model_param_list_create.Rdmodel_param_list_create creates list of model parameters to be used
within equilibrium_init_create
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,
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,
km = 11,
cm = 0.05,
betaL = 21.2,
num_int = 1,
itn_cov = 0,
irs_cov = 0,
ITN_IRS_on = -1,
DY = 365,
d_ITN0 = 0.41,
r_ITN0 = 0.56,
r_ITN1 = 0.24,
r_IRS0 = 0.6,
d_IRS0 = 1,
irs_half_life = 0.5 * DY,
itn_half_life = 2.64 * DY,
IRS_interval = 1 * DY,
ITN_interval = 3 * DY,
...
)Death rate for expoential population distribtuion, i.e. 1/Mean Population Age. Default = 0.0001305
Age-dependent biting parameter. Default = 0.85
Age-dependent biting parameter. Default = 2920
Variance of the log heterogeneity in biting rates. Default = 1.67
Maximum age in days. Default = 100*365
Rate of leaving asymptomatic infection. Default = 0.00512821
Rate of leaving treatment. Default = 0.2
Rate of leaving clinical disease. Default = 0.2
Rate of recovering from subpatent infection. Default = 0.00906627
Rate of leaving prophylaxis. Default = 0.06666667
Latent period of human infection. Default = 12
Lag from parasites to infectious gametocytes. Default = 12.5
Untreated disease contribution to infectiousness. Default = 0.0676909
Treated disease contribution to infectiousness. Default = 0.322 * cD
Subpatent disease contribution to infectiousness. Default = 0.006203
Parameter for infectiousness of state A. Default = 1.82425
Minimum probability due to maximum immunity. Default = 0.160527
Inverse of decay rate. Default = 3650
Scale parameter. Default = 1.577533
Shape parameter. Default = 0.476614
Duration in which immunity is not boosted. Default = 9.44512
Scale parameter relating age to immunity. Default = 8001.99
Time-scale at which immunity changes with age. Default = 0.007055
Shape parameter relating age to immunity. Default = 4.8183
PCR detection probability parameters state A. Default = 0.757
PCR detection probability parameters state U. Default = 0.186
Maximum probability due to no immunity. Default = 0.590076
Maximum relative reduction due to immunity. Default = 0.5
Inverse of decay rate. Default = 3650
Scale parameter. Default = 43.8787
Shape parameter. Default = 2.15506
Duration in which immunity is not boosted. Default = 7.19919
Maximum probability due to no immunity. Default = 0.791666
Maximum relative reduction due to immunity. Default = 0.000737
Inverse of decay rate. Default = 10950
Scale parameter. Default = 18.02366
Shape parameter. Default = 2.36949
Duration in which immunity is not boosted. Default = 6.06349
New-born immunity relative to mother’s. Default = 0.774368
Inverse of decay rate of maternal immunity. Default = 67.6952
Extrinsic incubation period. Default = 10
Duration of host seeking, assumed to be constant between species. Default = 0.69
Duration of mosquito resting after feed. Default = 2.31
Daily mortality of adult mosquitos. Default = 0.132
Anthrophagy probability. Default = 0.92
Endophily probability. Default = 0.86
Percentage of bites indoors and in bed. Default = 0.89
Percentage of bites indoors . Default = 0.97
Per capita daily mortality rate of early stage larvae (low density). Default = 0.0338
Per capita daily mortality rate of late stage larvae (low density). Default = 0.0348
Per capita daily mortality rate of pupae. Default = 0.249
Development time of early stage larvae. Default = 6.64
Development time of late stage larvae. Default = 3.72
Development time of pupae. Default = 0.643
Relative effect of density dependence on late instars relative to early instars. Default = 13.25
Seasonal carrying capacity. Default = 11
Seasonal birth rate. Default = 0.05
Number of eggs laid per day per mosquito. Default = 21.2
Number of intervention parameters. Default = 4
The proportion of people that use an ITN. Default = 0
The proportion of people living in houses that have been sprayed. Default = 0
Time of ITN and IRS to be activated. Default = -1, i.e. never.
Duration of year (days). Default = 365
Probability of dying with an encounter with ITN (max). Default = 0.41
Probability of repeating behaviour with ITN (max). Default = 0.56
Probability of repeating behaviour with ITN (min). Default = 0.24
Probability of repeating behaviour with IRS (min). Default = 0.6
Probability of dying with an encounter with IRS (max). Default = 1
IRS half life. Default = 0.5 * DY
ITN half life. Default = 2.64 * DY
How long before IRS is repeated, i.e. when IRS decay = 1. Default = 1 * DY
How long before ITN is repeated, i.e. when IRS decay = 1. Default = 3 * DY
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))