R/parameters.R
In mrc-ide/squire: SEIR transmission model of COVID-19
Defines functions
parameters_explicit_SEEIR
get_hosp_bed_capacity
get_ICU_bed_capacity
parameters_simple_SEEIR
Documented in
parameters_explicit_SEEIR
parameters_simple_SEEIR
# -----------------------------------------------------------------------------
#' Parmeters for the simple SEEIR model
#'
#' @param R0 Basic reproduction number
#' @param tt_R0 Change time points for R0
#' @param dt Time step
#' @param init Data.frame of initial conditions
#' @param dur_E Mean duration of incubation period (days)
#' @param dur_I Mean duration of infectious period (days) in simple model
#' @param population Population vector (for each age group)
#' @param contact_matrix_set Contact matrices used in simulation
#' @param tt_contact_matrix Time change points for matrix change
#' @param time_period Length of simulation
#' @param day_return Logical, do we want to return outut after each day rather
#' than each dt. Default = FALSE
#'
#' @return Paramater List
#' @export
#'
parameters_simple_SEEIR <- function(R0 = 3,
tt_R0 = 0,
dt = 0.1,
init = NULL,
dur_E = 4.58,
dur_I = 2.09,
day_return = FALSE,
population,
contact_matrix_set,
tt_contact_matrix = 0,
time_period = 365) {
# Initialise initial conditions
init <- init_check(init, population)
# Standardise contact matrix set
if(is.matrix(contact_matrix_set)){
contact_matrix_set <- list(contact_matrix_set)
}
# populate contact matrix set if not provided
if (length(contact_matrix_set) == 1) {
baseline <- contact_matrix_set[[1]]
contact_matrix_set <- vector("list", length(tt_contact_matrix))
for(i in seq_along(tt_contact_matrix)) {
contact_matrix_set[[i]] <- baseline
}
}
# Input checks
mc <- matrix_check(population, contact_matrix_set)
stopifnot(length(R0) == length(tt_R0))
stopifnot(length(contact_matrix_set) == length(tt_contact_matrix))
tc <- lapply(list(tt_R0, tt_contact_matrix), check_time_change, time_period)
pn1 <- pos_num(dt, "dt")
pn2 <- pos_num(dur_E, "dur_E")
pn3 <- pos_num(dur_I, "dur_I")
pn4 <- pos_num(time_period, "time_period")
# Convert and Generate Parameters As Required
gamma_E <- 2 * 1 / dur_E
gamma_I <- 1 / dur_I
beta_set <- beta_est_simple(dur_I, contact_matrix_set[[1]], R0)
# Convert contact matrices to input matrices
matrices_set <- matrix_set(contact_matrix_set, population)
# Collate Parameters Into List
pars <- list(S0 = init$S,
E0 = init$E,
E02 = init$E2,
I0 = init$I,
R0 = init$R,
gamma_E = gamma_E,
gamma_I = gamma_I,
tt_beta = tt_R0,
beta_set = beta_set,
N_age = length(population),
tt_matrix = tt_contact_matrix,
mix_mat_set = matrices_set,
contact_matrix_set = contact_matrix_set,
population = population,
day_return = day_return,
dt = dt)
class(pars) <- c("simple_SEEIR_parameters", "squire_parameters")
return(pars)
}
# Get ICU bed capacity
#' @noRd
get_ICU_bed_capacity <- function(country) {
beds <- get_healthcare_capacity(country)
ICU_beds <- beds$ICU_beds
population <- get_population(country)$n
ICU_bed_capacity <- round(ICU_beds * sum(population)/1000)
ICU_bed_capacity
}
# Get hospital bed capacity
#' @noRd
get_hosp_bed_capacity <- function(country = NULL) {
beds <- get_healthcare_capacity(country)
population <- get_population(country)$n
hosp_beds <- beds$hosp_beds
hosp_bed_capacity <- round(hosp_beds * sum(population)/1000)
}
# -----------------------------------------------------------------------------
#' Parmaters for explicit SEEIR model
#'
#' @details All durations are in days.
#'
#' @section Parameter Updates:
#'
#' Parameters detailing the age-dependent probability of disease
#' severity and durations of hospital durations have been updated in v0.5.0
#' of \code{squire} to reflect the changing understanding of COVID-19 transmission.
#' Parameter arguments are by default equal to \code{NULL}, which
#' causes the new updated parameters specified in \code{\link{default_probs}}
#' and \code{\link{default_durations}} to be used. If any provided parameters
#' are not \code{NULL}, these will be used. In order to ease previous fits and
#' code, function argument \code{walker_params} will use the parameters described
#' in \href{https://science.sciencemag.org/content/369/6502/413}{Walker et al. Science. 2020}
#' which can be viewed within the function \code{\link{parse_country_severity}}
#'
#'
#' @param population Population vector (for each age group). Default = NULL,
#' which will cause population to be sourced from \code{country}
#' @param country Character for country beign simulated. WIll be used to
#' generate \code{population} and \code{contact_matrix_set} if
#' unprovided. Either \code{country} or \code{population} and
#' \code{contact_matrix_set} must be provided.
#' @param contact_matrix_set Contact matrices used in simulation. Default =
#' NULL, which will generate this based on the \code{country}.
#' @param tt_contact_matrix Time change points for matrix change. Default = 0
#' @param R0 Basic Reproduction Number. Default = 3
#' @param tt_R0 Change time points for R0. Default = 0
#' @param beta_set Alternative parameterisation via beta rather than R0.
#' Default = NULL, which causes beta to be estimated from R0
#' @param time_period Length of simulation. Default = 365
#' @param dt Time Step. Default = 0.1
#' @param init Data.frame of initial conditions. Default = NULL
#' @param seeding_cases Initial number of cases seeding the epidemic
#' @param prob_hosp Probability of hospitalisation by age.
#' Default, NULL, will use
#' \code{c(0.000840764, 0.001182411, 0.001662887, 0.002338607,
#' 0.003288907, 0.004625365, 0.006504897, 0.009148183, 0.012865577,
#' 0.018093546, 0.025445917, 0.035785947, 0.050327683, 0.0707785,
#' 0.099539573, 0.1399878, 0.233470395)}
#' @param prob_severe Probability of developing severe symptoms by age.
