List for simulating drug usage for resistance/mft variables
drug_list_create(
resistance_flag = FALSE,
number_of_resistance_loci = 2,
artemisinin_loci = c(0),
cost_of_resistance = c(0.99, 0.99),
absolute_fitness_cost_flag = FALSE,
epistatic_logic = NULL,
number_of_drugs = 1,
drugs = list(drug_create_default_no_resistance()),
mft_flag = FALSE,
temporal_cycling = -1,
sequential_cycling = -1,
sequential_update = 3,
drug_choice = 0,
partner_drug_ratios = rep(1/number_of_drugs, number_of_drugs)
)Boolean are we simulating resistance
Numeric for number of res. loci
Numerics for barcode positions that confer artemisinin resistance
Numeric vector for fitness cost of each resistance loci.
Boolean are we simulating fitness costs as absolute (i.e. impactive onward transmission chance) or relative (resistant strains have decreases chance of being onwardly transmitted in mixed infections). Default = FALSE.
Is there compensatory relationships. i.e. what loci need to be true for resistance cost to exist. Default of NULL means that this becomes seq_len(number_of_resistance_loci), i.e. only dependent on their own loci. (TODO: Change this to be a list of length norl)
Numeric for number of drugs used
List of drugs that are being used, with each list element being
created by drug_create.
Boolean are we doing mft
Numeric for when in years a drug switch occurs
Numeric for what perc. treatment failure before switch
How long does it take in years for sequential to be implemented
What's the default drug choice to begin. Default = 0
Numeric vector for ratio of first line drugs used