Parameterise antimalarial resistance

Parameterise antimalarial resistance

set_antimalarial_resistance(
  parameters,
  drug,
  timesteps,
  artemisinin_resistance_proportion,
  partner_drug_resistance_proportion,
  slow_parasite_clearance_probability,
  early_treatment_failure_probability,
  late_clinical_failure_probability,
  late_parasitological_failure_probability,
  reinfection_during_prophylaxis_probability,
  slow_parasite_clearance_time
)

Arguments

parameters

the model parameters

drug

the index of the drug which resistance is being set, as set by the set_drugs() function, in the parameter list

timesteps

vector of time steps for each update to resistance proportion and resistance outcome probability

artemisinin_resistance_proportion

vector of updates to the proportions of infections that are artemisinin resistant at time t

partner_drug_resistance_proportion

vector of updates to the proportions of infections that are partner-drug resistant at time t

slow_parasite_clearance_probability

vector of updates to the proportion of artemisinin-resistant infections that result in early treatment failure

early_treatment_failure_probability

vector of updates to the proportion of artemisinin-resistant infections that result in slow parasite clearance

late_clinical_failure_probability

vector of updates to the proportion of partner-drug-resistant infections that result in late clinical failure

late_parasitological_failure_probability

vector of updates to the proportion of partner-drug-resistant infections that result in late parasitological failure

reinfection_during_prophylaxis_probability

vector of updates to the proportion of partner-drug-resistant infections that result in reinfection during prophylaxis

slow_parasite_clearance_time

single value representing the mean time individual's experiencing slow parasite clearance reside in the treated state