#' Default, NULL, will use
#' \code{c(0.000840764, 0.001182411, 0.001662887, 0.002338607,
#' 0.003288907, 0.004625365, 0.006504897, 0.009148183, 0.012865577,
#' 0.018093546, 0.025445917, 0.035785947, 0.050327683, 0.0707785,
#' 0.099539573, 0.1399878, 0.233470395)}
#' @param prob_non_severe_death_treatment Probability of death from non severe
#' treated infection. Default, NULL, will use
#' \code{c(0.181354223, 0.181354223, 0.181354223, 0.137454906,
#' 0.121938236, 0.122775613, 0.136057441, 0.160922182, 0.196987378,
#' 0.242011054, 0.289368845, 0.326537862, 0.337229819, 0.309082553,
#' 0.243794865, 0.160480254, 0.057084366)}
#' @param prob_severe_death_treatment Probability of death from severe infection
#' that is treated. Default, NULL, will use
#' \code{c(0.226668959, 0.252420241, 0.281097009, 0.413005389,
#' 0.518451493, 0.573413613, 0.576222065, 0.54253573, 0.493557696,
#' 0.447376527, 0.416666608, 0.411186639, 0.443382594, 0.538718871,
#' 0.570434076, 0.643352843, 0.992620047)}
#' @param prob_non_severe_death_no_treatment Probability of death in non severe
#' hospital inections that aren't treated. Default, NULL, will use
#' \code{rep(0.5, 17)}
#' @param prob_severe_death_no_treatment Probability of death from severe infection
#' that is not treated. Default, NULL, will use
#' \code{rep(0.95, 17)}
#' @param p_dist Preferentiality of age group receiving treatment relative to
#' other age groups when demand exceeds healthcare capacity.
#' @param dur_E Mean duration of incubation period (days). Default = 4.6
#' @param dur_R Mean duration of immunity (days). Default = Inf
#' @param dur_IMild Mean duration of mild infection (days). Default = 2.1
#' @param dur_ICase Mean duration from symptom onset to hospitil admission (days).
#' Default = 4.5
#' @param dur_get_ox_survive Mean duration of oxygen given survive. Default = 9
#' @param tt_dur_get_ox_survive Times at which dur_get_ox_survive changes
#' (Default = 0 = doesn't change)
#' @param dur_get_ox_die Mean duration of oxygen given death. Default = 9
#' @param tt_dur_get_ox_die Times at which dur_get_ox_die changes
#' (Default = 0 = doesn't change)
#' @param dur_not_get_ox_survive Mean duration without oxygen given survive.
#' Default = 4.5
#' @param dur_not_get_ox_die Mean duration without oxygen given death.
#' Default = 4.5
#' @param dur_get_mv_survive Mean duration of ventilation given survive.
#' Default = 14.8
#' @param tt_dur_get_mv_survive Times at which dur_get_mv_survive changes
#' (Default = 0 = doesn't change)
#' @param dur_get_mv_die Mean duration of ventilation given death. Default = 11.1
#' @param tt_dur_get_mv_die Times at which dur_get_mv_die changes
#' (Default = 0 = doesn't change)
#' @param dur_not_get_mv_survive Mean duration without ventilation given
#' survive. Default = 7.4
#' @param dur_not_get_mv_die Mean duration without ventilation given
#' death. Default = 1
#' @param dur_rec Duration of recovery after coming off ventilation. Default = 3
#' @param hosp_bed_capacity General bed capacity. Can be single number or vector if capacity time-varies.
#' @param ICU_bed_capacity ICU bed capacity. Can be single number or vector if capacity time-varies.
#' @param tt_hosp_beds Times at which hospital bed capacity changes (Default = 0 = doesn't change)
#' @param tt_ICU_beds Times at which ICU bed capacity changes (Default = 0 = doesn't change)
#'
#' @param walker_params Boolean for using parameters in Walker et al. Default = FALSE,
#' which uses parameter update as of November 2020. For full information see
#' parameters vignette
#'
#' @return Paramater List
#' @export
#'
parameters_explicit_SEEIR <- function(
# demography
country = NULL,
population = NULL,
tt_contact_matrix = 0,
contact_matrix_set = NULL,
# transmission
R0 = 3,
tt_R0 = 0,
beta_set = NULL,
# initial state, duration, reps
time_period = 365,
dt = 0.1,
init = NULL,
seeding_cases = NULL,
# parameters/probabilities
prob_hosp = NULL,
prob_severe = NULL,
prob_non_severe_death_treatment = NULL,
prob_non_severe_death_no_treatment = NULL,
prob_severe_death_treatment = NULL,
prob_severe_death_no_treatment = NULL,
p_dist = probs$p_dist,
walker_params = FALSE,
# durations
dur_E = NULL,
dur_IMild = NULL,
dur_ICase = NULL,
dur_get_ox_survive = NULL,
tt_dur_get_ox_survive = NULL,
dur_get_ox_die = NULL,
tt_dur_get_ox_die = NULL,
dur_not_get_ox_survive = NULL,
dur_not_get_ox_die = NULL,
dur_get_mv_survive = NULL,
tt_dur_get_mv_survive = NULL,
dur_get_mv_die = NULL,
tt_dur_get_mv_die = NULL,
dur_not_get_mv_survive = NULL,
dur_not_get_mv_die = NULL,
dur_rec = NULL,
dur_R = NULL,
# health system capacity
hosp_bed_capacity = NULL,
ICU_bed_capacity = NULL,
tt_hosp_beds = 0,
tt_ICU_beds = 0
) {
# Handle country population args
cpm <- parse_country_population_mixing_matrix(country = country,
population = population,
contact_matrix_set = contact_matrix_set)
country <- cpm$country
population <- cpm$population
contact_matrix_set <- cpm$contact_matrix_set
# Handle severity parameters and possible 80+ demographic adjustment
severity_params <- parse_country_severity(country = country,
prob_hosp = prob_hosp,
