Frequently asked questions

As you get started with emodpy-hiv, you may have questions. The most common questions are answered below. The most common questions are answered below. For questions related to functionality in related packages, see Frequently asked questions for idmtools, Frequently asked questions for emod-api, and Frequently asked questions for emodpy.

How do I set configuration parameters?

Define your own parameter-setting function such as set_param_fn and pass that function to the emodpy task creator as the param_custom_cb parameter. In that function, you can set the parameters directly. For example:

    config.parameters.Enable_Demographics_Reporting = 0  # just because I don't like our default for this

    # config hacks until schema fixes arrive
    config.parameters.pop( "Serialized_Population_Filenames" )
    config.parameters.pop( "Serialization_Time_Steps" )
    config.parameters.Report_HIV_Event_Channels_List = []
    config.parameters.Male_To_Female_Relative_Infectivity_Ages = [] # 15,25,35 ]
    config.parameters.Male_To_Female_Relative_Infectivity_Multipliers = [] # 5, 1, 0.5 ]
    # This one is crazy! :(
    config.parameters.Maternal_Infection_Transmission_Probability = 0

    return config


def build_camp():
    """
    Build a campaign input file for the DTK using emod_api.
    Right now this function creates the file and returns the filename. If calling code just needs an asset that's fine.

See examples/start_here/example.py. for additional information.

If you prefer something more modular, you can call a function in a standalone script/file that sets the configuration parameters.

Are there parameter defaults?

Great question. If you don’t set any configuration parameters, they will have defaults based on the schema. There are not yet configuration parameter defaults specific to HIV.

The HIV team has some demographic parameter defaults set using emodpy_hiv.demographics.DemographicsTemplates.AddDefaultSociety(). They can be seen below.

def set_society_configs( config ):
    print( "TBD: Should be adding some implicit config here." )
    return config

