Helper 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,
  ...
)

Arguments

n_days

Number of days for which the simulation will run.

tsd

Number of time-steps per day. Fewer is faster, more better approximates the continuous solution.

age_vector

Lower bound of each age category. See function for default.

het_brackets

Number of biting heterogeneity groups.

lag_rates

Number of sub-compartments within FOI and FOIv which approximate delay-differential equation. Higher values are a closer approximation, but computationally more expensive.

eta

Death rate for exponential population distribution, i.e. 1/Mean Population Age

rho

Age-dependent biting parameter

a0

Age-dependent biting parameter

sigma2

Variance of the log heterogeneity in biting rates

max_age

Upper boundary of oldest age category

rA

Rate of leaving asymptomatic infection

rT

Rate of leaving treatment

rD

Rate of leaving clinical disease

rU

Rate of recovering from subpatent infection

rP

Rate of leaving prophylaxis

dE

Latent period of human infection

delayGam

Lag from parasites to infectious gametocytes

cD

Untreated disease contribution to infectiousness

cT

Treated disease contribution to infectiousness

cU

Subpatent disease contribution to infectiousness

gamma1

Parameter for infectiousness of state A

d1

Minimum probability due to maximum immunity

dID

Inverse of decay rate

ID0

Scale parameter

kD

Shape parameter

uD

Duration in which immunity is not boosted

aD

Scale parameter relating age to immunity

fD0

Time-scale at which immunity changes with age

gammaD

Shape parameter relating age to immunity

alphaA

PCR detection probability parameters state A

alphaU

PCR detection probability parameters state U

b0

Maximum probability due to no immunity

b1

Maximum relative reduction due to immunity

dB

Inverse of decay rate

IB0

Scale parameter

kB

Shape parameter

uB

Duration in which immunity is not boosted

phi0

Maximum probability due to no immunity

phi1

Maximum relative reduction due to immunity

dCA

Inverse of decay rate

IC0

Scale parameter

kC

Shape parameter

uCA

Duration in which immunity is not boosted

PM

New-born immunity relative to mothers

dCM

Inverse of decay rate of maternal immunity

delayMos

Extrinsic incubation period

tau1

Duration of host seeking, assumed to be constant between species

tau2

Duration of mosquito resting after feed

mu0

Daily mortality of adult mosquitoes

Q0

Anthrophagy probability

chi

Endophily probability

bites_Bed

Percentage of bites indoors and in bed

bites_Indoors

Percentage of bites indoors

muEL

Per capita daily mortality rate of early stage larvae (low density)

muLL

Per capita daily mortality rate of late stage larvae (low density)

muPL

Per capita daily mortality rate of pupae

dEL

Development time of early stage larvae

dLL

Development time of late stage larvae

dPL

Development time of pupae

gammaL

Relative effect of density dependence on late instars relative to early instars

betaL

Number of eggs laid per day per mosquito

ft

Percentage of population that gets treated

clin_inc_rendering_min_ages

Vector of values (or singe value) of lower age boundaries for clinical incidence output (days)

clin_inc_rendering_max_ages

Vector of values (or singe value) of upper age boundaries for clinical incidence output (days)

prevalence_rendering_min_ages

Vector of values (or singe value) of lower age boundaries for prevalence output (days)

prevalence_rendering_max_ages

Vector of values (or singe value) of upper age boundaries for prevalence output (days)

...

Additional arguments

Examples

#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)