Population-level malaria summary report (MalariaSummaryReport.json)¶
The malaria summary report is a JSON-formatted report that provides a summary of malaria data across the population, and grouped into different bins such as age, parasitemia, and infectiousness.
The output file is named MalariaSummaryReport.json, and is produced via the libmalariasummary_report_plugin.dll file. See Custom reporters for information on using using dynamic link library (DLL) files.
Configuration¶
To generate this report, the following parameters must be configured.
Parameter |
Data type |
Min |
Max |
Default |
Description |
|---|---|---|---|---|---|
Start_Day |
float |
0 |
3.40E+38 |
0 |
The day to start collecting data for the report. |
Duration_Days |
float |
0 |
3.40E+38 |
3.40E+38 |
The duration of simulation days over which to report events. |
Report_Description |
string |
NA |
NA |
NA |
Name of the report (it augments the filename of the report). If multiple CSV reports are being generated, this allows the user to distinguish one report from another. |
Nodeset_Config |
JSON object |
NA |
NA |
NA |
An object that specifies in which nodes the interventions will be distributed. |
Event_Trigger_List |
list of strings |
NA |
NA |
NA |
The list of event triggers for the events included in the report. |
Reporting_Interval |
integer |
1 |
1000000 |
1000000 |
Defines the cadence of the report by specifying how many time steps to collect data before writing to the file. This will limit system memory usage and is advised when large output files are expected. |
Max_Number_Reports |
integer |
0 |
1000000 |
1 |
The maximum number of report output files that will be produced for a given campaign. |
Pretty_Format |
enum |
NA |
NA |
F |
Possible values are T (true) and F (false); T will cause the file to be written in pretty JSON format; F will save space. |
Age_Bins |
array of integers |
0 |
MAX_HUMAN_AGE |
[10,20,30,40,50,60,70,80,90,100,1000] |
The age bins (in years, in ascending order) to aggregate within and report. |
Parasitemia_Bins |
float |
-3.40E+38 |
3.40E+38 |
[50,500,5000,50000,FLT_MAX] |
Parasitemia Bins to aggregate within and report. A value greater than or equal to zero in the first bin indicates that the uninfected people should be added to this bin. The values must be in ascending order. |
Infectiousness_Bins |
float |
-3.40E+38 |
3.40E+38 |
[20,40,60,80,100] |
Infectiousness bins to aggregate within and report. |
Individual_Property_Filter |
string |
NA |
NA |
(empty string) |
IndividualProperty (and value) to filter on; default of empty string means no filter. |
Output file data¶
These output files may be very large. They contain several sections of data:
Metadata
DataByTime
DataByTimeAndAgeBins
DataByTimeAndPfPRBinsAndAgeBins
DataByTimeAndInfectiousnessBinsAndPfPRBinsAndAgeBins
Metadata¶
This section contains the group of parameters used to configure the report, and includes the following data channels:
Parameter |
Data type |
Description |
|---|---|---|
Start_Day |
integer |
The first day that the first interval started. |
Reporting_Interval |
integer |
The number of days to accumulate data. |
Age Bins |
array of integers |
The max age in years per bin, listed in ascending order. Note that by using a large value for the last bin, it will collect all remaining people. |
Parasitemia Bins |
array of integers |
The max parasite density in infected red blood cells per microliter per bin, listed in ascending order. |
Gametocytemia Bins |
array of integers |
The max gametocyte density in infected red blood cells per microliter per bin, listed in ascending order. |
Infectiousness Bins |
array of integers |
The max percent infectiousness of each bin, listed in ascending order. |
DataByTime¶
This section contains a group of statistics where there is just one entry for each reporting interval. The following statistics are collected:
Parameter |
Description |
|---|---|
Time Of Report |
Each entry is the final day of the reporting interval, in days. |
Annual EIR |
The average Entomological Inoculation Rate (EIR) per day. |
PfPR_2to10 |
The percentage of individuals who’s age is 2 < age < 10 and have BLOOD_SMEAR_PARASITES diagnostic returning a positive number of parasites. |
No Infection Streak |
The maximum number of days without an infection during the interval. |
Fraction Days Under 1pct Infected |
The percentage of days during the interval in which the percentage of infected individuals was less than 1%. |
DataByTimeAndAgeBins¶
This section contains statistics in two-dimensional arrays by Time (the reporting interval) and Age Bin.