def AddDefaultSociety( demog ):
    """
    Adds a PFA config based on IDM defaults.
    """
    setting = {
        "Society" : {
            "Concurrency_Configuration" : 
            {
                "Probability_Person_Is_Behavioral_Super_Spreader" : 0,
                "Individual_Property_Name": "NONE", 
                "NONE": 
                {
                    "Extra_Relational_Flag_Type": "Independent"
                }
            },
            "TRANSITORY" :
            {
                "Concurrency_Parameters" :
                {
                    "NONE": 
                    {
                        "Max_Simultaneous_Relationships_Female": 1,
                        "Max_Simultaneous_Relationships_Male"  : 1,
                        "Prob_Extra_Relationship_Female"       : 0,
                        "Prob_Extra_Relationship_Male"         : 0
                    }
                },
                "Relationship_Parameters" :
                {
                    "Coital_Act_Rate" : 0.33,
                    "Condom_Usage_Probability" :
                    {
                        "Min": 0.10,
                        "Max": 0.90,
                        "Mid": 2000,
                        "Rate": 1
                    },
                    "Duration_Weibull_Heterogeneity": 0.833333333,
                    "Duration_Weibull_Scale": 0.956774771214,
                    "Migration_Actions" : [ "TERMINATE" ],
                    "Migration_Actions_Distribution" : [ 1.0 ]
                },
                "Pair_Formation_Parameters" :
                {
                    "Formation_Rate_Type" : "CONSTANT",
                    "Formation_Rate_Constant": 0.0014424307254,
                    "Update_Period" : 0.0,
                    "Extra_Relational_Rate_Ratio_Male": 1,
                    "Extra_Relational_Rate_Ratio_Female": 1,
                    "Number_Age_Bins_Male"   : 20,
                    "Number_Age_Bins_Female" : 20,
                    "Age_of_First_Bin_Edge_Male"   : 17.5,
                    "Age_of_First_Bin_Edge_Female" : 17.5,
                    "Years_Between_Bin_Edges_Male"   : 2.5,
                    "Years_Between_Bin_Edges_Female" : 2.5,
                    "Joint_Probabilities" :
                    [
                        [ 0.045567, 0.035956, 0.019793, 0.007568, 0.002328, 0.000551, 0.000059, 0.000018, 0.000004, 0.000001, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.044738, 0.036352, 0.021958, 0.010123, 0.003782, 0.001001, 0.000184, 0.000073, 0.000022, 0.000004, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.041749, 0.037081, 0.028094, 0.017609, 0.008170, 0.002469, 0.000642, 0.000267, 0.000090, 0.000021, 0.000002, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.034883, 0.034782, 0.032721, 0.025031, 0.013417, 0.004969, 0.001732, 0.000707, 0.000251, 0.000079, 0.000018, 0.000004, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.022317, 0.025265, 0.028532, 0.025516, 0.016489, 0.008321, 0.003780, 0.001533, 0.000572, 0.000213, 0.000062, 0.000012, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.009200, 0.013361, 0.019412, 0.020918, 0.016811, 0.011010, 0.005957, 0.002611, 0.001029, 0.000369, 0.000102, 0.000020, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.002873, 0.006137, 0.011340, 0.014349, 0.013829, 0.010947, 0.007060, 0.003720, 0.001602, 0.000506, 0.000122, 0.000031, 0.000004, 0.000001, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.001060, 0.002528, 0.005183, 0.007796, 0.009413, 0.009220, 0.007328, 0.004767, 0.002392, 0.000882, 0.000305, 0.000121, 0.000038, 0.000008, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.000282, 0.000827, 0.002074, 0.004090, 0.006305, 0.007459, 0.007090, 0.005534, 0.003443, 0.001782, 0.000873, 0.000393, 0.000140, 0.000032, 0.000002, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.000148, 0.000373, 0.001016, 0.002362, 0.004162, 0.005612, 0.006176, 0.005583, 0.004120, 0.002630, 0.001522, 0.000769, 0.000319, 0.000097, 0.000021, 0.000004, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.000077, 0.000166, 0.000484, 0.001276, 0.002467, 0.003661, 0.004442, 0.004384, 0.003574, 0.002614, 0.001800, 0.001118, 0.000585, 0.000245, 0.000083, 0.000020, 0.000002, 0.000000, 0.000000, 0.000000 ],
