R/parameters.R
In mrc-ide/ZikaModel: Zika odin model
Defines functions
parameters_deterministic_model
Documented in
parameters_deterministic_model
# -----------------------------------------------------------------------------
#' The function creates a list of user-defined parameters.
#'
#' @title Create a list of parameters
#'
#' @param YL Duration of a calendar year. Default = 365.
#' @param DT Time step size. Default = 1.
#' @param time_period Length of simulation. Default = 365.
#' @param NP Number of patches. Default = 21.
#' @param agec Numeric vector of age group widths.
#' Default = c(1, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10).
#' @param 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).
#' @param season Logical for controlling the effect of seasonality.
#' TRUE = maximum effect of seasonality.
#' FALSE = no effect of seasonality. Default = FALSE
#' @param age_per Time (weeks) between age updates. Default = 1.
#' @param N_human Human population in each patch. Default = 30000000.
#' @param incub Intrinsic Incubation Period (days). Default = 5.5.
#' @param inf_per Total duration of human infectiousness (days). Default = 6.
#' @param nu Inverse of virus generation time (1 / days).
#' Virus generation time = serial interval. Default = 1 / 21.
#' @param Omega Intensity of density dependence of mosquito larvae mortality rate.
#' 0 = no density dependence. Default = 1.
#' @param DeltaBase Adult mosquito mortality rate. Default = 0.2.
#' @param Sigma Larval mosquito mortality rate. Default = 0.025
#' @param Epsilon Larval mean development rate (1 / larvae mean development time in days).
#' Default = 1/19.
#' @param Rm Mosquito reproduction number (based on adult female fecundity and
#' mortality rates). Default = 2.69.
#' @param 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.
#' @param 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
#' @param eip_mean Mean Extrinsic Incubation Period (days). Default = 8.4.
#' @param Kappa Mosquito biting rate. Default = 0.5.
#' @param 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).
#' @param Beta_mh_1 Per bite transmission probability from mosquitoes to humans.
#' Arbitrarily assigned. Default = 0.7.
#' @param propMwtControl Increase in mortality of adult wild type mosquitoes induced
#' by a \emph{general} type of intervention. Default = 0.
#' @param TimeMwtControlOn Year of start of control of adult wild type mosquitoes.
#' Default = 2.
#' @param TimeMwtControlOff Year of end of control of adult wild type mosquitoes.
#' Default = 3.
#' @param Wb_cyto Degree of cytoplasmic incompatibility induced by Wolbachia.
#' Default = 1.
#' @param Wb_mat Degree of vertical transmission of Wolbachia. Default = 1.
#' @param Wb_fM Increase in mortality induced by Wolbachia. Default = 0.95.
#' @param Wb_fF Reduction in fecundity induced by Wolbachia. Default = 0.95.
#' @param Wb_relsusc1 Infectivity of a human host to Wolbachia infected mosquitoes
#' (time T after host infection). Default = 0.9.
#' @param Wb_relinf1 Infectiousness of Wolbachia-infected mosquitoes time T after
#' infection. Default = 0.75.
#' @param Wb_starttime Time of first release of Wolbachia-infected mosquiotes (years).
#' Default = 1.
#' @param Wb_introlevel Ratio of Wolbachia-infected to wild type mosquitoes at
#' introduction. (Not the proportion of Wolbachia AFTER introduction). Default = 0.
#' @param Wb_introduration Duration of Wolbachia release (days). Default = 60.
#' @param vacc_child_coverage Proportion of children vaccinated. Default = 0.
#' @param vacc_child_starttime Time when vaccination starts. Default = 30.
#' @param vacc_child_stoptime Time when vaccination ends. Default = 30.
#' @param vaccine_child_age Vector of binary indicators for routine vaccination
#' of age groups. 1 = vaccinate, 0 = do not vaccinate. Same length as \code{agec}.
#' Default = NULL.
#' @param vacc_cu_coverage Proportion of children who undergo catch up vaccination.
#' Default = 0.
#' @param vacc_cu_time Time when catch up vaccination occurs. Default = 30.
#' @param vaccine_cu_age Vector of binary indicators for catch up vaccination
#' of age groups. 1 = vaccinate, 0 = do not vaccinate. Same length as \code{agec}.
#' Default = c(0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0), from 9 to 49.
#' @param vacceff_prim Efficacy of vaccination in reducing infection. Default = 0.75.
#' @param rho_prim Decay of protection from vaccine. Default = 1.
#' @param other_foi Default = 0.025.
