Frequently asked questions¶
As you get started with emodpy-hiv, you may have questions. 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_fnand pass that function to the emodpy task creator as theparam_custom_cbparameter. 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 config.parameters['logLevel_default'] = "WARNING" # 'LogLevel_Default' is not in scheme, so need to use the old style dict keys return config def build_camp(): """ Build a campaign input file for the DTK using emod_api.
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.from copy import deepcopy societies = dict() societies["default"] = { "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, 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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, 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"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" } } } } } societies["PFA-Southern-Africa"] = { "IndividualProperties": [ { "Property": "Risk", "Values": ["LOW", "MEDIUM", "HIGH"], "Initial_Distribution": [0.6669671396606822, 0.3330328603393178, 0] } ], "Society": { "Concurrency_Configuration": { "Probability_Person_Is_Behavioral_Super_Spreader": 0, "Individual_Property_Name": "Risk", "HIGH": { "Extra_Relational_Flag_Type": "Correlated", "Correlated_Relationship_Type_Order": [ "COMMERCIAL", "TRANSITORY", "INFORMAL", "MARITAL" ] }, "LOW": { 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0.005534, 0.003443, 0.001782, 0.000873, 0.000393, 0.00014, 3.2e-05, 2e-06, 0.0, 0.0, 0.0, 0.0, 0.0 ], [ 0.000148, 0.000373, 0.001016, 0.002362, 0.004162, 0.005612, 0.006176, 0.005583, 0.00412, 0.00263, 0.001522, 0.000769, 0.000319, 9.7e-05, 2.1e-05, 4e-06, 0.0, 0.0, 0.0, 0.0 ], [ 7.7e-05, 0.000166, 0.000484, 0.001276, 0.002467, 0.003661, 0.004442, 0.004384, 0.003574, 0.002614, 0.0018, 0.001118, 0.000585, 0.000245, 8.3e-05, 2e-05, 2e-06, 0.0, 0.0, 0.0 ], [ 9.6e-05, 0.000144, 0.000302, 0.000669, 0.001252, 0.001963, 0.002577, 0.002736, 0.002445, 0.002074, 0.00175, 0.001355, 0.000895, 0.000496, 0.000222, 7.1e-05, 1.7e-05, 3e-06, 0.0, 0.0 ], [ 0.000219, 0.000202, 0.000201, 0.000291, 0.00054, 0.001013, 0.001555, 0.001784, 0.001668, 0.001522, 0.001453, 0.001358, 0.00117, 0.000855, 0.000475, 0.000195, 6.3e-05, 1.3e-05, 0.0, 0.0 ], [ 0.00032, 0.00025, 0.000144, 9.7e-05, 0.000205, 0.000567, 0.001037, 0.00123, 0.00111, 0.000997, 0.001033, 0.001178, 0.001296, 0.00115, 0.000755, 0.000381, 0.00015, 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0.00082, 0.000946, 0.00101 ] ], "Assortivity": { "Axes": [ "LOW", "MEDIUM", "HIGH" ], "Group": "INDIVIDUAL_PROPERTY", "Property_Name": "Risk", "Weighting_Matrix_RowMale_ColumnFemale": [ [0.6097767084, 0.3902232916, 0], [0.3902232916, 0.6097767084, 0.6097767084], [0, 0.6097767084, 0.3902232916] ] } } } } } def add_society_from_template(demog, key="default"): demog.raw['Defaults'].update(deepcopy(societies[key])) def add_default_society(demog): """ Adds a PFA config based on IDM defaults. """ add_society_from_template(demog)
- 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.