prob_severe = prob_severe,
prob_non_severe_death_treatment = prob_non_severe_death_treatment,
prob_severe_death_treatment = prob_severe_death_treatment,
prob_non_severe_death_no_treatment = prob_non_severe_death_no_treatment,
prob_severe_death_no_treatment = prob_severe_death_no_treatment,
walker_params = walker_params)
prob_hosp <- severity_params$prob_hosp
prob_severe <- severity_params$prob_severe
prob_non_severe_death_treatment <- severity_params$prob_non_severe_death_treatment
prob_severe_death_treatment <- severity_params$prob_severe_death_treatment
prob_non_severe_death_no_treatment <- severity_params$prob_non_severe_death_no_treatment
prob_severe_death_no_treatment <- severity_params$prob_severe_death_no_treatment
# Handle duration of hospitalisation parameters
duration_params <- parse_durations(
dur_get_ox_survive = dur_get_ox_survive,
tt_dur_get_ox_survive = tt_dur_get_ox_survive,
dur_get_ox_die = dur_get_ox_die,
tt_dur_get_ox_die = tt_dur_get_ox_die,
dur_not_get_ox_survive = dur_not_get_ox_survive,
dur_not_get_ox_die = dur_not_get_ox_die,
dur_get_mv_survive = dur_get_mv_survive,
tt_dur_get_mv_survive = tt_dur_get_mv_survive,
dur_get_mv_die = dur_get_mv_die,
tt_dur_get_mv_die = tt_dur_get_mv_die,
dur_not_get_mv_survive = dur_not_get_mv_survive,
dur_not_get_mv_die = dur_not_get_mv_die,
dur_rec = dur_rec,
dur_R = dur_R,
dur_E = dur_E,
dur_IMild = dur_IMild,
dur_ICase = dur_ICase,
walker_params = walker_params)
dur_get_ox_survive <- duration_params$dur_get_ox_survive
tt_dur_get_ox_survive <- duration_params$tt_dur_get_ox_survive
dur_get_ox_die <- duration_params$dur_get_ox_die
tt_dur_get_ox_die <- duration_params$tt_dur_get_ox_die
dur_not_get_ox_survive <- duration_params$dur_not_get_ox_survive
dur_not_get_ox_die <- duration_params$dur_not_get_ox_die
dur_get_mv_survive <- duration_params$dur_get_mv_survive
tt_dur_get_mv_survive <- duration_params$tt_dur_get_mv_survive
dur_get_mv_die <- duration_params$dur_get_mv_die
tt_dur_get_mv_die <- duration_params$tt_dur_get_mv_die
dur_not_get_mv_survive <- duration_params$dur_not_get_mv_survive
dur_not_get_mv_die <- duration_params$dur_not_get_mv_die
dur_rec <- duration_params$dur_rec
dur_R <- duration_params$dur_R
dur_E <- duration_params$dur_E
dur_IMild <- duration_params$dur_IMild
dur_ICase <- duration_params$dur_ICase
# Standardise contact matrix set
if(is.matrix(contact_matrix_set)){
contact_matrix_set <- list(contact_matrix_set)
}
# populate contact matrix set if not provided
if (length(contact_matrix_set) == 1) {
baseline <- contact_matrix_set[[1]]
contact_matrix_set <- vector("list", length(tt_contact_matrix))
for(i in seq_along(tt_contact_matrix)) {
contact_matrix_set[[i]] <- baseline
}
}
# populate hospital and ICU bed capacity if not provided
if (is.null(hosp_bed_capacity)) {
if (!is.null(country)) {
beds <- get_healthcare_capacity(country)
hosp_beds <- beds$hosp_beds
hosp_bed_capacity <- rep(round(hosp_beds * sum(population)/1000), length(tt_hosp_beds))
} else {
hosp_bed_capacity <- round(5 * sum(population)/1000)
}
}
if (is.null(ICU_bed_capacity)) {
if (!is.null(country)) {
beds <- get_healthcare_capacity(country)
ICU_beds <- beds$ICU_beds
ICU_bed_capacity <- rep(round(ICU_beds * sum(population)/1000), length(tt_ICU_beds))
} else {
ICU_bed_capacity <- round(3 * hosp_bed_capacity/100)
}
}
# Initial state and matrix formatting
# ----------------------------------------------------------------------------
# Initialise initial conditions
if (!is.null(seeding_cases)) {
assert_int(seeding_cases)
mod_init <- init_check_explicit(init, population, seeding_cases)
} else {
mod_init <- init_check_explicit(init, population)
}
# Convert contact matrices to input matrices
matrices_set <- matrix_set_explicit(contact_matrix_set, population)
mc <- matrix_check(population[-1], contact_matrix_set)
# Input checks
# ----------------------------------------------------------------------------
stopifnot(length(R0) == length(tt_R0))
stopifnot(length(contact_matrix_set) == length(tt_contact_matrix))
stopifnot(length(hosp_bed_capacity) == length(tt_hosp_beds))
stopifnot(length(ICU_bed_capacity) == length(tt_ICU_beds))
stopifnot(length(dur_get_mv_survive) == length(tt_dur_get_mv_survive))
stopifnot(length(dur_get_ox_survive) == length(tt_dur_get_ox_survive))
stopifnot(length(dur_get_mv_die) == length(tt_dur_get_mv_die))
stopifnot(length(dur_get_ox_die) == length(tt_dur_get_ox_die))
tc <- lapply(list(tt_R0/dt, tt_contact_matrix/dt,
tt_hosp_beds/dt, tt_ICU_beds/dt,
tt_dur_get_mv_survive/dt,
tt_dur_get_ox_survive/dt,
tt_dur_get_mv_die/dt,
tt_dur_get_ox_die/dt
),
check_time_change, time_period/dt)
assert_pos(dt)
assert_pos(dur_E)
assert_pos(dur_IMild)
assert_pos(dur_ICase)
assert_pos(dur_get_ox_survive)
assert_pos(dur_get_ox_die)
assert_pos(dur_not_get_ox_survive)
assert_pos(dur_not_get_ox_die)
assert_pos(dur_get_mv_survive)
assert_pos(dur_get_mv_die)
assert_pos(dur_not_get_mv_survive)
assert_pos(dur_not_get_mv_die)
assert_pos(time_period)
assert_pos(hosp_bed_capacity)
assert_pos(ICU_bed_capacity)
assert_length(prob_hosp, length(population))
assert_length(prob_severe, length(population))