Parameter |
Description |
|---|---|
PfPR by Age Bin |
The percentage of individuals who have BLOOD_SMEAR_PARASITES diagnostic returning a positive number of parasites. |
Pf Gametocyte Prevalence by Age Bin |
The percentage of individuals who have a BLOOD_SMEAR_GAMETOCYTES diagnostic return a value > 0.02. |
Mean Log Parasite Density |
The average Log10 parasite density of the population for that age bin. |
Annual Clinical Incidence by Age Bin |
The percentage of the population per day that has clinical symptoms. |
Annual Severe Incidence by Age Bin |
The percentage of the population per day that has severe symptoms. |
Average Population by Age Bin |
The average population of the people in the given age bin over the reporting internal/period. |
Annual Severe Incidence by Anemia by Age Bin |
The percentage of the population per day who have severe symptoms caused by Anemia. |
Annual Severe Incidence by Parasites by Age Bin |
The percentage of the population per day who have severe symptoms caused by Parasites. |
Annual Severe Incidence by Fever by Age Bin |
The percentage of the population per day who have severe symptoms caused by Fever. |
Annual Severe Anemia |
The percentage of the population per day whose hemoglobin count is less than 5. |
Annual Moderate Anemia |
The percentage of the population per day whose hemoglobin count is less than 8. |
Annual Mild Anemia |
The percentage of the population per day whose hemoglobin count is less than 11. |
DataByTimeAndPfPRBinsAndAgeBins¶
This section contains statistics in three-dimensional arrays: Time (the reporting interval), Parasitemia Bins, and Age Bins.
Parameter |
Description |
|---|---|
PfPR by Parasitemia and Age Bin |
The average number of individuals whose parasite density and age fall into this bin. |
PfPR by Gametocytemia and Age Bin |
The average number of individuals whose gametocyte density and age fall into this bin. |
Smeared PfPR by Parasitemia and Age Bin |
The average number of individuals whose parasite density (from the smear) and age fall into this bin. |
Smeared PfPR by Gametocytemia and Age Bin |
The average number of individuals whose gametocyte density (from the smear) and age fall into this bin. |
Smeared True PfPR by Parasitemia and Age Bin |
The average number of individuals whose parasite density (true value from the smear) and age fall into this bin. |
Smeared True PfPR by Gametocytemia and Age Bin |
The average number of individuals whose gametocyte density (true value from the smear) and age fall into this bin. |
DataByTimeAndInfectiousnessBinsAndPfPRBinsAndAgeBins¶
This section contains statistics in four-dimensional arrays: Time (the reporting interval), Infectiousness, Parasitemia Bins, and Age Bins.
Parameter |
Description |
|---|---|
Infectiousness by Gametocytemia and Age Bin |
The average number of individuals whose infectiousness, parasite density, and age fall into this bin. |
Age scaled Infectiousness by Gametocytemia and Age Bin |
Adjusted infectiousness for age-dependent Surface Area Biting. |
Infectiousness by smeared Gametocytemia and Age Bin |
The average number of individuals whose infectiousness, gametocyte density (from the smear) and age fall into this bin. |
Smeared Infectiousness by smeared Gametocytemia and Age Bin |
Both the infectiousness and the gametocyte densities are smeared when selecting the bin. |
Age scaled Smeared Infectiousness by smeared Gametocytemia and Age Bin |
Infectiousness is indexed by smearing the infectiousness with age-based Surface Area Biting and adjusted for Binomial Infectiousness. |
Example¶
The following is a sample of a MalariaSummaryReport.json file.