                        [ 0.000096, 0.000144, 0.000302, 0.000669, 0.001252, 0.001963, 0.002577, 0.002736, 0.002445, 0.002074, 0.001750, 0.001355, 0.000895, 0.000496, 0.000222, 0.000071, 0.000017, 0.000003, 0.000000, 0.000000 ],
                        [ 0.000219, 0.000202, 0.000201, 0.000291, 0.000540, 0.001013, 0.001555, 0.001784, 0.001668, 0.001522, 0.001453, 0.001358, 0.001170, 0.000855, 0.000475, 0.000195, 0.000063, 0.000013, 0.000000, 0.000000 ],
                        [ 0.000320, 0.000250, 0.000144, 0.000097, 0.000205, 0.000567, 0.001037, 0.001230, 0.001110, 0.000997, 0.001033, 0.001178, 0.001296, 0.001150, 0.000755, 0.000381, 0.000150, 0.000037, 0.000004, 0.000001 ],
                        [ 0.000227, 0.000170, 0.000077, 0.000015, 0.000051, 0.000253, 0.000535, 0.000648, 0.000582, 0.000560, 0.000678, 0.000905, 0.001125, 0.001143, 0.000924, 0.000598, 0.000283, 0.000086, 0.000021, 0.000010 ],
                        [ 0.000062, 0.000046, 0.000021, 0.000004, 0.000014, 0.000069, 0.000146, 0.000177, 0.000176, 0.000240, 0.000395, 0.000600, 0.000804, 0.000943, 0.000951, 0.000756, 0.000428, 0.000183, 0.000088, 0.000063 ],
                        [ 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000015, 0.000076, 0.000194, 0.000361, 0.000551, 0.000720, 0.000808, 0.000735, 0.000536, 0.000355, 0.000253, 0.000212 ],
                        [ 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000004, 0.000021, 0.000070, 0.000186, 0.000351, 0.000496, 0.000586, 0.000621, 0.000607, 0.000555, 0.000489, 0.000451 ],
                        [ 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000015, 0.000077, 0.000184, 0.000305, 0.000424, 0.000543, 0.000649, 0.000717, 0.000746, 0.000754 ],
                        [ 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000005, 0.000024, 0.000074, 0.000178, 0.000331, 0.000500, 0.000666, 0.000820, 0.000946, 0.001010 ]
                    ],
                    "Assortivity" :
                    {
                        "Group" : "NO_GROUP"
                    }
                }
            },
            "INFORMAL" :
            {
                "Concurrency_Parameters" :
                {
                    "NONE": 
                    {
                        "Max_Simultaneous_Relationships_Female": 1,
                        "Max_Simultaneous_Relationships_Male"  : 1,
                        "Prob_Extra_Relationship_Female"       : 0,
                        "Prob_Extra_Relationship_Male"         : 0
                    }
                },
                "Relationship_Parameters" :
                {
                    "Coital_Act_Rate" : 0.33,
                    "Condom_Usage_Probability" :
                    {
                        "Min": 0.10,
                        "Max": 0.90,
                        "Mid": 2000,
                        "Rate": 1
                    },
                    "Duration_Weibull_Heterogeneity": 0.5,
                    "Duration_Weibull_Scale": 2.03104913138,
                    "Migration_Actions" : [ "TERMINATE" ],
                    "Migration_Actions_Distribution" : [ 1.0 ]
                },
                "Pair_Formation_Parameters" :
                {
                    "Formation_Rate_Type" : "CONSTANT",
                    "Formation_Rate_Constant": 0.00146753349399999,
                    "Update_Period" : 0.0,
                    "Extra_Relational_Rate_Ratio_Male": 1,
                    "Extra_Relational_Rate_Ratio_Female": 1,
                    "Number_Age_Bins_Male"   : 20,
                    "Number_Age_Bins_Female" : 20,
                    "Age_of_First_Bin_Edge_Male"   : 17.5,
                    "Age_of_First_Bin_Edge_Female" : 17.5,
                    "Years_Between_Bin_Edges_Male"   : 2.5,
                    "Years_Between_Bin_Edges_Female" : 2.5,
                    "Joint_Probabilities" :
                    [