#' @param other_prop_immune Propotion of population with pre-existing immunity.
#' Default = 0.
#' @param propTransGlobal Proportion of transmission between all patches.
#' Default = 0.0005.
#' @param propTransNN Proportion of transmission with nearest-neighbor patches.
#' Default = 0.
#' @param BG_FOI Force of infection on humans resulting from imported cases in
#' travelers visiting from elsewhere. Default = 1e-8.
#' @param phi_prim Degree of cross-immunity (not applicable for Zika). Default = 1.
#' @param dis_pri Proportion of infections which are symptomatic. Default = 0.2.
#' @param mc_baseline Baseline per birth microcephaly incidence rate.
#' Default = 0.0002.
#' @param AGE_REC Default = 2.
#' @param PropDiseaseReported Reporting rate of symptomatic cases. Default = 0.1.
#'
#' @return Parameter list
#'
#' @export
parameters_deterministic_model <- function(
# initial state, duration, patches
YL = 365,
DT = 1,
time_period = 365,
NP = 21,
# demography
agec = default_demog$agec,
death = default_demog$death,
# seasonality
season = FALSE,
# humans
age_per = 1,
N_human = 30000000,
incub = 5.5,
inf_per = 6,
nu = 1/21,
# mosquitoes
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,
# general control
propMwtControl = 0,
TimeMwtControlOn = 1.5,
TimeMwtControlOff = 2.5,
# wolbachia
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,
# vaccination
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,
# FOI
other_foi = 0.025,
other_prop_immune = 0,
propTransGlobal = 0.0005,
propTransNN = 0,
BG_FOI = 1e-8,
phi_prim = 1,
# disease
dis_pri = 0.2,
mc_baseline = 0.0002,
AGE_REC = 2,
PropDiseaseReported = 1) {
# Check parameters
if(!is.null(vaccine_child_age)) {
assert_same_length(vaccine_child_age, agec)
}
assert_same_length(vaccine_cu_age, agec)
pars_to_equlibrium_init_create <- list(NP = NP,
YL = YL,
DT = DT,
N_human = N_human,
other_prop_immune = other_prop_immune,
other_foi = other_foi)
# generate initial state variables from equilibrium solution
state_init <- equilibrium_init_create(agec,
death,
pars_to_equlibrium_init_create)
amp_phas <- ZikaModel::amplitudes_phases # Amplitude and phase of seasonal forcing for each patch.
amp_phas[, "phase"] <- amp_phas[, "phase"] * YL
Wb_introtime <- c()
for (i in seq_len(NP - 1)){
Wb_introtime[i] <- Wb_starttime # + trunc(6 * (i - 1) / NP) * 0.5
}
Wb_introtime[NP] <- 1000
vacc_cu_rndtime <- trunc(vacc_cu_time*YL/age_per)*age_per
dis_pri_values <- c()
dis_pri_values[1:2] <- dis_pri
rho1_values <- c()
rho1_values[1] <- rho_prim
rho1_values[2] <- rho_prim * (1 - vacceff_prim)
phi_prim_values <- c()
phi_prim_values[1:2] <- phi_prim
pTG_bigpatch <- propTransGlobal / 10
na <- as.integer(length(agec)) # number of age groups
if(!is.null(vaccine_child_age)) {
vaccine_child_age_2 <- c(0, vaccine_child_age)
} else {
vaccine_child_age_2 <- rep(0, na + 1)
}
if(!is.null(vaccine_cu_age)) {
vaccine_cu_age_2 <- c(0, vaccine_cu_age)
} else {
vaccine_cu_age_2 <- rep(0, na + 1)
