from numpy import log as log
[docs]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