assert_length(prob_non_severe_death_treatment, length(population))
assert_length(prob_non_severe_death_no_treatment, length(population))
assert_length(prob_severe_death_treatment, length(population))
assert_length(prob_severe_death_no_treatment, length(population))
assert_length(p_dist, length(population))
assert_numeric(prob_hosp, length(population))
assert_numeric(prob_severe, length(population))
assert_numeric(prob_non_severe_death_treatment, length(population))
assert_numeric(prob_non_severe_death_no_treatment, length(population))
assert_numeric(prob_severe_death_treatment, length(population))
assert_numeric(prob_severe_death_no_treatment, length(population))
assert_numeric(p_dist, length(population))
assert_leq(prob_hosp, 1)
assert_leq(prob_severe, 1)
assert_leq(prob_non_severe_death_treatment, 1)
assert_leq(prob_non_severe_death_no_treatment, 1)
assert_leq(prob_severe_death_treatment, 1)
assert_leq(prob_severe_death_no_treatment, 1)
assert_leq(p_dist, 1)
assert_greq(prob_hosp, 0)
assert_greq(prob_severe, 0)
assert_greq(prob_non_severe_death_treatment, 0)
assert_greq(prob_non_severe_death_no_treatment, 0)
assert_greq(prob_severe_death_treatment, 0)
assert_greq(prob_severe_death_no_treatment, 0)
assert_greq(p_dist, 0)
# Convert and Generate Parameters As Required
# ----------------------------------------------------------------------------
# durations
gamma_E = 2 * 1/dur_E
gamma_IMild = 1/dur_IMild
gamma_ICase = 2 * 1/dur_ICase
gamma_get_ox_survive = 2 * 1/dur_get_ox_survive
gamma_get_ox_die = 2 * 1/dur_get_ox_die
gamma_not_get_ox_survive = 2 * 1/dur_not_get_ox_survive
gamma_not_get_ox_die = 2 * 1/dur_not_get_ox_die
gamma_get_mv_survive = 2 * 1/dur_get_mv_survive
gamma_get_mv_die = 2 * 1/dur_get_mv_die
gamma_not_get_mv_survive = 2 * 1/dur_not_get_mv_survive
gamma_not_get_mv_die = 2 * 1/dur_not_get_mv_die
gamma_rec = 2 * 1/dur_rec
gamma_R = 2 * 1/dur_R
if (is.null(beta_set)) {
baseline_matrix <- process_contact_matrix_scaled_age(contact_matrix_set[[1]], population)
beta_set <- beta_est_explicit(dur_IMild = dur_IMild,
dur_ICase = dur_ICase,
prob_hosp = prob_hosp,
mixing_matrix = baseline_matrix,
R0 = R0)
}
# normalise to sum to 1
p_dist <- p_dist/mean(p_dist)
# Collate Parameters Into List
pars <- list(N_age = length(population),
S_0 = mod_init$S,
E1_0 = mod_init$E1,
E2_0 = mod_init$E2,
IMild_0 = mod_init$IMild,
ICase1_0 = mod_init$ICase1,
ICase2_0 = mod_init$ICase2,
IOxGetLive1_0 = mod_init$IOxGetLive1,
IOxGetLive2_0 = mod_init$IOxGetLive2,
IOxGetDie1_0 = mod_init$IOxGetDie1,
IOxGetDie2_0 = mod_init$IOxGetDie2,
IOxNotGetLive1_0 = mod_init$IOxNotGetLive1,
IOxNotGetLive2_0 = mod_init$IOxNotGetLive2,
IOxNotGetDie1_0 = mod_init$IOxNotGetDie1,
IOxNotGetDie2_0 = mod_init$IOxNotGetDie2,
IMVGetLive1_0 = mod_init$IMVGetLive1,
IMVGetLive2_0 = mod_init$IMVGetLive2,
IMVGetDie1_0 = mod_init$IMVGetDie1,
IMVGetDie2_0 = mod_init$IMVGetDie2,
IMVNotGetLive1_0 = mod_init$IMVNotGetLive1,
IMVNotGetLive2_0 = mod_init$IMVNotGetLive2,
IMVNotGetDie1_0 = mod_init$IMVNotGetDie1,
IMVNotGetDie2_0 = mod_init$IMVNotGetDie2,
IRec1_0 = mod_init$IRec1,
IRec2_0 = mod_init$IRec2,
R1_0 = mod_init$R1,
R2_0 = mod_init$R2,
D_0 = mod_init$D,
gamma_E = gamma_E,
gamma_IMild = gamma_IMild,
gamma_ICase = gamma_ICase,
gamma_get_ox_survive = gamma_get_ox_survive,
gamma_get_ox_die = gamma_get_ox_die,
gamma_not_get_ox_survive = gamma_not_get_ox_survive,
gamma_not_get_ox_die = gamma_not_get_ox_die,
gamma_get_mv_survive = gamma_get_mv_survive,
gamma_get_mv_die = gamma_get_mv_die,
gamma_not_get_mv_survive = gamma_not_get_mv_survive,
gamma_not_get_mv_die = gamma_not_get_mv_die,
gamma_rec = gamma_rec,
gamma_R = gamma_R,
prob_hosp = prob_hosp,
prob_severe = prob_severe,
prob_non_severe_death_treatment = prob_non_severe_death_treatment,
prob_non_severe_death_no_treatment = prob_non_severe_death_no_treatment,
prob_severe_death_treatment = prob_severe_death_treatment,
prob_severe_death_no_treatment = prob_severe_death_no_treatment,
p_dist = p_dist,
mix_mat_set = matrices_set,
hosp_beds = hosp_bed_capacity,
ICU_beds = ICU_bed_capacity,
beta_set = beta_set,
tt_hosp_beds = round(tt_hosp_beds/dt),
tt_ICU_beds = round(tt_ICU_beds/dt),
tt_matrix = round(tt_contact_matrix/dt),
tt_beta = round(tt_R0/dt),
tt_dur_get_mv_survive = round(tt_dur_get_mv_survive/dt),
tt_dur_get_ox_survive = round(tt_dur_get_ox_survive/dt),
tt_dur_get_mv_die = round(tt_dur_get_mv_die/dt),
tt_dur_get_ox_die = round(tt_dur_get_ox_die/dt),
dt = dt,
population = population,
contact_matrix_set = contact_matrix_set,
dur_E = dur_E,
dur_IMild = dur_IMild,
dur_ICase = dur_ICase,
dur_get_ox_survive = dur_get_ox_survive,
dur_get_ox_die = dur_get_ox_die,
dur_not_get_ox_survive = dur_not_get_ox_survive,
dur_not_get_ox_die = dur_not_get_ox_die,
dur_get_mv_survive = dur_get_mv_survive,
dur_get_mv_die = dur_get_mv_die,
dur_not_get_mv_survive = dur_not_get_mv_survive,
dur_not_get_mv_die = dur_not_get_mv_die,
dur_rec = dur_rec,
dur_R = dur_R)
class(pars) <- c("explicit_SEEIR_parameters", "squire_parameters")
return(pars)
}
mrc-ide/squire documentation built on Sept. 10, 2022, 1:11 a.m.
