get_parameters creates a named list of parameters for use in the model. These parameters are passed to process functions. These parameters are explained in "The US President's Malaria Initiative, Plasmodium falciparum transmission and mortality: A modelling study."

get_parameters(overrides = list())

Arguments

overrides

a named list of parameter values to use instead of defaults The parameters are defined below.

initial state proportions:

  • s_proportion - the proportion of human_population that begin as susceptible; default = 0.420433246

  • d_proportion - the proportion of human_population that begin with clinical disease; default = 0.007215064

  • a_proportion - the proportion of human_population that begin as asymptomatic; default = 0.439323667

  • u_proportion - the proportion of human_population that begin as subpatents; default = 0.133028023

  • t_proportion - the proportion of human_population that begin treated; default = 0

human fixed state transitions:

  • dd - the delay for humans to move from state D to A; default = 5

  • dt - the delay for humans to move from state Tr to S; default = 5

  • da - the delay for humans to move from state A to U; default = 195

  • du - the delay for humans to move from state U to S; default = 110

human demography parameters:

  • human_population - the initial number of humans to model; default = 100

  • average_age - the average age of humans (in timesteps), this is only used if custom_demography is FALSE; default = 7665

  • custom_demography - population demography given; default = FALSE

initial immunity values:

  • init_icm - the immunity from clinical disease at birth; default = 0

  • init_ivm - the immunity from severe disease at birth; default = 0

  • init_ib - the initial pre-erythrocitic immunity; default = 0

  • init_ica - the initial acquired immunity from clinical disease; default = 0

  • init_iva - the initial acquired immunity from severe disease; default = 0

  • init_id - the initial acquired immunity to detectability; default = 0

immunity decay rates:

  • rm - decay rate for maternal immunity to clinical disease; default = 67.6952

  • rvm - decay rate for maternal immunity to severe disease; default = 76.8365

  • rb - decay rate for acquired pre-erythrocytic immunity; default = 3650

  • rc - decay rate for acquired immunity to clinical disease; default = 10950

  • rva - decay rate for acquired immunity to severe disease; default = 10950

  • rid - decay rate for acquired immunity to detectability; default = 3650

immunity boost grace periods:

  • ub - period in which pre-erythrocytic immunity cannot be boosted; default = 7.2

  • uc - period in which clinical immunity cannot be boosted; default = 6.06

  • uv - period in which severe immunity cannot be boosted; default = 11.4321

  • ud - period in which immunity to detectability cannot be boosted; default = 9.44512

maternal immunity parameters:

  • pcm - new-born clinical immunity relative to mother's; default = 0.774368

  • pvm - new-born severe immunity relative to mother's; default = 0.195768

unique biting rate:

  • a0 - age dependent biting parameter; default = 2920

  • rho - age dependent biting parameter; default = 0.85

  • sigma_squared - heterogeneity parameter; default = 1.67

  • n_heterogeneity_groups - number discretised groups for heterogeneity, used for sampling mothers; default = 5

probability of pre-erythrocytic infection:

  • b0 - maximum probability due to no immunity; default = 0.59

  • b1 - maximum reduction due to immunity; default = 0.5

  • ib0 - scale parameter; default = 43.9

  • kb - shape parameter; default = 2.16

probability of detection by light-microscopy when asymptomatic:

  • fd0 - time-scale at which immunity changes with age; default = 0.007055

  • ad - scale parameter relating age to immunity; default = 7993.5

  • gammad - shape parameter relating age to immunity; default = 4.8183

  • d1 - minimum probability due to immunity; default = 0.160527

  • id0 - scale parameter; default = 1.577533

  • kd - shape parameter; default = 0.476614

probability of clinical infection:

  • phi0 - maximum probability due to no immunity; default = 0.792

  • phi1 - maximum reduction due to immunity; default = 0.00074

  • ic0 - scale parameter; default = 18.02366

  • kc - shape parameter; default = 2.36949

probability of severe infection:

  • theta0 - maximum probability due to no immunity; default = 0.0749886

  • theta1 - maximum reduction due to immunity; default = 0.0001191

  • iv0 - scale parameter; default = 1.09629

  • kv - shape parameter; default = 2.00048

  • fv0 - age dependent modifier; default = 0.141195

  • av - age dependent modifier; default = 2493.41

  • gammav - age dependent modifier; default = 2.91282

infectivity towards mosquitoes:

  • cd - infectivity of clinically diseased humans towards mosquitoes; default = 0.068

  • gamma1 - parameter for infectivity of asymptomatic humans; default = 1.82425

  • cu - infectivity of sub-patent infection; default = 0.0062

  • ct - infectivity of treated infection; default = 0.021896

mosquito fixed state transitions (including mortality):

  • del - the delay for mosquitoes to move from state E to L; default = 6.64

  • dl - the delay for mosquitoes to move from state L to P; default = 3.72

  • dpl - the delay mosquitoes to move from state P to Sm; default = 0.643

  • me - early stage larval mortality rate; default = 0.0338

  • ml - late stage larval mortality rate; default = 0.0348

  • mup - the rate at which pupal mosquitoes die; default = 0.249

  • mum - the rate at which developed mosquitoes die; default (An. gambiae) = .132

vector biology: species specific values are vectors please set species parameters using the convenience function set_species

  • beta - the average number of eggs laid per female mosquito per day; default = 21.2

  • total_M - the initial number of adult mosquitos in the simulation; default = 1000

  • init_foim - the FOIM used to calculate the equilibrium state for mosquitoes; default = 0

  • species - names of the species in the simulation; default = "gamb"

  • species_proportions - the relative proportions of each species; default = 1

  • blood_meal_rates - the blood meal rates for each species; default = 1/3

  • Q0 - proportion of blood meals taken on humans; default = 0.92

  • foraging_time - time spent taking blood meals; default = 0.69

seasonality and carrying capacity parameters: please set flexible carrying capacity using the convenience function set_carrying_capacity

  • model_seasonality - boolean switch TRUE iff the simulation models seasonal rainfall; default = FALSE

  • g0 - rainfall fourier parameter; default = 2

  • g - rainfall fourier parameter; default = 0.3, 0.6, 0.9

  • h - rainfall fourier parameters; default = 0.1, 0.4, 0.7

  • gamma - effect of density dependence on late instars relative to early instars; default = 13.25

  • rainfall_floor - the minimum rainfall value (must be above 0); default 0.001

  • carrying_capacity; default = FALSE

  • carrying_capacity_timesteps; default = NULL

  • carrying_capacity_values; default = NULL#'

parasite incubation periods:

  • de - duration of the human latent period of infection; default = 12

  • delay_gam - lag from parasites to infectious gametocytes; default = 12.5

  • dem - extrinsic incubation period in mosquito population model; default = 10

treatment parameters: please set treatment parameters with the convenience functions set_drugs and set_clinical_treatment

  • drug_efficacy - a vector of efficacies for available drugs; default = turned off

  • drug_rel_c - a vector of relative onward infectiousness values for drugs; default = turned off

  • drug_prophylaxis_shape - a vector of shape parameters for weibull curves to model prophylaxis for each drug; default = turned off

  • drug_prophylaxis_scale - a vector of scale parameters for weibull curves to model prophylaxis for each drug; default = turned off

  • clinical_treatment_drugs - a vector of drugs that are available for clinically diseased (these values refer to the index in drug_* parameters); default = NULL, NULL, NULL

  • clinical_treatment_coverage - a vector of coverage values for each drug; default = NULL, NULL, NULL

MDA, SMC and PMC parameters: please set these parameters with the convenience functions set_mda, set_smc and set_pmc, with peak_season_offset

bednet, irs and mosquito feeding cycle parameters: please set vector control strategies using set_bednets and set_spraying

  • bednets - boolean for if bednets are enabled; default = FALSE

  • phi_bednets - proportion of bites taken in bed; default = 0.85

  • k0 - proportion of females bloodfed with no net; default = 0.699

  • spraying - boolean for if indoor spraying is enabled; default = FALSE

  • phi_indoors - proportion of bites taken indoors; default = 0.90

PEV parameters: please set vaccine strategies with the convenience functions set_pev_epi and set_mass_pev

  • pev_doses - the dosing schedule before the vaccine takes effect; default = c(0, 1.5 * 30, 3 * 30) default = 365