}
# Scaling factors (between 0 and 1) for effect of seasonality.
# 1 = maximum effect of seasonality.
# 0 = no effect of seasonality.
if(season) {
Kc_season <- 1
eip_season <- 1
Delta_season <- 1
} else {
Kc_season <- 0
eip_season <- 0
Delta_season <- 0
}
# Collate Parameters Into List
mp_list <- list(YL = YL,
DT = DT,
time_period = time_period,
NP = NP,
agec = agec,
death = death,
age_per = age_per,
incub = incub,
inf_per = inf_per,
nu = nu,
Omega = Omega,
DeltaBase = DeltaBase,
Sigma = Sigma,
Epsilon = Epsilon,
Rm = Rm,
Mwt_mean = Mwt_mean,
Mwt_cv = Mwt_cv,
eip_mean = eip_mean,
Kappa = Kappa,
Beta_hm_1 = Beta_hm_1,
Beta_mh_1 = Beta_mh_1,
propMwtControl = propMwtControl,
TimeMwtControlOn = TimeMwtControlOn,
TimeMwtControlOff = TimeMwtControlOff,
Wb_cyto = Wb_cyto,
Wb_mat = Wb_mat,
Wb_fM = Wb_fM,
Wb_fF = Wb_fF,
Wb_relsusc1 = Wb_relsusc1,
Wb_relinf1 = Wb_relinf1,
Wb_starttime = Wb_starttime,
Wb_introlevel = Wb_introlevel,
Wb_introduration = Wb_introduration,
vacc_child_coverage = vacc_child_coverage,
vacc_child_starttime = vacc_child_starttime,
vacc_child_stoptime = vacc_child_stoptime,
vacc_cu_coverage = vacc_cu_coverage,
vacc_cu_time = vacc_cu_time,
propTransGlobal = propTransGlobal,
propTransNN = propTransNN,
BG_FOI = BG_FOI,
dis1 = dis_pri_values,
rho1 = rho1_values,
phi1 = phi_prim_values,
mc_baseline = mc_baseline,
AGE_REC = AGE_REC,
PropDiseaseReported = PropDiseaseReported,
Wb_introtime = Wb_introtime,
vacc_cu_rndtime = vacc_cu_rndtime,
nn = state_init$nn,
na = state_init$na,
surv = state_init$surv,
mean_surv = state_init$mean_surv,
mean_age = state_init$mean_age,
av_age_s = state_init$av_age_s,
deathrt = state_init$deathrt,
lifeexpec = state_init$lifeexpec,
lifespan = state_init$lifespan,
N_eq = state_init$N_eq,
Nb = state_init$Nb,
init_S = state_init$init_S,
init_I1 = state_init$init_I1,
init_R1 = state_init$init_R1,
pTG_bigpatch = pTG_bigpatch,
vacc_child_age = vaccine_child_age_2,
vacc_cu_age = vaccine_cu_age_2,
Kc_season = Kc_season,
eip_season = eip_season,
Delta_season = Delta_season,
amplitudes_phases = amp_phas,
pi = pi)
return(mp_list)
}
mrc-ide/ZikaModel documentation built on Sept. 14, 2022, 8:51 a.m.
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Defines functions parameters_deterministic_model
Documented in parameters_deterministic_model
# -----------------------------------------------------------------------------
#' The function creates a list of user-defined parameters.
#'
#' @title Create a list of parameters
#'
#' @param YL Duration of a calendar year. Default = 365.
#' @param DT Time step size. Default = 1.
#' @param time_period Length of simulation. Default = 365.
#' @param NP Number of patches. Default = 21.
#' @param agec Numeric vector of age group widths.
#' Default = c(1, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10).
#' @param 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).
#' @param season Logical for controlling the effect of seasonality.
#' TRUE = maximum effect of seasonality.
#' FALSE = no effect of seasonality. Default = FALSE
#' @param age_per Time (weeks) between age updates. Default = 1.
#' @param N_human Human population in each patch. Default = 30000000.
#' @param incub Intrinsic Incubation Period (days). Default = 5.5.
#' @param inf_per Total duration of human infectiousness (days). Default = 6.
#' @param nu Inverse of virus generation time (1 / days).
#' Virus generation time = serial interval. Default = 1 / 21.
#' @param Omega Intensity of density dependence of mosquito larvae mortality rate.
#' 0 = no density dependence. Default = 1.
#' @param DeltaBase Adult mosquito mortality rate. Default = 0.2.
#' @param Sigma Larval mosquito mortality rate. Default = 0.025
#' @param Epsilon Larval mean development rate (1 / larvae mean development time in days).
#' Default = 1/19.
#' @param Rm Mosquito reproduction number (based on adult female fecundity and
#' mortality rates). Default = 2.69.
#' @param 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.
#' @param 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
#' @param eip_mean Mean Extrinsic Incubation Period (days). Default = 8.4.
#' @param Kappa Mosquito biting rate. Default = 0.5.
#' @param 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).
#' @param Beta_mh_1 Per bite transmission probability from mosquitoes to humans.
#' Arbitrarily assigned. Default = 0.7.
#' @param propMwtControl Increase in mortality of adult wild type mosquitoes induced
#' by a \emph{general} type of intervention. Default = 0.
#' @param TimeMwtControlOn Year of start of control of adult wild type mosquitoes.