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Defines functions parameters_explicit_SEEIR get_hosp_bed_capacity get_ICU_bed_capacity parameters_simple_SEEIR
Documented in parameters_explicit_SEEIR parameters_simple_SEEIR
# -----------------------------------------------------------------------------
#' Parmeters for the simple SEEIR model
#'
#' @param R0 Basic reproduction number
#' @param tt_R0 Change time points for R0
#' @param dt Time step
#' @param init Data.frame of initial conditions
#' @param dur_E Mean duration of incubation period (days)
#' @param dur_I Mean duration of infectious period (days) in simple model
#' @param population Population vector (for each age group)
#' @param contact_matrix_set Contact matrices used in simulation
#' @param tt_contact_matrix Time change points for matrix change
#' @param time_period Length of simulation
#' @param day_return Logical, do we want to return outut after each day rather
#' than each dt. Default = FALSE
#'
#' @return Paramater List
#' @export
#'
parameters_simple_SEEIR <- function(R0 = 3,
tt_R0 = 0,
dt = 0.1,
init = NULL,
dur_E = 4.58,
dur_I = 2.09,
day_return = FALSE,
population,
contact_matrix_set,
tt_contact_matrix = 0,
time_period = 365) {
# Initialise initial conditions
init <- init_check(init, population)
# Standardise contact matrix set
if(is.matrix(contact_matrix_set)){
contact_matrix_set <- list(contact_matrix_set)
}
# populate contact matrix set if not provided
if (length(contact_matrix_set) == 1) {
baseline <- contact_matrix_set[[1]]
contact_matrix_set <- vector("list", length(tt_contact_matrix))
for(i in seq_along(tt_contact_matrix)) {
contact_matrix_set[[i]] <- baseline
}
}
# Input checks
mc <- matrix_check(population, contact_matrix_set)
stopifnot(length(R0) == length(tt_R0))
stopifnot(length(contact_matrix_set) == length(tt_contact_matrix))
tc <- lapply(list(tt_R0, tt_contact_matrix), check_time_change, time_period)
pn1 <- pos_num(dt, "dt")
pn2 <- pos_num(dur_E, "dur_E")
pn3 <- pos_num(dur_I, "dur_I")
pn4 <- pos_num(time_period, "time_period")
# Convert and Generate Parameters As Required
gamma_E <- 2 * 1 / dur_E
gamma_I <- 1 / dur_I
beta_set <- beta_est_simple(dur_I, contact_matrix_set[[1]], R0)
# Convert contact matrices to input matrices
matrices_set <- matrix_set(contact_matrix_set, population)
# Collate Parameters Into List
pars <- list(S0 = init$S,
E0 = init$E,
E02 = init$E2,
I0 = init$I,
R0 = init$R,
gamma_E = gamma_E,
gamma_I = gamma_I,
tt_beta = tt_R0,
beta_set = beta_set,
N_age = length(population),
tt_matrix = tt_contact_matrix,
mix_mat_set = matrices_set,
contact_matrix_set = contact_matrix_set,
population = population,
day_return = day_return,
dt = dt)
class(pars) <- c("simple_SEEIR_parameters", "squire_parameters")
return(pars)
}
# Get ICU bed capacity
#' @noRd
get_ICU_bed_capacity <- function(country) {
beds <- get_healthcare_capacity(country)
ICU_beds <- beds$ICU_beds
population <- get_population(country)$n
ICU_bed_capacity <- round(ICU_beds * sum(population)/1000)
ICU_bed_capacity
}
# Get hospital bed capacity
#' @noRd
get_hosp_bed_capacity <- function(country = NULL) {
beds <- get_healthcare_capacity(country)
population <- get_population(country)$n
hosp_beds <- beds$hosp_beds
hosp_bed_capacity <- round(hosp_beds * sum(population)/1000)
}
# -----------------------------------------------------------------------------
#' Parmaters for explicit SEEIR model
#'
#' @details All durations are in days.
#'
#' @section Parameter Updates:
#'
#' Parameters detailing the age-dependent probability of disease
#' severity and durations of hospital durations have been updated in v0.5.0
#' of \code{squire} to reflect the changing understanding of COVID-19 transmission.
