get_parameters.RdHelper function to provide defaults for most necessary values required for running the malariasimple model
get_parameters(
n_days = 100,
tsd = 4,
age_vector = c(0, 0.25, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5, 6, 7, 8.5, 10, 20, 30, 40,
60, 80) * 365,
het_brackets = 5,
lag_rates = 10,
eta = 1/(21 * 365),
rho = 0.85,
a0 = 2920,
sigma2 = 1.67,
max_age = 100 * 365,
rA = 1/195,
rT = 0.2,
rD = 0.2,
rU = 1/110.299,
rP = 1/15,
dE = 12,
delayGam = 12.5,
cD = 0.0676909,
cT = 0.322 * cD,
cU = 0.006203,
gamma1 = 1.82425,
d1 = 0.160527,
dID = 3650,
ID0 = 1.577533,
kD = 0.476614,
uD = 9.44512,
aD = 8001.99,
fD0 = 0.007055,
gammaD = 4.8183,
alphaA = 0.75735,
alphaU = 0.185624,
b0 = 0.590076,
b1 = 0.5,
dB = 3650,
IB0 = 43.8787,
kB = 2.15506,
uB = 7.19919,
phi0 = 0.791666,
phi1 = 0.000737,
dCA = 10950,
IC0 = 18.02366,
kC = 2.36949,
uCA = 6.06349,
PM = 0.774368,
dCM = 67.6952,
delayMos = 10,
tau1 = 0.69,
tau2 = 2.31,
mu0 = 0.132,
Q0 = 0.92,
chi = 0.86,
bites_Bed = 0.89,
bites_Indoors = 0.97,
muEL = 0.0338,
muLL = 0.0348,
muPL = 0.249,
dEL = 6.64,
dLL = 3.72,
dPL = 0.643,
gammaL = 13.25,
betaL = 21.2,
ft = 0,
clin_inc_rendering_min_ages = NULL,
clin_inc_rendering_max_ages = NULL,
prevalence_rendering_min_ages = NULL,
prevalence_rendering_max_ages = NULL,
...
)Number of days for which the simulation will run.
Number of time-steps per day. Fewer is faster, more better approximates the continuous solution.
Lower bound of each age category. See function for default.
Number of biting heterogeneity groups.
Number of sub-compartments within FOI and FOIv which approximate delay-differential equation. Higher values are a closer approximation, but computationally more expensive.
Death rate for exponential population distribution, i.e. 1/Mean Population Age
Age-dependent biting parameter
Age-dependent biting parameter
Variance of the log heterogeneity in biting rates
Upper boundary of oldest age category
Rate of leaving asymptomatic infection
Rate of leaving treatment
Rate of leaving clinical disease
Rate of recovering from subpatent infection
Rate of leaving prophylaxis
Latent period of human infection
Lag from parasites to infectious gametocytes
Untreated disease contribution to infectiousness
Treated disease contribution to infectiousness
Subpatent disease contribution to infectiousness
Parameter for infectiousness of state A
Minimum probability due to maximum immunity
Inverse of decay rate
Scale parameter
Shape parameter
Duration in which immunity is not boosted
Scale parameter relating age to immunity
Time-scale at which immunity changes with age
Shape parameter relating age to immunity
PCR detection probability parameters state A
PCR detection probability parameters state U
Maximum probability due to no immunity
Maximum relative reduction due to immunity
Inverse of decay rate
Scale parameter
Shape parameter
Duration in which immunity is not boosted
Maximum probability due to no immunity
Maximum relative reduction due to immunity
Inverse of decay rate
Scale parameter
Shape parameter
Duration in which immunity is not boosted
New-born immunity relative to mothers
Inverse of decay rate of maternal immunity
Extrinsic incubation period
Duration of host seeking, assumed to be constant between species
Duration of mosquito resting after feed
Daily mortality of adult mosquitoes
Anthrophagy probability
Endophily probability
Percentage of bites indoors and in bed
Percentage of bites indoors
Per capita daily mortality rate of early stage larvae (low density)
Per capita daily mortality rate of late stage larvae (low density)
Per capita daily mortality rate of pupae
Development time of early stage larvae
Development time of late stage larvae
Development time of pupae
Relative effect of density dependence on late instars relative to early instars
Number of eggs laid per day per mosquito
Percentage of population that gets treated
Vector of values (or singe value) of lower age boundaries for clinical incidence output (days)
Vector of values (or singe value) of upper age boundaries for clinical incidence output (days)
Vector of values (or singe value) of lower age boundaries for prevalence output (days)
Vector of values (or singe value) of upper age boundaries for prevalence output (days)
Additional arguments
#Output default model for clinical incidence in range [0-10] and 2+
params <- get_parameters(n_days = 500,
clin_inc_rendering_min_ages = c(0,2*365),
clin_inc_rendering_max_ages = c(10*365,Inf)) |>
set_equilibrium(init_EIR = 10)