get_parameters: Get model parameters

In mrc-ide/malariasimulation: An individual based model for malaria

Get model parameters

Description

get_parameters creates a named list of parameters for use in the model. These parameters are passed to process functions.

The default parameters, which are for Plasmodium falciparum, are explained in "The US President's Malaria Initiative, Plasmodium falciparum transmission and mortality: A modelling study."

Plasmodium vivax specific parameters are explained in "Mathematical modelling of the impact of expanding levels of malaria control interventions on Plasmodium vivax." by White, Michael T., et al.

Usage

get_parameters(overrides = list(), parasite = "falciparum")

Arguments

overrides

a named list of parameter values to use instead of defaults

parasite

Plasmodium parasite species ("falciparum" or "vivax"); default = "falciparum" The parameters are defined below. parasite parameter parasite - parasite species (falciparum or vivax); default = "falciparum" 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 (p.f only); default = 110 duration of pcr detectable infections: du (p.v only): dpcr_max - Maximum duration of PCR-detectable infections: default = 53.69 dpcr_min - Minimum duration of PCR-detectable infections: default = 10 kpcr - Shape parameter: default = 4.021 apcr50 - Scale parameter: default = 9.8 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_ib - the initial pre-erythrocitic immunity (p.f only); default = 0 init_iaa - the initial acquired anti-parasite immunity (p.v only): default = 0 init_iam - the initial anti-parasite immunity at birth (p.v only); default = 0 init_ica - the initial acquired immunity from clinical disease; default = 0 init_icm - the initial clinical immunity at birth; default = 0 init_iva - the initial acquired immunity from severe disease (p.f only); default = 0 init_ivm - the initial severe immunity from severe disease at birth (p.f only); default = 0 init_id - the initial acquired immunity to lm detectability (p.f only); default = 0 immunity decay rates: rb - decay rate for acquired pre-erythrocytic immunity (p.f only); default = 3650 ra - decay rate for acquired anti-parasite immunity (p.v only); default = 3650 rc - decay rate for acquired immunity to clinical disease; default = 10950 rva - decay rate for acquired immunity to severe disease (p.f only); default = 10950 rm - decay rate for maternal immunity to clinical disease (or p.v: maternal clinical and anti-parasite immunities); default = 67.6952 rvm - decay rate for maternal immunity to severe disease (p.f only); default = 76.8365 rid - decay rate for acquired immunity to lm-detectability (p.f only); default = 3650 immunity boost grace periods: ub - period in which pre-erythrocytic immunity cannot be boosted (p.f only); default = 7.2 ua - period in which anti-parasite immunity cannot be boosted (p.v only); default = 44.09 uc - period in which clinical immunity cannot be boosted; default = 6.06 uv - period in which severe immunity cannot be boosted (p.f only); default = 11.4321 ud - period in which immunity to detectability cannot be boosted (p.f only); default = 9.44512 maternal immunity parameters: pcm - new-born clinical immunity (or p.v: clinical and anti-parasite immunities) relative to mother's; default = 0.774368 pvm - new-born severe immunity relative to mother's (p.f only); 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 (p.f only): 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 pre-erythrocytic infection (p.v only): b - probability of pre-erythrocytic infection: default = 0.25 probability of detection by light-microscopy when asymptomatic (p.f only): 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 light-microscopy detectable infections due to anti-parasite immunity (p.v only): philm_max - maximum probability due to no immunity; default = 0.9329 philm_min - maximum reduction due to immunity; default = 0.0131 alm50 - scale parameter; default = 17.3 klm - shape parameter; default = 3.202 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 (p.f only): 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 ca - infectivity of asymptomatic humans towards mosquitoes (p.v only); default = 0.1 gamma1 - parameter for infectivity of asymptomatic humans; default = 1.82425 cu - infectivity of subpatent 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 hypnozoite batch parameters (p.v only): f - hypnozoite batch relapse rate; default = 0.02439024 gammal - hypnozoite batch clearance rate; default = 0.002610966 init_hyp - initial hypnozoite batch number; default = 0 kmax - maximum number of hypnozoite batches for use in the equilibrium solution; 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 drug_hypnozoite_efficacy - a vector of efficacies targeting hypnozoites; default = turned off drug_hypnozoite_prophylaxis_shape - a vector of shape parameters for weibull curves to model prophylaxis against hypnozoite batch formation (days); default = turned off drug_hypnozoite_prophylaxis_scale - a vector of scale parameters for weibull curves to model prophylaxis against hypnozoite batch formation (days); 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 n_with_hypnozoites_rendering_min_ages - the minimum ages for number with hypnozoites outputs (p.v only); default = numeric(0) n_with_hypnozoites_rendering_max_ages - the corresponding max ages; default = numeric(0) Age structured mean immunity (/hyponozoite) rendering: ib_rendering_min_ages - the minimum ages for blood immunity outputs (p.f only); default = numeric(0) ib_rendering_max_ages - the corresponding max ages; default = numeric(0) id_rendering_min_ages - the minimum ages for acquired detectability immunity (p.f); default = numeric(0) id_rendering_max_ages - the corresponding max ages; default = numeric(0) iaa_rendering_min_ages - the minimum ages for antiparasite immunity (p.v only); default = numeric(0) iam_rendering_max_ages - the corresponding max ages; default = numeric(0) ica_rendering_min_ages - the minimum ages for acquired clinical immunity outputs; default = numeric(0) ica_rendering_max_ages - the corresponding max ages; default = numeric(0) iva_rendering_min_ages - the minimum ages for acquired severe immunity outputs (p.f only); default = numeric(0) iva_rendering_max_ages - the corresponding max ages; default = numeric(0) idm_rendering_min_ages - the minimum ages for maternal antiparasite immunity outputs (p.v only); default = numeric(0) idm_rendering_max_ages - the corresponding max ages; default = numeric(0) icm_rendering_min_ages - the minimum ages for maternal clinical immunity outputs; default = numeric(0) icm_rendering_max_ages - the corresponding max ages; default = numeric(0) ivm_rendering_min_ages - the minimum ages for maternal severe immunity outputs (p.f only); default = numeric(0) ivm_rendering_max_ages - the corresponding max ages; default = numeric(0) hypnozoites_rendering_min_ages - the minimum ages average hypnozoite batches outputs (p.v only); default = numeric(0) hypnozoites_rendering_max_ages - the corresponding max ages; default = numeric(0) 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

mrc-ide/malariasimulation documentation built on Feb. 18, 2025, 8:43 a.m.