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.
Define your own parameter-setting function such as
set_param_fn and pass
that function to the emodpy task creator as the
parameter. In that function, you can set the parameters directly. For
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 config.parameters.Incubation_Period_Distribution = "CONSTANT_DISTRIBUTION" return config def build_camp(): """
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.
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
They can be seen in demographics/DemographicsTemplates.py.
You can use the following code:
def build_campaign(): import emod_api.campaign as camp camp.set_schema( manifest.schema_path ) # don't worry about this for now import emodpy_hiv.interventions.outbreak as ob event = ob.new_intervention( timestep=365, camp=camp, coverage=0.01 ) camp.add( event ) return camp
The code above creates a new intervention from the outbreak submodule that causes 1% of the population to get an infection at timestep 365, and then adds that to the campaign. The only remaining thing to do is pass the ‘build_campaign’ function to the task creator function (‘from_default2’ ). To see the documentation for the hiv outbreak module go here.
We’re going to divide this into 4 steps:
Import the art module for creating the ART intervention.
Create the ART intervention the way you want it.
import and emod_api.interventions.common module for distribution interventions.
Invoke the ScheduledCampaignEvent function.
Let’s look at the code that will go into your build_campaign function::
def build_campaign(): import emod_api.campaign as camp camp.set_schema( manifest.schema_path ) # don't worry about this for now import emodpy_hiv.interventions.art as art import emod_api.interventions.common as com art_iv = art.new_intervention( camp ) event1 = com.ScheduledCampaignEvent( camp, Start_Day=123, Intervention_List=[ art_iv ] ) camp.add( event ) event2 = com.ScheduledCampaignEvent( camp, Start_Day=366, Node_Ids=[ 1 ], Number_Repetitions = 10 Timesteps_Between_Repetitions = 14, Property_Restrictions = "Risk=High", Demographic_Coverage = 0.04, Target_Age_Min=20*365, Target_Age_Max=25*365, Target_Gender = "Male", Intervention_List=[ art_iv ]) ) camp.add( event )
The first 4 lines take care of our imports and initializating the campaign module with the schema. The next line creates the simplest possible intervention. Then we create a campaign event that distributes the ART intervention at timestep 123, and we add this to the campaign. Because we leave all the targeting parameters unspecified, the function uses the defaults, which basically means “everybody”. In event2, we use all of the targeting and scheduling parameters to distributing ART every 2 weeks, 10 times in a row, starting at t=366, just in node 1, to 4% of the males between the ages of 20 and 25 in the “High Risk” group based on individual properties. Now in practice the repetitions don’t make much sense because we’re targeting the same people each rep as we got the first time, but it makes the point.
The key part here is to use the TriggeredCampaignEvent function instead of ScheduledCampaignEvent. Let’s look at the code::
def build_campaign(): import emod_api.campaign as camp camp.set_schema( manifest.schema_path ) # don't worry about this for now import emodpy_hiv.interventions.art as art import emod_api.interventions.common as com art_iv = art.new_intervention( camp ) event1 = com.TriggeredCampaignEvent( camp, Start_Day=123, Event_Trigger="NewInfection", Intervention_List=[ art_iv ] ) camp.add( event )
So we can see that the code is very similar, but we pass a new parameter to this new function, Event_Trigger. This can be any built-in event known to the model – usually related to health events – or an ad-hoc one you publish from another campaign event.
Yes. There is a function to do most of the above for you. But you still create and pass the intervention itself.
You can use the BroadcastEvent function and use that as the intervention or just one of multiple interventions.
What if I want to have a delay between the trigger (signal) and when the intervention is actually distributed?¶
You may want to use this function.
First, find the test intervention. This code should now seem unsurprising.:
def build_campaign(): import emod_api.campaign as camp camp.set_schema( manifest.schema_path ) import emodpy_hiv.interventions.art as art import emodpy_hiv.interventions.rapiddiag as diag import emod_api.interventions.common as com diagnostic = diag.new_intervention( camp ) art_iv = art.new_intervention( camp ) test_event = com.TriggeredCampaignEvent( camp, Start_Day=1, Event_Trigger="NewInfection", Intervention_List=[ diagnostic ] ) treat_event = com.TriggeredCampaignEvent( camp, Start_Day=1, Event_Trigger="TestedPositive", Intervention_List=[ art_iv ] ) camp.add( test_event ) camp.add( treat_event )
Testing everyone who is infected is obviously a bit naive but it just shows the idea.
Not at this time.
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.
pip install emodpy_hiv –upgrade –upgrade-strategy eager