                        [ 0.021820, 0.016798, 0.008474, 0.002572, 0.000566, 0.000133, 0.000012, 0.000002, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.022878, 0.018808, 0.011747, 0.005706, 0.002183, 0.000534, 0.000061, 0.000012, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.025094, 0.023590, 0.019998, 0.013835, 0.006582, 0.001817, 0.000321, 0.000075, 0.000008, 0.000003, 0.000001, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.024383, 0.026075, 0.027147, 0.022210, 0.012255, 0.004504, 0.001348, 0.000349, 0.000061, 0.000025, 0.000008, 0.000002, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.017162, 0.021429, 0.026924, 0.025626, 0.017250, 0.008852, 0.003661, 0.001076, 0.000252, 0.000092, 0.000027, 0.000006, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.008432, 0.013738, 0.021613, 0.024180, 0.019887, 0.013033, 0.006651, 0.002503, 0.000812, 0.000255, 0.000063, 0.000019, 0.000004, 0.000001, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.003736, 0.007791, 0.014370, 0.018571, 0.018491, 0.014865, 0.009391, 0.004734, 0.001979, 0.000629, 0.000170, 0.000062, 0.000019, 0.000006, 0.000002, 0.000001, 0.000001, 0.000000, 0.000000, 0.000000 ],
                        [ 0.001699, 0.003707, 0.007467, 0.011553, 0.014397, 0.014112, 0.010869, 0.006905, 0.003605, 0.001505, 0.000575, 0.000218, 0.000079, 0.000034, 0.000017, 0.000010, 0.000004, 0.000001, 0.000000, 0.000000 ],
                        [ 0.000649, 0.001503, 0.003405, 0.006352, 0.009457, 0.010871, 0.010096, 0.007985, 0.005372, 0.003070, 0.001478, 0.000581, 0.000222, 0.000103, 0.000053, 0.000030, 0.000012, 0.000002, 0.000000, 0.000000 ],
                        [ 0.000253, 0.000604, 0.001471, 0.003029, 0.005049, 0.006871, 0.007949, 0.007848, 0.006588, 0.004633, 0.002576, 0.001130, 0.000463, 0.000197, 0.000093, 0.000050, 0.000020, 0.000004, 0.000000, 0.000000 ],
                        [ 0.000096, 0.000274, 0.000712, 0.001492, 0.002634, 0.004087, 0.005552, 0.006489, 0.006506, 0.005362, 0.003450, 0.001796, 0.000819, 0.000328, 0.000137, 0.000067, 0.000025, 0.000006, 0.000001, 0.000000 ],
                        [ 0.000066, 0.000224, 0.000546, 0.000969, 0.001526, 0.002331, 0.003383, 0.004556, 0.005399, 0.005125, 0.003806, 0.002370, 0.001298, 0.000621, 0.000278, 0.000118, 0.000045, 0.000015, 0.000004, 0.000001 ],
                        [ 0.000034, 0.000126, 0.000314, 0.000562, 0.000882, 0.001325, 0.001955, 0.002844, 0.003711, 0.003916, 0.003386, 0.002613, 0.001862, 0.001172, 0.000606, 0.000252, 0.000098, 0.000039, 0.000012, 0.000003 ],
                        [ 0.000009, 0.000033, 0.000107, 0.000275, 0.000523, 0.000781, 0.001072, 0.001508, 0.002033, 0.002423, 0.002583, 0.002548, 0.002296, 0.001748, 0.001030, 0.000478, 0.000199, 0.000073, 0.000021, 0.000006 ],
                        [ 0.000000, 0.000000, 0.000021, 0.000106, 0.000244, 0.000370, 0.000495, 0.000703, 0.001023, 0.001429, 0.001860, 0.002219, 0.002354, 0.002059, 0.001414, 0.000786, 0.000357, 0.000120, 0.000030, 0.000008 ],
                        [ 0.000000, 0.000000, 0.000006, 0.000028, 0.000066, 0.000112, 0.000179, 0.000309, 0.000527, 0.000843, 0.001243, 0.001692, 0.002040, 0.002018, 0.001612, 0.001064, 0.000557, 0.000218, 0.000067, 0.000018 ],
                        [ 0.000000, 0.000000, 0.000000, 0.000000, 0.000003, 0.000013, 0.000053, 0.000161, 0.000337, 0.000537, 0.000769, 0.001088, 0.001424, 0.001582, 0.001485, 0.001178, 0.000762, 0.000404, 0.000178, 0.000078 ],
                        [ 0.000000, 0.000000, 0.000000, 0.000000, 0.000001, 0.000003, 0.000034, 0.000143, 0.000303, 0.000410, 0.000468, 0.000594, 0.000806, 0.001025, 0.001160, 0.001107, 0.000884, 0.000635, 0.000444, 0.000350 ],
                        [ 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000024, 0.000119, 0.000259, 0.000338, 0.000354, 0.000400, 0.000512, 0.000665, 0.000808, 0.000863, 0.000843, 0.000852, 0.000910, 0.000951 ],
                        [ 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000020, 0.000101, 0.000223, 0.000309, 0.000345, 0.000378, 0.000427, 0.000485, 0.000549, 0.000625, 0.000753, 0.001001, 0.001315, 0.001501 ]
                    ],
                    "Assortivity" :
                    {
                        "Group" : "NO_GROUP"
                    }
                }
            },
            "MARITAL" :
            {
                "Concurrency_Parameters" :
                {
                    "NONE": 
                    {
                        "Max_Simultaneous_Relationships_Female": 1,
                        "Max_Simultaneous_Relationships_Male"  : 1,
                        "Prob_Extra_Relationship_Female"       : 0,