#' Parameter arguments are by default equal to \code{NULL}, which
#' causes the new updated parameters specified in \code{\link{default_probs}}
#' and \code{\link{default_durations}} to be used. If any provided parameters
#' are not \code{NULL}, these will be used. In order to ease previous fits and
#' code, function argument \code{walker_params} will use the parameters described
#' in \href{https://science.sciencemag.org/content/369/6502/413}{Walker et al. Science. 2020}
#' which can be viewed within the function \code{\link{parse_country_severity}}
#'
#'
#' @param population Population vector (for each age group). Default = NULL,
#' which will cause population to be sourced from \code{country}
#' @param country Character for country beign simulated. WIll be used to
#' generate \code{population} and \code{contact_matrix_set} if
#' unprovided. Either \code{country} or \code{population} and
#' \code{contact_matrix_set} must be provided.
#' @param contact_matrix_set Contact matrices used in simulation. Default =
#' NULL, which will generate this based on the \code{country}.
#' @param tt_contact_matrix Time change points for matrix change. Default = 0
#' @param R0 Basic Reproduction Number. Default = 3
#' @param tt_R0 Change time points for R0. Default = 0
#' @param beta_set Alternative parameterisation via beta rather than R0.
#' Default = NULL, which causes beta to be estimated from R0
#' @param time_period Length of simulation. Default = 365
#' @param dt Time Step. Default = 0.1
#' @param init Data.frame of initial conditions. Default = NULL
#' @param seeding_cases Initial number of cases seeding the epidemic
#' @param prob_hosp Probability of hospitalisation by age.
#' Default, NULL, will use
#' \code{c(0.000840764, 0.001182411, 0.001662887, 0.002338607,
#' 0.003288907, 0.004625365, 0.006504897, 0.009148183, 0.012865577,
#' 0.018093546, 0.025445917, 0.035785947, 0.050327683, 0.0707785,
#' 0.099539573, 0.1399878, 0.233470395)}
#' @param prob_severe Probability of developing severe symptoms by age.
#' Default, NULL, will use
#' \code{c(0.000840764, 0.001182411, 0.001662887, 0.002338607,
#' 0.003288907, 0.004625365, 0.006504897, 0.009148183, 0.012865577,
#' 0.018093546, 0.025445917, 0.035785947, 0.050327683, 0.0707785,
#' 0.099539573, 0.1399878, 0.233470395)}
#' @param prob_non_severe_death_treatment Probability of death from non severe
#' treated infection. Default, NULL, will use
#' \code{c(0.181354223, 0.181354223, 0.181354223, 0.137454906,
#' 0.121938236, 0.122775613, 0.136057441, 0.160922182, 0.196987378,
#' 0.242011054, 0.289368845, 0.326537862, 0.337229819, 0.309082553,
#' 0.243794865, 0.160480254, 0.057084366)}
#' @param prob_severe_death_treatment Probability of death from severe infection
#' that is treated. Default, NULL, will use
#' \code{c(0.226668959, 0.252420241, 0.281097009, 0.413005389,
#' 0.518451493, 0.573413613, 0.576222065, 0.54253573, 0.493557696,
#' 0.447376527, 0.416666608, 0.411186639, 0.443382594, 0.538718871,
#' 0.570434076, 0.643352843, 0.992620047)}
#' @param prob_non_severe_death_no_treatment Probability of death in non severe
#' hospital inections that aren't treated. Default, NULL, will use
#' \code{rep(0.5, 17)}
#' @param prob_severe_death_no_treatment Probability of death from severe infection
#' that is not treated. Default, NULL, will use
#' \code{rep(0.95, 17)}
#' @param p_dist Preferentiality of age group receiving treatment relative to
#' other age groups when demand exceeds healthcare capacity.
#' @param dur_E Mean duration of incubation period (days). Default = 4.6
#' @param dur_R Mean duration of immunity (days). Default = Inf
#' @param dur_IMild Mean duration of mild infection (days). Default = 2.1
#' @param dur_ICase Mean duration from symptom onset to hospitil admission (days).
#' Default = 4.5
#' @param dur_get_ox_survive Mean duration of oxygen given survive. Default = 9
#' @param tt_dur_get_ox_survive Times at which dur_get_ox_survive changes
#' (Default = 0 = doesn't change)
#' @param dur_get_ox_die Mean duration of oxygen given death. Default = 9
#' @param tt_dur_get_ox_die Times at which dur_get_ox_die changes
#' (Default = 0 = doesn't change)
#' @param dur_not_get_ox_survive Mean duration without oxygen given survive.
#' Default = 4.5
#' @param dur_not_get_ox_die Mean duration without oxygen given death.
#' Default = 4.5
#' @param dur_get_mv_survive Mean duration of ventilation given survive.
#' Default = 14.8
#' @param tt_dur_get_mv_survive Times at which dur_get_mv_survive changes
#' (Default = 0 = doesn't change)
#' @param dur_get_mv_die Mean duration of ventilation given death. Default = 11.1
#' @param tt_dur_get_mv_die Times at which dur_get_mv_die changes
#' (Default = 0 = doesn't change)
#' @param dur_not_get_mv_survive Mean duration without ventilation given
#' survive. Default = 7.4
#' @param dur_not_get_mv_die Mean duration without ventilation given
#' death. Default = 1
#' @param dur_rec Duration of recovery after coming off ventilation. Default = 3
#' @param hosp_bed_capacity General bed capacity. Can be single number or vector if capacity time-varies.
#' @param ICU_bed_capacity ICU bed capacity. Can be single number or vector if capacity time-varies.
