The function creates a list of user-defined parameters.
Usage
parameters_deterministic_model(
YL = 365,
DT = 1,
time_period = 365,
NP = 21,
agec = default_demog$agec,
death = default_demog$death,
season = FALSE,
age_per = 1,
N_human = 3e+07,
incub = 5.5,
inf_per = 6,
nu = 1/21,
Omega = 1,
DeltaBase = 0.2,
Sigma = 0.025,
Epsilon = 1/19,
Rm = 2.69,
Mwt_mean = 1.5,
Mwt_cv = 0.15,
eip_mean = 8.4,
Kappa = 0.5,
Beta_hm_1 = 0.7,
Beta_mh_1 = 0.7,
propMwtControl = 0,
TimeMwtControlOn = 1.5,
TimeMwtControlOff = 2.5,
Wb_cyto = 1,
Wb_mat = 1,
Wb_fM = 0.95,
Wb_fF = 0.95,
Wb_relsusc1 = 0.9,
Wb_relinf1 = 0.5,
Wb_starttime = 1,
Wb_introlevel = 0,
Wb_introduration = 60,
vacc_child_coverage = 0,
vacc_child_starttime = 30,
vacc_child_stoptime = 30,
vaccine_child_age = NULL,
vacc_cu_coverage = 0,
vacc_cu_time = 30,
vaccine_cu_age = c(0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0),
vacceff_prim = 0.75,
rho_prim = 1,
other_foi = 0.025,
other_prop_immune = 0,
propTransGlobal = 5e-04,
propTransNN = 0,
BG_FOI = 1e-08,
phi_prim = 1,
dis_pri = 0.2,
mc_baseline = 2e-04,
AGE_REC = 2,
PropDiseaseReported = 1
)Arguments
- YL
Duration of a calendar year. Default = 365.
- DT
Time step size. Default = 1.
- time_period
Length of simulation. Default = 365.
- NP
Number of patches. Default = 21.
- agec
Numeric vector of age group widths. Default = c(1, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10).
- death
Numeric vector of mortality rates. Default = deathrt <- c(1e-10, 1e-10, 1e-10, 0.00277068683332695, 0.0210680857689784, 0.026724997685722, 0.0525354529367476, 0.0668013582441452, 0.119271483740379, 0.279105747097929, 0.390197266957464).
- season
Logical for controlling the effect of seasonality. TRUE = maximum effect of seasonality. FALSE = no effect of seasonality. Default = FALSE
- age_per
Time (weeks) between age updates. Default = 1.
- N_human
Human population in each patch. Default = 30000000.
- incub
Intrinsic Incubation Period (days). Default = 5.5.
- inf_per
Total duration of human infectiousness (days). Default = 6.
- nu
Inverse of virus generation time (1 / days). Virus generation time = serial interval. Default = 1 / 21.
- Omega
Intensity of density dependence of mosquito larvae mortality rate. 0 = no density dependence. Default = 1.
- DeltaBase
Adult mosquito mortality rate. Default = 0.2.
- Sigma
Larval mosquito mortality rate. Default = 0.025
- Epsilon
Larval mean development rate (1 / larvae mean development time in days). Default = 1/19.
- Rm
Mosquito reproduction number (based on adult female fecundity and mortality rates). Default = 2.69.
- Mwt_mean
Mean of the lognorm distribution of the at-equilibrium number of adult female mosquitos per person, per patch, without seasonality. Default = 1.5.
- Mwt_cv
Standard deviation of the lognorm distribution of the at-equilibrium number of adult female mosquitos per person, per patch, without seasonality. Default = 0.15
- eip_mean
Mean Extrinsic Incubation Period (days). Default = 8.4.
- Kappa
Mosquito biting rate. Default = 0.5.
- Beta_hm_1
Per bite transmission probability from humans to mosquitoes. Default = 0.7. This value is assigned to give a mean reproduction number, R0, across patches of 2.3 (with seasonal forcing).
- Beta_mh_1
Per bite transmission probability from mosquitoes to humans. Arbitrarily assigned. Default = 0.7.
- propMwtControl
Increase in mortality of adult wild type mosquitoes induced by a general type of intervention. Default = 0.
- TimeMwtControlOn
Year of start of control of adult wild type mosquitoes. Default = 2.
- TimeMwtControlOff
Year of end of control of adult wild type mosquitoes. Default = 3.
- Wb_cyto
Degree of cytoplasmic incompatibility induced by Wolbachia. Default = 1.
- Wb_mat
Degree of vertical transmission of Wolbachia. Default = 1.
- Wb_fM
Increase in mortality induced by Wolbachia. Default = 0.95.
- Wb_fF
Reduction in fecundity induced by Wolbachia. Default = 0.95.
- Wb_relsusc1
Infectivity of a human host to Wolbachia infected mosquitoes (time T after host infection). Default = 0.9.
- Wb_relinf1
Infectiousness of Wolbachia-infected mosquitoes time T after infection. Default = 0.75.
- Wb_starttime
Time of first release of Wolbachia-infected mosquiotes (years). Default = 1.
- Wb_introlevel
Ratio of Wolbachia-infected to wild type mosquitoes at introduction. (Not the proportion of Wolbachia AFTER introduction). Default = 0.
- Wb_introduration
Duration of Wolbachia release (days). Default = 60.
- vacc_child_coverage
Proportion of children vaccinated. Default = 0.
- vacc_child_starttime
Time when vaccination starts. Default = 30.
- vacc_child_stoptime
Time when vaccination ends. Default = 30.
- vaccine_child_age
Vector of binary indicators for routine vaccination of age groups. 1 = vaccinate, 0 = do not vaccinate. Same length as
agec. Default = NULL.- vacc_cu_coverage
Proportion of children who undergo catch up vaccination. Default = 0.
- vacc_cu_time
Time when catch up vaccination occurs. Default = 30.
- vaccine_cu_age
Vector of binary indicators for catch up vaccination of age groups. 1 = vaccinate, 0 = do not vaccinate. Same length as
agec. Default = c(0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0), from 9 to 49.- vacceff_prim
Efficacy of vaccination in reducing infection. Default = 0.75.
- rho_prim
Decay of protection from vaccine. Default = 1.
- other_foi
Default = 0.025.
- other_prop_immune
Propotion of population with pre-existing immunity. Default = 0.
- propTransGlobal
Proportion of transmission between all patches. Default = 0.0005.
- propTransNN
Proportion of transmission with nearest-neighbor patches. Default = 0.
- BG_FOI
Force of infection on humans resulting from imported cases in travelers visiting from elsewhere. Default = 1e-8.
- phi_prim
Degree of cross-immunity (not applicable for Zika). Default = 1.
- dis_pri
Proportion of infections which are symptomatic. Default = 0.2.
- mc_baseline
Baseline per birth microcephaly incidence rate. Default = 0.0002.
- AGE_REC
Default = 2.
- PropDiseaseReported
Reporting rate of symptomatic cases. Default = 0.1.