#' Default = 2.
#' @param TimeMwtControlOff Year of end of control of adult wild type mosquitoes.
#' Default = 3.
#' @param Wb_cyto Degree of cytoplasmic incompatibility induced by Wolbachia.
#' Default = 1.
#' @param Wb_mat Degree of vertical transmission of Wolbachia. Default = 1.
#' @param Wb_fM Increase in mortality induced by Wolbachia. Default = 0.95.
#' @param Wb_fF Reduction in fecundity induced by Wolbachia. Default = 0.95.
#' @param Wb_relsusc1 Infectivity of a human host to Wolbachia infected mosquitoes
#' (time T after host infection). Default = 0.9.
#' @param Wb_relinf1 Infectiousness of Wolbachia-infected mosquitoes time T after
#' infection. Default = 0.75.
#' @param Wb_starttime Time of first release of Wolbachia-infected mosquiotes (years).
#' Default = 1.
#' @param Wb_introlevel Ratio of Wolbachia-infected to wild type mosquitoes at
#' introduction. (Not the proportion of Wolbachia AFTER introduction). Default = 0.
#' @param Wb_introduration Duration of Wolbachia release (days). Default = 60.
#' @param vacc_child_coverage Proportion of children vaccinated. Default = 0.
#' @param vacc_child_starttime Time when vaccination starts. Default = 30.
#' @param vacc_child_stoptime Time when vaccination ends. Default = 30.
#' @param vaccine_child_age Vector of binary indicators for routine vaccination
#' of age groups. 1 = vaccinate, 0 = do not vaccinate. Same length as \code{agec}.
#' Default = NULL.
#' @param vacc_cu_coverage Proportion of children who undergo catch up vaccination.
#' Default = 0.
#' @param vacc_cu_time Time when catch up vaccination occurs. Default = 30.
#' @param vaccine_cu_age Vector of binary indicators for catch up vaccination
#' of age groups. 1 = vaccinate, 0 = do not vaccinate. Same length as \code{agec}.
#' Default = c(0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0), from 9 to 49.
#' @param vacceff_prim Efficacy of vaccination in reducing infection. Default = 0.75.
#' @param rho_prim Decay of protection from vaccine. Default = 1.
#' @param other_foi Default = 0.025.
#' @param other_prop_immune Propotion of population with pre-existing immunity.
#' Default = 0.
#' @param propTransGlobal Proportion of transmission between all patches.
#' Default = 0.0005.
#' @param propTransNN Proportion of transmission with nearest-neighbor patches.
#' Default = 0.
#' @param BG_FOI Force of infection on humans resulting from imported cases in
#' travelers visiting from elsewhere. Default = 1e-8.
#' @param phi_prim Degree of cross-immunity (not applicable for Zika). Default = 1.
#' @param dis_pri Proportion of infections which are symptomatic. Default = 0.2.
#' @param mc_baseline Baseline per birth microcephaly incidence rate.
#' Default = 0.0002.
#' @param AGE_REC Default = 2.
#' @param PropDiseaseReported Reporting rate of symptomatic cases. Default = 0.1.
#'
#' @return Parameter list
#'
#' @export
parameters_deterministic_model <- function(
# initial state, duration, patches
YL = 365,
DT = 1,
time_period = 365,
NP = 21,
# demography
agec = default_demog$agec,
death = default_demog$death,
# seasonality
season = FALSE,
# humans
age_per = 1,
N_human = 30000000,
incub = 5.5,
inf_per = 6,
nu = 1/21,
# mosquitoes
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,
# general control
propMwtControl = 0,
TimeMwtControlOn = 1.5,
TimeMwtControlOff = 2.5,
# wolbachia
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,
# vaccination
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,
# FOI
other_foi = 0.025,
other_prop_immune = 0,
propTransGlobal = 0.0005,
propTransNN = 0,
BG_FOI = 1e-8,
phi_prim = 1,
# disease
dis_pri = 0.2,
mc_baseline = 0.0002,
AGE_REC = 2,
PropDiseaseReported = 1) {
# Check parameters
if(!is.null(vaccine_child_age)) {
assert_same_length(vaccine_child_age, agec)
}
assert_same_length(vaccine_cu_age, agec)
pars_to_equlibrium_init_create <- list(NP = NP,
YL = YL,
DT = DT,
N_human = N_human,
other_prop_immune = other_prop_immune,
other_foi = other_foi)
# generate initial state variables from equilibrium solution
state_init <- equilibrium_init_create(agec,
death,
pars_to_equlibrium_init_create)
amp_phas <- ZikaModel::amplitudes_phases # Amplitude and phase of seasonal forcing for each patch.
