imperial_model_param_list_create: Model Parameter List Creation

Description

model_param_list_create creates list of model parameters to be used within equilibrium_init_create

Usage

imperial_model_param_list_create(
  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,
  theta0 = 0.0749886,
  theta1 = 0.0001191,
  iv0 = 1.09629,
  kv = 2.00048,
  av = 2493.41,
  gammaV = 2.91282,
  fvS = 0.141195,
  pctMort = 0.215,
  phi0 = 0.791666,
  phi1 = 0.000737,
  dCA = 10950,
  IC0 = 18.02366,
  kC = 2.36949,
  uCA = 6.06349,
  PM = 0.774368,
  dCM = 67.6952,
  dVM = 76.8365,
  dVA = 30 * 365,
  PVM = 0.195768,
  uVA = 11.4321,
  tau1 = 0.69,
  tau2 = 2.31,
  muF = 0.132,
  nEIP = 3,
  qEIP = 1/10,
  Q0 = 0.92,
  DY = 365,
  thetaB = 0.89,
  thetaI = 0.97,
  r_llin = 0.56,
  s_llin = 0.03,
  r_irs = 0.6,
  s_irs = 0,
  qE = 1/3,
  nE = 2,
  qL = 1/7,
  nL = 3,
  qP = 1/1,
  nP = 2,
  muE = 0.05,
  muL = 0.15,
  muP = 0.05,
  muM = 0.132,
  eps = 58.9,
  nu = 1/(4/24),
  NH = 1000,
  ...
)

Value

A named vector of all baseline parameters required by the Imperial malaria model.

This function creates all of the necessary parameters for the Imperial model. Parameters furnished by MGDrivE will be removed from this function. Adapted from: https://github.com/mrc-ide/deterministic-malaria-model/blob/master/R/model_parameters.R

A newer version of the model also includes parameters for severe disease. See: https://github.com/mrc-ide/malariasimulation for details.

Arguments

eta: Death rate for expoential population distribtuion, i.e. 1/Mean Population Age. Default = 0.0001305
rho: Age-dependent biting parameter. Default = 0.85
a0: Age-dependent biting parameter. Default = 2920
sigma2: Variance of the log heterogeneity in biting rates. Default = 1.67
max_age: Maximum age in days. Default = 100*365
rA: Rate of leaving asymptomatic infection. Default = 0.00512821
rT: Rate of leaving treatment. Default = 0.2
rD: Rate of leaving clinical disease. Default = 0.2
rU: Rate of recovering from subpatent infection. Default = 0.00906627
rP: Rate of leaving prophylaxis. Default = 0.06666667
dE: Latent period of human infection. Default = 12
delayGam: Lag from parasites to infectious gametocytes. Default = 12.5
cD: Untreated disease contribution to infectiousness. Default = 0.0676909
cT: Treated disease contribution to infectiousness. Default = 0.322 * cD
cU: Subpatent disease contribution to infectiousness. Default = 0.006203
gamma1: Parameter for infectiousness of state A. Default = 1.82425
d1: Minimum probability due to maximum immunity. Default = 0.160527
dID: Inverse of decay rate. Default = 3650
ID0: Scale parameter. Default = 1.577533
kD: Shape parameter. Default = 0.476614
uD: Duration in which immunity is not boosted. Default = 9.44512
aD: Scale parameter relating age to immunity. Default = 8001.99
fD0: Time-scale at which immunity changes with age. Default = 0.007055
gammaD: Shape parameter relating age to immunity. Default = 4.8183
alphaA: PCR detection probability parameters state A. Default = 0.757
alphaU: PCR detection probability parameters state U. Default = 0.186
b0: Maximum probability due to no immunity. Default = 0.590076
b1: Maximum relative reduction due to immunity. Default = 0.5
dB: Inverse of decay rate. Default = 3650
IB0: Scale parameter. Default = 43.8787
kB: Shape parameter. Default = 2.15506
uB: Duration in which immunity is not boosted. Default = 7.19919
theta0: Maximum probability of severe infection due to no immunity. Default = 0.0749886
theta1: Maximum reduction due to to immunity. Default = 0.0001191
iv0: Scale parameter. Default = 1.09629
kv: Shape parameter. Default = 2.00048
av: Age-dependent modifier. Default = 2493.41
gammaV: Age-dependent modifier. Default = 2.91282
fvS: Age-dependent modifier. Default = 0.141195
pctMort: Percentage of severe cases that die. Default = 0.215
phi0: Maximum probability due to no immunity. Default = 0.791666
phi1: Maximum relative reduction due to immunity. Default = 0.000737
dCA: Inverse of decay rate. Default = 10950
IC0: Scale parameter. Default = 18.02366
kC: Shape parameter. Default = 2.36949
uCA: Duration in which immunity is not boosted. Default = 6.06349
PM: New-born immunity relative to mother’s. Default = 0.774368
dCM: Inverse of decay rate of maternal immunity. Default = 67.6952
dVM: Inverse of decay rate. Default = 76.8365
dVA: Inverse of decay rate. Default = 30 * 365
PVM: New-born immunity to severe disease relative to mothers. Default = 0.195768
uVA: Duration in which immunity to severe disease is not boosted. Default = 11.4321
tau1: Duration of host seeking, assumed to be constant between species. Default = 0.69
tau2: Duration of mosquito resting after feed. Default = 2.31
muF: Daily mortality of adult mosquitos. Default = 0.132
nEIP: Number of Erlang-distributed EIP compartments. Default = 6
qEIP: Inverse of the mean duration of the EIP. Default = 1/10 (days)
Q0: Anthrophagy probability. Default = 0.92
DY: number of days in a year. Default = 365
thetaB: proportion of bites on a person in bed. Default = 0.89
thetaI: proportion of bites on a person outdoors. Default = 0.97
r_llin: probability of repeating a feeding attempt due to LLINs. Default = 0.56
s_llin: probability of feeding and surviving in presence of LLINs. Default = 0.03
r_irs: probability of repeating a feeding attempt due to IRS. Default = 0.60
s_irs: probability of feeding and surviving in presence of IRS. Default = 0
qE: mosquito egg lifecycle parameter. Default = 1/3
nE: mosquito egg lifecycle parameter. Default = 2
qL: mosquito larval lifecycle parameter. Default = 1/7
nL: mosquito larval lifecycle parameter. Default = 3
qP: mosquito pupae lifecycle parameter. Default = 1/1
nP: mosquito pupae lifecycle parameter. Default = 2
muE: death rate of egg stage. Default = 0.05
muL: death rate of larval stage. Default = 0.15
muP: death rate of pupae stage. Default = 0.05
muM: death rate of male adult stage. Default = 0.132
eps: eggs laid per day. Default = 58.9
nu: mosquito lifecycle parameter. Default = 1/(4/24
NH: number of humans. Default = 1000
...: Any other parameters needed for non-standard model. If they share the same name as any of the defined parameters model_param_list_create will stop. You can either write any extra parameters you like individually, e.g. model_param_list_create(extra1 = 1, extra2 = 2) and these parameteres will appear appended to the returned list, or you can pass explicitly the ellipsis argument as a list created before, e.g. model_param_list_create(...=list(extra1 = 1, extra2 = 2))