Source code for emodpy_tbhiv.interventions.drugs

from numpy import log as log



def add_tb_drug_type(config, drug_name, duration, cure_proportion, death_proportion,
                     resistance_proportion, inactivation_proportion, relapse_proportion,
                     reduced_transmit=1, reduced_acquire=1,
                     cure_proportion_hiv=None, death_proportion_hiv=None,
                     resistance_proportion_hiv=None, relapse_proportion_hiv=None,
                     inactivation_proportion_hiv=None, mdr_cure_proportion=None,
                     mdr_death_proportion=None, mdr_inactivation_proportion=None,
                     mdr_relapse_proportion=None):
    """
    Add a drug definition to the simulation. This does not deliver the drug to anyone, and also
    doesn't mean we're going to use it. It's like putting it in the reference section.

    """

    def converttorate(proportion, interval):
        return -log(1.0 - proportion) / interval

    if cure_proportion_hiv is None:
        cure_proportion_hiv = cure_proportion
    if inactivation_proportion_hiv is None:
        inactivation_proportion_hiv = inactivation_proportion
    if relapse_proportion_hiv is None:
        relapse_proportion_hiv = relapse_proportion
    if death_proportion_hiv is None:
        death_proportion_hiv = death_proportion
    if resistance_proportion_hiv is None:
        resistance_proportion_hiv = resistance_proportion

    if mdr_cure_proportion is None:
        mdr_cure_proportion = cure_proportion
    if mdr_inactivation_proportion is None:
        mdr_inactivation_proportion = inactivation_proportion
    if mdr_relapse_proportion is None:
        mdr_relapse_proportion = relapse_proportion
    if mdr_death_proportion is None:
        mdr_death_proportion = death_proportion

    rate_res = converttorate(resistance_proportion, duration)
    rate_res_hiv = converttorate(resistance_proportion_hiv, duration)

    total_rate = converttorate(cure_proportion + inactivation_proportion + death_proportion + relapse_proportion,
                               duration)
    rate_cure = cure_proportion * total_rate
    rate_relapse = relapse_proportion * total_rate
    rate_death = death_proportion * total_rate
    rate_inactivation = inactivation_proportion * total_rate

    total_ratehiv = converttorate(cure_proportion_hiv + inactivation_proportion_hiv +
                                  death_proportion_hiv + relapse_proportion_hiv, duration)
    rate_curehiv = cure_proportion_hiv * total_ratehiv
    rate_relapsehiv = relapse_proportion_hiv * total_ratehiv
    rate_deathhiv = death_proportion_hiv * total_ratehiv
    rate_inactivationhiv = inactivation_proportion_hiv * total_ratehiv

    total_rate_mdr = converttorate(mdr_cure_proportion + mdr_inactivation_proportion +
                                   mdr_death_proportion + mdr_relapse_proportion, duration)
    rate_curemdr = mdr_cure_proportion * total_rate_mdr
    rate_relapsemdr = mdr_relapse_proportion * total_rate_mdr
    rate_deathmdr = mdr_death_proportion * total_rate_mdr
    rate_inactivationmdr = mdr_inactivation_proportion * total_rate_mdr

    drug_dict = {drug_name: dict(TB_Drug_Cure_Rate=rate_cure, TB_Drug_Cure_Rate_MDR=rate_curemdr,
                                 TB_Drug_Cure_Rate_HIV=rate_curehiv, TB_Drug_Inactivation_Rate=rate_inactivation,
                                 TB_Drug_Inactivation_Rate_MDR=rate_inactivationmdr,
                                 TB_Drug_Inactivation_Rate_HIV=rate_inactivationhiv,
                                 TB_Drug_Mortality_Rate=rate_death, TB_Drug_Mortality_Rate_MDR=rate_deathmdr,
                                 TB_Drug_Mortality_Rate_HIV=rate_deathhiv, TB_Drug_Relapse_Rate=rate_relapse,
                                 TB_Drug_Relapse_Rate_MDR=rate_relapsemdr, TB_Drug_Relapse_Rate_HIV=rate_relapsehiv,
                                 TB_Drug_Resistance_Rate=rate_res, TB_Drug_Resistance_Rate_HIV=rate_res_hiv,
                                 TB_Drug_Primary_Decay_Time_Constant=duration, TB_Reduced_Acquire=reduced_acquire,
                                 TB_Reduced_Transmit=reduced_transmit)
                 }
    current_drug_params = config.parameters.TBHIV_Drug_Params
    if drug_name in current_drug_params:
        print( f"Overriding pre-existing configuration for drug {drug_name}." )
    current_drug_params[drug_name] = drug_dict[drug_name]
    config.parameters.TBHIV_Drug_Params = current_drug_params


def _add_tb_drug(config, drug_name):
    
    """
    Tell the simulation which drugs we're going to use. Optionally override parameters in the process.
    This function is deprecated. The functionality provided here is now done automatically for you.

    """
    current_drug_names = config.parameters.TBHIV_Drug_Types
    if drug_name not in current_drug_names:
        current_drug_names.append(drug_name)
        config.parameters.TBHIV_Drug_Types = current_drug_names