	0	0	0	0
50	2	F	10	arm3	T	294	294	0.00601945	111251	1.08511	0.0165306	1	294
50	2	F	100	arm1	F	341	0	0	0	0	0	0	0
50	2	F	100	arm1	T	156	156	0.00205657	139663	0.371027	0.0165171	1	156
50	2	F	100	arm2	F	914	0	0	0	0	0	0	0
50	2	F	100	arm2	T	626	626	0.00205598	140771	0.371019	0.0165549	1	626
50	2	F	100	arm3	F	2728	0	0	0	0	0	0	0
50	2	F	100	arm3	T	271	271	0.00205597	140890	0.370996	0.0165068	1	271