{
"Metadata": {
"Start_Day": 0,
"Reporting_Interval": 73,
"Age Bins": [
25,
50,
75,
125
],
"Parasitemia Bins": [
500,
50000,
9999999
],
"Gametocytemia Bins": [
500,
50000,
9999999
],
"Infectiousness Bins": [
50,
100
]
},
"DataByTime": {
"Time Of Report": [
73,
146,
219
],
"Annual EIR": [
3.162024962367,
17.51441525354,
11.87080321251
],
"PfPR_2to10": [
0.1704726251755,
0.4665846270352,
0.7762127578304
],
"No Infection Streak": [
0,
0,
0
],
"Fraction Days Under 1pct Infected": [
0,
0,
0
]
},
"DataByTimeAndAgeBins": {
"PfPR by Age Bin": [
[
0.1339885339885,
0.09905544651619,
0.09631578947368,
0.05854084753167
],
[
0.4092613233357,
0.3057670056635,
0.301073312716,
0.3378867014865
],
[
0.6964023568685,
0.4945852743663,
0.5197093551317,
0.5671100362757
]
],
"Pf Gametocyte Prevalence by Age Bin": [
[
0.101678951679,
0.0721908734053,
0.07070175438596,
0.0349497597204
],
[
0.3455263957848,
0.2407892332988,
0.2230307440422,
0.2619525914022
],
[
0.6942707181209,
0.4758303587634,
0.511353315168,
0.5461507456671
]
],
"Mean Log Parasite Density": [
[
2.306478442565,
1.629361294962,
1.661861693924,
1.524076431545
],
[
2.401303822193,
1.681284855785,
1.677762827268,
1.61520629859
],
[
2.423047828561,
1.609734215751,
1.605083507743,
1.682926607454
]
],
"Annual Clinical Incidence by Age Bin": [
[
1.741298153531,
0.2686457410455,
0.3201754391193,
0.1594582796097
],
[
4.401155002415,
0.9113330598921,
0.863198146224,
0.4399356991053
],
[
6.150984396227,
0.8612136561424,
0.7293369323015,
1.618299007416
]
],
"Annual Severe Incidence by Age Bin": [
[
1.091113864444,
0.08954858034849,
0.1921052634716,
0
],
[
3.017934858799,
0.4445527121425,
0.3319992870092,
0.1466452330351
],
[
3.611317807809,
0.3312360215932,
0.4641235023737,
0.4413542747498
]
],
"Average Population by Age Bin": [
[
669.0410958904,
223.3424657534,
78.08219178082,
31.35616438356
],
[
675.9589041096,
224.9452054795,
75.30136986301,
34.09589041096
],
[
681.1917808219,
226.4246575342,
75.41095890411,
33.98630136986
]
],
"Annual Severe Incidence by Anemia by Age Bin": [
[
0,
0,
0,
0
],
[
0,
0,
0,
0
],
[
0.007340076845139,
0,
0,
0
]
],
"Annual Severe Incidence by Parasites by Age Bin": [
[
0,
0,
0,
0
],
[
0,
0,
0,
0
],
[
0.007340076845139,
0,
0,
0
]
],
"Annual Severe Incidence by Fever by Age Bin": [
[
1.091113864444,
0.08954858034849,
0.1921052634716,
0
],
[
3.017934858799,
0.4445527121425,
0.3319992870092,
0.1466452330351
],
[
3.596637654118,
0.3312360215932,
0.4641235023737,
0.4413542747498
]
],
"Annual Severe Anemia": [
[
0,
0,
0,
0
],
[
0,
0,
0,
0
],
[
0,
0,
0,
0
]
],
"Annual Moderate Anemia": [
[
0.05978706106544,
0,
0,
0
],
[
1.33144184947,
0,
0,
0
],
[
9.461359053385,
0,
0,
0
]
],
"Annual Mild Anemia": [
[
4.087940300349,
0,
0,
0
],
[
21.04417812079,
0,
0,
0
],
[
43.99642060976,
0,
0,
0
]
]
},
"DataByTimeAndPfPRBinsAndAgeBins": {
"PfPR by Parasitemia and Age Bin": [
