get_parameters: Get model parameters

In pahanc/malariasimulation_Ace_params: 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. These parameters are explained in "The US President's Malaria Initiative, Plasmodium falciparum transmission and mortality: A modelling study."

Usage

get_parameters(overrides = list())

Arguments

overrides

a named list of parameter values to use instead of defaults The parameters are defined below. 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 Ph; default = 5 da - the delay for humans to move from state A to U; default = 200 du - the delay for humans to move from state U to S; default = 110 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 mup - the rate at which pupal mosquitoes die; default = 0.249 mum - the rate at which developed mosquitoes die; default = 0.1253333 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 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 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 immunity reducing probability of detection: 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 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 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 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 mortality parameters: average_age - the average age of humans (in timesteps), this is only used if custom_demography is FALSE; default = 7663 pcm - new-born clinical immunity relative to mother's; default = 0.774368 pvm - new-born severe immunity relative to mother's; default = 0.195768 me - early stage larval mortality rate; default = 0.0338 ml - late stage larval mortality rate; default = 0.0348 carrying capacity parameters: 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 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 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 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 vector biology: species specific values are vectors 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 = "All" species_proportions - the relative proportions of each species; default = 1 blood_meal_rates - the blood meal rates for each species; default = 0.3333333333 Q0 - proportion of blood meals taken on humans; default = 0.92 foraging_time - time spent taking blood meals; default = 0.69 feeding cycle: please set vector control strategies using set_betnets 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 treatment parameters: please set treatment parameters with the convenience functions in drug_parameters.R 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 RTS,S paramters: please set RTS,S strategies with the convenience functions in vaccine_parameters.R:set_rtss_epi vaccine_parameters.R:set_mass_rtss rtss_doses - the dosing schedule before the vaccine takes effect; default = c(0, 1.5 * 30, 3 * 30) default = 365 rtss_vmax - the maximum efficacy of the vaccine; default = 0.93 rtss_alpha - shape parameter for the vaccine efficacy model; default = 0.74 rtss_beta - scale parameter for the vaccine efficacy model; default = 99.4 rtss_cs - peak parameters for the antibody model (mean and std. dev); default = 6.37008, 0.35 rtss_cs_boost - peak parameters for the antibody model for booster rounds (mean and std. dev); default = 5.56277, 0.35 rtss_rho - delay parameters for the antibody model (mean and std. dev); default = 2.37832, 1.00813 rtss_rho_boost - delay parameters for the antibody model for booster rounds (mean and std. dev); default = 1.03431, 1.02735 rtss_ds - delay parameters for the antibody model, short-term weaning (mean and std. dev); default = 3.74502, 0.341185 (White MT et al. 2015 Lancet ID) rtss_dl - delay parameters for the antibody model, long-term weaning (mean and std. dev); default = 6.30365, 0.396515 (White MT et al. 2015 Lancet ID) MDA and SMC parameters: please set these parameters with the convenience functions in mda_parameters.R TBV parameters: please set TBV parameters with the convenience functions in vaccine_parameters.R: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 rendering: All values are in timesteps and all ranges are inclusive prevalence_rendering_min_ages - the minimum ages for clinical prevalence outputs; default = 730 prevalence_rendering_max_ages - the corresponding max ages; default = 3650 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 miscellaneous: human_population - the initial number of humans to model; default = 100 human_population_timesteps - the timesteps at which the population should change; default = 0 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 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

pahanc/malariasimulation_Ace_params documentation built on March 12, 2024, 2:21 a.m.