#' @param tt_hosp_beds Times at which hospital bed capacity changes (Default = 0 = doesn't change)
#' @param tt_ICU_beds Times at which ICU bed capacity changes (Default = 0 = doesn't change)
#'
#' @param walker_params Boolean for using parameters in Walker et al. Default = FALSE,
#' which uses parameter update as of November 2020. For full information see
#' parameters vignette
#'
#' @return Paramater List
#' @export
#'
parameters_explicit_SEEIR <- function(
# demography
country = NULL,
population = NULL,
tt_contact_matrix = 0,
contact_matrix_set = NULL,
# transmission
R0 = 3,
tt_R0 = 0,
beta_set = NULL,
# initial state, duration, reps
time_period = 365,
dt = 0.1,
init = NULL,
seeding_cases = NULL,
# parameters/probabilities
prob_hosp = NULL,
prob_severe = NULL,
prob_non_severe_death_treatment = NULL,
prob_non_severe_death_no_treatment = NULL,
prob_severe_death_treatment = NULL,
prob_severe_death_no_treatment = NULL,
p_dist = probs$p_dist,
walker_params = FALSE,
# durations
dur_E = NULL,
dur_IMild = NULL,
dur_ICase = NULL,
dur_get_ox_survive = NULL,
tt_dur_get_ox_survive = NULL,
dur_get_ox_die = NULL,
tt_dur_get_ox_die = NULL,
dur_not_get_ox_survive = NULL,
dur_not_get_ox_die = NULL,
dur_get_mv_survive = NULL,
tt_dur_get_mv_survive = NULL,
dur_get_mv_die = NULL,
tt_dur_get_mv_die = NULL,
dur_not_get_mv_survive = NULL,
dur_not_get_mv_die = NULL,
dur_rec = NULL,
dur_R = NULL,
# health system capacity
hosp_bed_capacity = NULL,
ICU_bed_capacity = NULL,
tt_hosp_beds = 0,
tt_ICU_beds = 0
) {
# Handle country population args
cpm <- parse_country_population_mixing_matrix(country = country,
population = population,
contact_matrix_set = contact_matrix_set)
country <- cpm$country
population <- cpm$population
contact_matrix_set <- cpm$contact_matrix_set
# Handle severity parameters and possible 80+ demographic adjustment
severity_params <- parse_country_severity(country = country,
prob_hosp = prob_hosp,
prob_severe = prob_severe,
prob_non_severe_death_treatment = prob_non_severe_death_treatment,
prob_severe_death_treatment = prob_severe_death_treatment,
prob_non_severe_death_no_treatment = prob_non_severe_death_no_treatment,
prob_severe_death_no_treatment = prob_severe_death_no_treatment,
walker_params = walker_params)
prob_hosp <- severity_params$prob_hosp
prob_severe <- severity_params$prob_severe
prob_non_severe_death_treatment <- severity_params$prob_non_severe_death_treatment
prob_severe_death_treatment <- severity_params$prob_severe_death_treatment
prob_non_severe_death_no_treatment <- severity_params$prob_non_severe_death_no_treatment
prob_severe_death_no_treatment <- severity_params$prob_severe_death_no_treatment
# Handle duration of hospitalisation parameters
duration_params <- parse_durations(
dur_get_ox_survive = dur_get_ox_survive,
tt_dur_get_ox_survive = tt_dur_get_ox_survive,
dur_get_ox_die = dur_get_ox_die,
tt_dur_get_ox_die = tt_dur_get_ox_die,
dur_not_get_ox_survive = dur_not_get_ox_survive,
dur_not_get_ox_die = dur_not_get_ox_die,
dur_get_mv_survive = dur_get_mv_survive,
tt_dur_get_mv_survive = tt_dur_get_mv_survive,
dur_get_mv_die = dur_get_mv_die,
tt_dur_get_mv_die = tt_dur_get_mv_die,
dur_not_get_mv_survive = dur_not_get_mv_survive,
dur_not_get_mv_die = dur_not_get_mv_die,
dur_rec = dur_rec,
dur_R = dur_R,
dur_E = dur_E,
dur_IMild = dur_IMild,
dur_ICase = dur_ICase,
walker_params = walker_params)
dur_get_ox_survive <- duration_params$dur_get_ox_survive
tt_dur_get_ox_survive <- duration_params$tt_dur_get_ox_survive
dur_get_ox_die <- duration_params$dur_get_ox_die
tt_dur_get_ox_die <- duration_params$tt_dur_get_ox_die
dur_not_get_ox_survive <- duration_params$dur_not_get_ox_survive
dur_not_get_ox_die <- duration_params$dur_not_get_ox_die
dur_get_mv_survive <- duration_params$dur_get_mv_survive
tt_dur_get_mv_survive <- duration_params$tt_dur_get_mv_survive
dur_get_mv_die <- duration_params$dur_get_mv_die
tt_dur_get_mv_die <- duration_params$tt_dur_get_mv_die
dur_not_get_mv_survive <- duration_params$dur_not_get_mv_survive
dur_not_get_mv_die <- duration_params$dur_not_get_mv_die
dur_rec <- duration_params$dur_rec
dur_R <- duration_params$dur_R
dur_E <- duration_params$dur_E
dur_IMild <- duration_params$dur_IMild
dur_ICase <- duration_params$dur_ICase
# Standardise contact matrix set
if(is.matrix(contact_matrix_set)){
contact_matrix_set <- list(contact_matrix_set)
}
# populate contact matrix set if not provided
if (length(contact_matrix_set) == 1) {
baseline <- contact_matrix_set[[1]]
contact_matrix_set <- vector("list", length(tt_contact_matrix))
for(i in seq_along(tt_contact_matrix)) {
contact_matrix_set[[i]] <- baseline
}
}
# populate hospital and ICU bed capacity if not provided
if (is.null(hosp_bed_capacity)) {
if (!is.null(country)) {
beds <- get_healthcare_capacity(country)
hosp_beds <- beds$hosp_beds
hosp_bed_capacity <- rep(round(hosp_beds * sum(population)/1000), length(tt_hosp_beds))
} else {
hosp_bed_capacity <- round(5 * sum(population)/1000)
}
}
if (is.null(ICU_bed_capacity)) {
if (!is.null(country)) {