[
[
0.2156224406224,
0.2732458292444,
0.2470175438596,
0.1799912625601
],
[
0.04694922194922,
0.005642787046124,
0.005789473684211,
0.001310615989515
],
[
0.0009213759213759,
0,
0,
0
]
],
[
[
0.512513932516,
0.6836368065282,
0.6470802255776,
0.7127360385697
],
[
0.1522342689229,
0.02052250167468,
0.01691831908314,
0.01044596223383
],
[
0.004519201540176,
0,
0,
0
]
],
[
[
0.6575100046253,
0.9105814023837,
0.9227974568574,
0.9621120515921
],
[
0.2662738552497,
0.02014640934116,
0.02288828337875,
0.03385731559855
],
[
0.005268767470388,
0,
0,
0
]
]
],
"PfPR by Gametocytemia and Age Bin": [
[
[
0.231981981982,
0.2774165848871,
0.2522807017544,
0.1813018785496
],
[
0.03151105651106,
0.001472031403337,
0.0005263157894737,
0
],
[
0,
0,
0,
0
]
],
[
[
0.5678792177526,
0.6973996711528,
0.6556303438239,
0.7219766974689
],
[
0.1013881852265,
0.006759637050119,
0.00836820083682,
0.001205303334673
],
[
0,
0,
0,
0
]
],
[
[
0.6901079896233,
0.9226208482062,
0.9375113533152,
0.9794437726723
],
[
0.238944637722,
0.008106963518664,
0.008174386920981,
0.01652559451834
],
[
0,
0,
0,
0
]
]
],
"Smeared PfPR by Parasitemia and Age Bin": [
[
[
0.2155814905815,
0.2731231599607,
0.2470175438596,
0.1799912625601
],
[
0.02661752661753,
0.004600098135427,
0.005087719298246,
0.001310615989515
],
[
0.02129402129402,
0.001165358194308,
0.0007017543859649,
0
]
],
[
[
0.5121288884385,
0.6835150112661,
0.6470802255776,
0.7127360385697
],
[
0.07591447968386,
0.01583338408136,
0.01273421866473,
0.00964242667738
],
[
0.08122403485662,
0.00481091285549,
0.00418410041841,
0.0008035355564484
]
],
[
[
0.6564844048505,
0.9105814023837,
0.9235240690282,
0.9621120515921
],
[
0.1494962495224,
0.01675842458709,
0.01743869209809,
0.02700523982265
],
[
0.1230719729724,
0.003387984754069,
0.0047229791099,
0.006852075775897
]
]
],
"Smeared PfPR by Gametocytemia and Age Bin": [
[
[
0.2318386568387,
0.2772325809617,
0.2521052631579,
0.1813018785496
],
[
0.02223587223587,
0.001656035328754,
0.0007017543859649,
0
],
[
0.009418509418509,
0,
0,
0
]
],
[
[
0.5678589522748,
0.6966688995798,
0.6549026741859,
0.7219766974689
],
[
0.06651129800385,
0.007490408623105,
0.009095870474804,
0.001205303334673
],
[
0.03489715270037,
0,
0,
0
]
],
[
[
0.6902889778189,
0.9221368503842,
0.9378746594005,
0.9774284562676
],
[
0.1544834797997,
0.008590961340674,
0.007811080835604,
0.01854091092301
],
[
0.08428016972671,
0,
0,
0
]
]
],
"Smeared True PfPR by Parasitemia and Age Bin": [
[
[
0.2124488124488,
0.2658856722277,
0.2410526315789,
0.176496286588
],
[
0.04928337428337,
0.012941609421,
0.01175438596491,
0.004805591961555
],
[
0.001760851760852,
6.133464180569e-05,
0,
0
]
],
[
[
0.5028675651028,
0.6659155958833,
0.6308895761324,
0.6958617918843
],
[
0.1583341777282,
0.03781742890202,
0.03310896852829,
0.02732020891924
],
[
0.008065660147938,
0.0004262834175751,
0,
0
]
],
[
[