                        "Prob_Extra_Relationship_Male"         : 0
                    }
                },
                "Relationship_Parameters" :
                {
                    "Coital_Act_Rate" : 0.33,
                    "Condom_Usage_Probability" :
                    {
                        "Min": 0.10,
                        "Max": 0.90,
                        "Mid": 2001,
                        "Rate": 1
                    },
                    "Duration_Weibull_Heterogeneity": 0.666666667,
                    "Duration_Weibull_Scale": 22.154455184937,
                    "Migration_Actions" : [ "TERMINATE" ],
                    "Migration_Actions_Distribution" : [ 1.0 ]
                },
                "Pair_Formation_Parameters" :
                {
                    "Formation_Rate_Type" : "CONSTANT",
                    "Formation_Rate_Constant": 0.0000914427211999999,
                    "Update_Period" : 0.0,
                    "Extra_Relational_Rate_Ratio_Male": 1,
                    "Extra_Relational_Rate_Ratio_Female": 1,
                    "Number_Age_Bins_Male"   : 20,
                    "Number_Age_Bins_Female" : 20,
                    "Age_of_First_Bin_Edge_Male"   : 17.5,
                    "Age_of_First_Bin_Edge_Female" : 17.5,
                    "Years_Between_Bin_Edges_Male"   : 2.5,
                    "Years_Between_Bin_Edges_Female" : 2.5,
                    "Joint_Probabilities" :
                    [
                        [ 0.001014, 0.000773, 0.000377, 0.000102, 0.000016, 0.000003, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.001467, 0.001149, 0.000618, 0.000222, 0.000062, 0.000012, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.002110, 0.001740, 0.001116, 0.000633, 0.000393, 0.000235, 0.000098, 0.000020, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.002212, 0.002054, 0.001796, 0.001620, 0.001472, 0.001076, 0.000489, 0.000098, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.001684, 0.001953, 0.002461, 0.003028, 0.003301, 0.002735, 0.001514, 0.000551, 0.000155, 0.000031, 0.000001, 0.000005, 0.000009, 0.000009, 0.000005, 0.000001, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.001040, 0.001617, 0.002774, 0.004255, 0.005423, 0.005206, 0.003661, 0.001972, 0.000775, 0.000155, 0.000005, 0.000024, 0.000047, 0.000047, 0.000024, 0.000005, 0.000000, 0.000000, 0.000000, 0.000000 ],
                        [ 0.000569, 0.001200, 0.002613, 0.004826, 0.007094, 0.007849, 0.006726, 0.004557, 0.002234, 0.000711, 0.000183, 0.000092, 0.000101, 0.000097, 0.000050, 0.000013, 0.000002, 0.000000, 0.000000, 0.000000 ],
                        [ 0.000339, 0.000830, 0.002079, 0.004396, 0.007285, 0.009393, 0.009818, 0.008106, 0.004974, 0.002315, 0.000877, 0.000269, 0.000126, 0.000108, 0.000063, 0.000025, 0.000008, 0.000002, 0.000000, 0.000000 ],
                        [ 0.000293, 0.000570, 0.001407, 0.003244, 0.006069, 0.009393, 0.011954, 0.011712, 0.008762, 0.005333, 0.002674, 0.001056, 0.000371, 0.000138, 0.000062, 0.000038, 0.000016, 0.000003, 0.000000, 0.000000 ],
                        [ 0.000253, 0.000419, 0.000970, 0.002268, 0.004615, 0.008232, 0.012061, 0.013764, 0.012690, 0.009880, 0.006410, 0.003391, 0.001375, 0.000352, 0.000070, 0.000039, 0.000016, 0.000003, 0.000000, 0.000000 ],
                        [ 0.000159, 0.000333, 0.000802, 0.001727, 0.003427, 0.006363, 0.010138, 0.013505, 0.015301, 0.014457, 0.011223, 0.007178, 0.003560, 0.001263, 0.000358, 0.000087, 0.000009, 0.000002, 0.000000, 0.000000 ],
                        [ 0.000075, 0.000230, 0.000598, 0.001230, 0.002345, 0.004316, 0.007261, 0.011034, 0.014582, 0.015942, 0.014559, 0.011288, 0.007231, 0.003733, 0.001443, 0.000304, 0.000009, 0.000002, 0.000000, 0.000000 ],
                        [ 0.000027, 0.000102, 0.000300, 0.000684, 0.001367, 0.002505, 0.004362, 0.007309, 0.010903, 0.013882, 0.015276, 0.014404, 0.011428, 0.007354, 0.003388, 0.000935, 0.000171, 0.000046, 0.000007, 0.000002 ],
                        [ 0.000005, 0.000020, 0.000090, 0.000286, 0.000658, 0.001226, 0.002235, 0.004148, 0.007018, 0.010488, 0.013644, 0.015020, 0.013925, 0.010445, 0.005801, 0.002345, 0.000792, 0.000218, 0.000037, 0.000010 ],