TBV parameters: please set TBV parameters with the convenience functions in set_tbv

  • tbv_mt - effect on treated infectiousness; default = 35

  • tbv_md - effect on diseased infectiousness; default = 46.7

  • tbv_ma - effect on asymptomatic infectiousness; default = 3.6

  • tbv_mu - effect on subpatent infectiousness; default = 0.8

  • tbv_k - scale parameter for effect on infectiousness; default = 0.9

  • tbv_tau - peak antibody parameter; default = 22

  • tbv_rho - antibody component parameter; default = 0.7

  • tbv_ds - antibody short-term delay parameter; default = 45

  • tbv_dl - antibody long-term delay parameter; default = 591

  • tbv_tra_mu - transmission reduction parameter; default = 12.63

  • tbv_gamma1 - transmission reduction parameter; default = 2.5

  • tbv_gamma2 - transmission reduction parameter; default = 0.06

Antimalarial resistance parameters: please set antimalarial resistance parameters with the convenience functions in set_antimalarial_resistance

  • antimalarial_resistance - boolean for if antimalarial resistance is enabled; default = FALSE

  • antimalarial_resistance_drug - vector of drugs for which resistance can be parameterised; default = NULL

  • antimalarial_resistance_timesteps - vector of time steps on which resistance updates occur; default = NULL

  • artemisinin_resistant_proportion - vector of proportions of infections resistant to the artemisinin component of a given drug; default = NULL

  • partner_drug_resistance_proportion - vector of proportions of infections resistant to the parter drug component of a given drug; default = NULL

  • slow_parasite_clearance_probability - vector of probabilities of slow parasite clearance for a given drug; default = NULL

  • early_treatment_failure_probability - vector of probabilities of early treatment failure for a given drug; default = NULL

  • late_clinical_failure_probability - vector of probabilities of late clinical failure for a given drug; default = NULL

  • late_parasitological_failure_probability - vector of probabilities of late parasitological failure for a given drug; default = NULL

  • reinfection_during_prophylaxis_probability - vector of probabilities of reinfection during prophylaxis for a given drug; default = NULL

  • dt_slow_parasite_clearance - the delay for humans experiencing slow parasite clearance to move from state Tr to S; default = NULL

rendering: All values are in timesteps and all ranges are inclusive. Please set rendered age groups using the convenience function

  • age_group_rendering_min_ages - the minimum ages for population size outputs; default = turned off

  • age_group_rendering_max_ages - the corresponding max ages; default = turned off

  • incidence_rendering_min_ages - the minimum ages for incidence outputs (includes asymptomatic microscopy +); default = turned off

  • incidence_rendering_max_ages - the corresponding max ages; default = turned off

  • clinical_incidence_rendering_min_ages - the minimum ages for clinical incidence outputs (symptomatic); default = 0

  • clinical_incidence_rendering_max_ages - the corresponding max ages; default = 1825

  • severe_incidence_rendering_min_ages - the minimum ages for severe incidence outputs; default = turned off

  • severe_incidence_rendering_max_ages - the corresponding max ages; default = turned off

  • prevalence_rendering_min_ages - the minimum ages for clinical prevalence outputs; default = 730

  • prevalence_rendering_max_ages - the corresponding max ages; default = 3650

mixing:

  • rdt_intercept - the y intercept for the log logit relationship betweeen rdt and PCR prevalence; default = -0.968

  • rdt_coeff - the coefficient for the log logit relationship betweeen rdt and PCR prevalence; default = 1.186

miscellaneous:

  • mosquito_limit - the maximum number of mosquitoes to allow for in the simulation; default = 1.00E+05

  • individual_mosquitoes - boolean whether adult mosquitoes are modeled individually or compartmentally; default = TRUE

  • human_population_timesteps - the timesteps at which the population should change; default = 0

  • r_tol - the relative tolerance for the ode solver; default = 1e-4

  • a_tol - the absolute tolerance for the ode solver; default = 1e-4

  • ode_max_steps - the max number of steps for the solver; default = 1e6

  • enable_heterogeneity - boolean whether to include heterogeneity in biting rates; default = TRUE