0.6451022583305,
0.8832960251679,
0.8986376021798,
0.9338976219266
],
[
0.273412834074,
0.0470082884627,
0.04668483197094,
0.06207174526401
],
[
0.01053753494078,
0.0004234980942586,
0.0003633060853769,
0
]
]
],
"Smeared True PfPR by Gametocytemia and Age Bin": [
[
[
0.2295864045864,
0.2739205103042,
0.249298245614,
0.1804281345566
],
[
0.03355855855856,
0.004968105986261,
0.003508771929825,
0.00087374399301
],
[
0.0003480753480753,
0,
0,
0
]
],
[
[
0.55768568244,
0.6868643809756,
0.6450791340731,
0.711530735235
],
[
0.110163137096,
0.01692954144084,
0.0187374931781,
0.0116512655685
],
[
0.001418583443105,
0.0003653857864929,
0.0001819174094961,
0
]
],
[
[
0.6753272869869,
0.9037449331478,
0.9171662125341,
0.9532446594115
],
[
0.2512920546182,
0.0269223788493,
0.0283378746594,
0.04272470777912
],
[
0.002433285740141,
6.049972775123e-05,
0.0001816530426885,
0
]
]
]
},
"DataByTimeAndInfectiousnessBinsAndPfPRBinsAndAgeBins": {
"Infectiousness by Gametocytemia and Age Bin": [
[
[
[
0.1968468468468,
0.2587708537782,
0.2326315789474,
0.176496286588
],
[
0.0001228501228501,
0,
0,
0
],
[
0,
0,
0,
0
]
],
[
[
0.03513513513514,
0.01864573110893,
0.01964912280702,
0.004805591961555
],
[
0.03138820638821,
0.001472031403337,
0.0005263157894737,
0
],
[
0,
0,
0,
0
]
]
],
[
[
[
0.4628635120073,
0.6436270629073,
0.5995997816991,
0.6777822418642
],
[
0.001013273887932,
0,
0,
0
],
[
0,
0,
0,
0
]
],
[
[
0.1050157057453,
0.05377260824554,
0.0560305621248,
0.04419445560466
],
[
0.1003749113385,
0.006759637050119,
0.00836820083682,
0.001205303334673
],
[
0,
0,
0,
0
]
]
],
[
[
[
0.4698855752408,
0.8167463246415,
0.8207084468665,
0.8363563079403
],
[
0.00166911335894,
0,
0,
0
],
[
0,
0,
0,
0
]
],
[
[
0.2202224143825,
0.1058745235646,
0.1168029064487,
0.143087464732
],
[
0.237275524363,
0.008106963518664,
0.008174386920981,
0.01652559451834
],
[
0,
0,
0,
0
]
]
]
],
"Age scaled Infectiousness by Gametocytemia and Age Bin": [
[
[
[
0.2228705978706,
0.2587708537782,
0.2326315789474,
0.176496286588
],
[
0.02727272727273,
0,
0,
0
],
[
0,
0,
0,
0
]
],
[
[
0.009111384111384,
0.01864573110893,
0.01964912280702,
0.004805591961555
],
[
0.004238329238329,
0.001472031403337,
0.0005263157894737,
0
],
[
0,
0,
0,
0
]
]
],
[
[
[
0.538453744047,
0.6436270629073,
0.5995997816991,
0.6777822418642
],
[
0.0857432363968,
0,
0,
0
],
[
0,
0,
0,
0
]
],
[
[
0.02942547370554,
0.05377260824554,
0.0560305621248,
0.04419445560466
],
[
0.01564494882967,
0.006759637050119,
0.00836820083682,
0.001205303334673
],
[
0,
0,
0,
0
]
]
],
[
[
[
0.6135700927062,
0.8167463246415,
0.8207084468665,
0.8363563079403
],
[
0.2018822772337,
0,
0,
0
],
[
0,
0,
0,
0
]
],
[
[
0.07653789691717,
0.1058745235646,
0.1168029064487,
0.143087464732
],
[
0.03706236048827,
0.008106963518664,
0.008174386920981,
0.01652559451834
],
[
0,
0,
0,
0
]
]
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