                        [ 0.000000, 0.000000, 0.000020, 0.000102, 0.000273, 0.000549, 0.001102, 0.002260, 0.004239, 0.007138, 0.010432, 0.012966, 0.013724, 0.011826, 0.007974, 0.004455, 0.002233, 0.000958, 0.000324, 0.000092 ],
                        [ 0.000000, 0.000000, 0.000013, 0.000063, 0.000163, 0.000314, 0.000611, 0.001249, 0.002433, 0.004383, 0.006909, 0.009408, 0.011056, 0.010813, 0.008887, 0.006737, 0.004916, 0.003067, 0.001322, 0.000382 ],
                        [ 0.000000, 0.000000, 0.000018, 0.000088, 0.000203, 0.000312, 0.000455, 0.000764, 0.001380, 0.002449, 0.003925, 0.005568, 0.007040, 0.007909, 0.008149, 0.008144, 0.007639, 0.005738, 0.002924, 0.001208 ],
                        [ 0.000000, 0.000000, 0.000018, 0.000088, 0.000198, 0.000288, 0.000365, 0.000502, 0.000770, 0.001238, 0.001911, 0.002730, 0.003684, 0.004800, 0.006002, 0.007105, 0.007580, 0.006558, 0.004455, 0.003100 ],
                        [ 0.000000, 0.000000, 0.000009, 0.000044, 0.000105, 0.000175, 0.000244, 0.000316, 0.000417, 0.000601, 0.000889, 0.001276, 0.001787, 0.002479, 0.003318, 0.004175, 0.004909, 0.005365, 0.005540, 0.005586 ],
                        [ 0.000000, 0.000000, 0.000002, 0.000012, 0.000038, 0.000096, 0.000173, 0.000228, 0.000270, 0.000355, 0.000509, 0.000729, 0.001011, 0.001347, 0.001743, 0.002217, 0.002961, 0.004339, 0.006055, 0.007062 ]
                    ],
                    "Assortivity" :
                    {
                        "Group" : "NO_GROUP"
                    }
                }
            },
            "COMMERCIAL" :
            {
                "Concurrency_Parameters" :
                {
                    "NONE": 
                    {
                        "Max_Simultaneous_Relationships_Female": 0,
                        "Max_Simultaneous_Relationships_Male"  : 0,
                        "Prob_Extra_Relationship_Female"       : 0,
                        "Prob_Extra_Relationship_Male"         : 0
                    }
                },
                "Relationship_Parameters" :
                {
                    "Coital_Act_Rate" : 0.33,
                    "Condom_Usage_Probability" :
                    {
                        "Min": 0.10,
                        "Max": 0.90,
                        "Mid": 2000,
                        "Rate": 1
                    },
                    "Duration_Weibull_Heterogeneity": 0.833333333,
                    "Duration_Weibull_Scale": 0.956774771214,
                    "Migration_Actions" : [ "TERMINATE" ],
                    "Migration_Actions_Distribution" : [ 1.0 ]
                },
                "Pair_Formation_Parameters" :
                {
                    "Formation_Rate_Type" : "CONSTANT",
                    "Formation_Rate_Constant": 0.0,
                    "Update_Period" : 7.0,
                    "Extra_Relational_Rate_Ratio_Male": 1,
                    "Extra_Relational_Rate_Ratio_Female": 1,
                    "Number_Age_Bins_Male"   : 2,
                    "Number_Age_Bins_Female" : 2,
                    "Age_of_First_Bin_Edge_Male"   : 50,
                    "Age_of_First_Bin_Edge_Female" : 50,
                    "Years_Between_Bin_Edges_Male"   : 35,
                    "Years_Between_Bin_Edges_Female" : 35,
                    "Joint_Probabilities" :
                    [
                        [ 0, 1 ],
                        [ 1, 0 ]
                    ],
                    "Assortivity" :
                    {
                        "Group" : "NO_GROUP"
                    }
                }
            }
        }
    }
    demog.raw['Defaults'].update( setting )
    #demog.SetNodeDefaultFromTemplate( setting, set_society_configs )

I see lots of HIV_SIM examples. Are there any STI_SIM examples?

Not at this time.

I pip installed emodpy-hiv, but I want to make changes. How should I do that?

Install at a command prompt using the following:

python package_setup.py develop

This method is the most popular and proven, though there are some other options. Installing this way means that the emodpy-hiv module in site-packages actually points to the same code as you have checked out in git. For more detail, see this Stack Overflow post.

However, we aim to get the desired changes quickly tested and included in the versioned module we release via pip install.