get_parameters.Rdget_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())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