amp_phas[, "phase"] <- amp_phas[, "phase"] * YL
Wb_introtime <- c()
for (i in seq_len(NP - 1)){
Wb_introtime[i] <- Wb_starttime # + trunc(6 * (i - 1) / NP) * 0.5
}
Wb_introtime[NP] <- 1000
vacc_cu_rndtime <- trunc(vacc_cu_time*YL/age_per)*age_per
dis_pri_values <- c()
dis_pri_values[1:2] <- dis_pri
rho1_values <- c()
rho1_values[1] <- rho_prim
rho1_values[2] <- rho_prim * (1 - vacceff_prim)
phi_prim_values <- c()
phi_prim_values[1:2] <- phi_prim
pTG_bigpatch <- propTransGlobal / 10
na <- as.integer(length(agec)) # number of age groups
if(!is.null(vaccine_child_age)) {
vaccine_child_age_2 <- c(0, vaccine_child_age)
} else {
vaccine_child_age_2 <- rep(0, na + 1)
}
if(!is.null(vaccine_cu_age)) {
vaccine_cu_age_2 <- c(0, vaccine_cu_age)
} else {
vaccine_cu_age_2 <- rep(0, na + 1)
}
# Scaling factors (between 0 and 1) for effect of seasonality.
# 1 = maximum effect of seasonality.
# 0 = no effect of seasonality.
if(season) {
Kc_season <- 1
eip_season <- 1
Delta_season <- 1
} else {
Kc_season <- 0
eip_season <- 0
Delta_season <- 0
}
# Collate Parameters Into List
mp_list <- list(YL = YL,
DT = DT,
time_period = time_period,
NP = NP,
agec = agec,
death = death,
age_per = age_per,
incub = incub,
inf_per = inf_per,
nu = nu,
Omega = Omega,
DeltaBase = DeltaBase,
Sigma = Sigma,
Epsilon = Epsilon,
Rm = Rm,
Mwt_mean = Mwt_mean,
Mwt_cv = Mwt_cv,
eip_mean = eip_mean,
Kappa = Kappa,
Beta_hm_1 = Beta_hm_1,
Beta_mh_1 = Beta_mh_1,
propMwtControl = propMwtControl,
TimeMwtControlOn = TimeMwtControlOn,
TimeMwtControlOff = TimeMwtControlOff,
Wb_cyto = Wb_cyto,
Wb_mat = Wb_mat,
Wb_fM = Wb_fM,
Wb_fF = Wb_fF,
Wb_relsusc1 = Wb_relsusc1,
Wb_relinf1 = Wb_relinf1,
Wb_starttime = Wb_starttime,
Wb_introlevel = Wb_introlevel,
Wb_introduration = Wb_introduration,
vacc_child_coverage = vacc_child_coverage,
vacc_child_starttime = vacc_child_starttime,
vacc_child_stoptime = vacc_child_stoptime,
vacc_cu_coverage = vacc_cu_coverage,
vacc_cu_time = vacc_cu_time,
propTransGlobal = propTransGlobal,
propTransNN = propTransNN,
BG_FOI = BG_FOI,
dis1 = dis_pri_values,
rho1 = rho1_values,
phi1 = phi_prim_values,
mc_baseline = mc_baseline,
AGE_REC = AGE_REC,
PropDiseaseReported = PropDiseaseReported,
Wb_introtime = Wb_introtime,
vacc_cu_rndtime = vacc_cu_rndtime,
nn = state_init$nn,
na = state_init$na,
surv = state_init$surv,
mean_surv = state_init$mean_surv,
mean_age = state_init$mean_age,
av_age_s = state_init$av_age_s,
deathrt = state_init$deathrt,
lifeexpec = state_init$lifeexpec,
lifespan = state_init$lifespan,
N_eq = state_init$N_eq,
Nb = state_init$Nb,
init_S = state_init$init_S,
init_I1 = state_init$init_I1,
init_R1 = state_init$init_R1,
pTG_bigpatch = pTG_bigpatch,
vacc_child_age = vaccine_child_age_2,
vacc_cu_age = vaccine_cu_age_2,
Kc_season = Kc_season,
eip_season = eip_season,
Delta_season = Delta_season,
amplitudes_phases = amp_phas,
pi = pi)
return(mp_list)
}
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