beds <- get_healthcare_capacity(country)
ICU_beds <- beds$ICU_beds
ICU_bed_capacity <- rep(round(ICU_beds * sum(population)/1000), length(tt_ICU_beds))
} else {
ICU_bed_capacity <- round(3 * hosp_bed_capacity/100)
}
}
# Initial state and matrix formatting
# ----------------------------------------------------------------------------
# Initialise initial conditions
if (!is.null(seeding_cases)) {
assert_int(seeding_cases)
mod_init <- init_check_explicit(init, population, seeding_cases)
} else {
mod_init <- init_check_explicit(init, population)
}
# Convert contact matrices to input matrices
matrices_set <- matrix_set_explicit(contact_matrix_set, population)
mc <- matrix_check(population[-1], contact_matrix_set)
# Input checks
# ----------------------------------------------------------------------------
stopifnot(length(R0) == length(tt_R0))
stopifnot(length(contact_matrix_set) == length(tt_contact_matrix))
stopifnot(length(hosp_bed_capacity) == length(tt_hosp_beds))
stopifnot(length(ICU_bed_capacity) == length(tt_ICU_beds))
stopifnot(length(dur_get_mv_survive) == length(tt_dur_get_mv_survive))
stopifnot(length(dur_get_ox_survive) == length(tt_dur_get_ox_survive))
stopifnot(length(dur_get_mv_die) == length(tt_dur_get_mv_die))
stopifnot(length(dur_get_ox_die) == length(tt_dur_get_ox_die))
tc <- lapply(list(tt_R0/dt, tt_contact_matrix/dt,
tt_hosp_beds/dt, tt_ICU_beds/dt,
tt_dur_get_mv_survive/dt,
tt_dur_get_ox_survive/dt,
tt_dur_get_mv_die/dt,
tt_dur_get_ox_die/dt
),
check_time_change, time_period/dt)
assert_pos(dt)
assert_pos(dur_E)
assert_pos(dur_IMild)
assert_pos(dur_ICase)
assert_pos(dur_get_ox_survive)
assert_pos(dur_get_ox_die)
assert_pos(dur_not_get_ox_survive)
assert_pos(dur_not_get_ox_die)
assert_pos(dur_get_mv_survive)
assert_pos(dur_get_mv_die)
assert_pos(dur_not_get_mv_survive)
assert_pos(dur_not_get_mv_die)
assert_pos(time_period)
assert_pos(hosp_bed_capacity)
assert_pos(ICU_bed_capacity)
assert_length(prob_hosp, length(population))
assert_length(prob_severe, length(population))
assert_length(prob_non_severe_death_treatment, length(population))
assert_length(prob_non_severe_death_no_treatment, length(population))
assert_length(prob_severe_death_treatment, length(population))
assert_length(prob_severe_death_no_treatment, length(population))
assert_length(p_dist, length(population))
assert_numeric(prob_hosp, length(population))
assert_numeric(prob_severe, length(population))
assert_numeric(prob_non_severe_death_treatment, length(population))
assert_numeric(prob_non_severe_death_no_treatment, length(population))
assert_numeric(prob_severe_death_treatment, length(population))
assert_numeric(prob_severe_death_no_treatment, length(population))
assert_numeric(p_dist, length(population))
assert_leq(prob_hosp, 1)
assert_leq(prob_severe, 1)
assert_leq(prob_non_severe_death_treatment, 1)
assert_leq(prob_non_severe_death_no_treatment, 1)
assert_leq(prob_severe_death_treatment, 1)
assert_leq(prob_severe_death_no_treatment, 1)
assert_leq(p_dist, 1)
assert_greq(prob_hosp, 0)
assert_greq(prob_severe, 0)
assert_greq(prob_non_severe_death_treatment, 0)
assert_greq(prob_non_severe_death_no_treatment, 0)
assert_greq(prob_severe_death_treatment, 0)
assert_greq(prob_severe_death_no_treatment, 0)
assert_greq(p_dist, 0)
# Convert and Generate Parameters As Required
# ----------------------------------------------------------------------------
# durations
gamma_E = 2 * 1/dur_E
gamma_IMild = 1/dur_IMild
gamma_ICase = 2 * 1/dur_ICase
gamma_get_ox_survive = 2 * 1/dur_get_ox_survive
gamma_get_ox_die = 2 * 1/dur_get_ox_die
gamma_not_get_ox_survive = 2 * 1/dur_not_get_ox_survive
gamma_not_get_ox_die = 2 * 1/dur_not_get_ox_die
gamma_get_mv_survive = 2 * 1/dur_get_mv_survive
gamma_get_mv_die = 2 * 1/dur_get_mv_die
gamma_not_get_mv_survive = 2 * 1/dur_not_get_mv_survive
gamma_not_get_mv_die = 2 * 1/dur_not_get_mv_die
gamma_rec = 2 * 1/dur_rec
gamma_R = 2 * 1/dur_R
if (is.null(beta_set)) {
baseline_matrix <- process_contact_matrix_scaled_age(contact_matrix_set[[1]], population)
beta_set <- beta_est_explicit(dur_IMild = dur_IMild,
dur_ICase = dur_ICase,
prob_hosp = prob_hosp,
mixing_matrix = baseline_matrix,
R0 = R0)
}
# normalise to sum to 1
p_dist <- p_dist/mean(p_dist)
# Collate Parameters Into List
pars <- list(N_age = length(population),
S_0 = mod_init$S,
E1_0 = mod_init$E1,
E2_0 = mod_init$E2,
IMild_0 = mod_init$IMild,
ICase1_0 = mod_init$ICase1,
ICase2_0 = mod_init$ICase2,
IOxGetLive1_0 = mod_init$IOxGetLive1,
IOxGetLive2_0 = mod_init$IOxGetLive2,
IOxGetDie1_0 = mod_init$IOxGetDie1,
IOxGetDie2_0 = mod_init$IOxGetDie2,
IOxNotGetLive1_0 = mod_init$IOxNotGetLive1,
IOxNotGetLive2_0 = mod_init$IOxNotGetLive2,
IOxNotGetDie1_0 = mod_init$IOxNotGetDie1,
IOxNotGetDie2_0 = mod_init$IOxNotGetDie2,
IMVGetLive1_0 = mod_init$IMVGetLive1,
IMVGetLive2_0 = mod_init$IMVGetLive2,
IMVGetDie1_0 = mod_init$IMVGetDie1,
IMVGetDie2_0 = mod_init$IMVGetDie2,
IMVNotGetLive1_0 = mod_init$IMVNotGetLive1,
IMVNotGetLive2_0 = mod_init$IMVNotGetLive2,
IMVNotGetDie1_0 = mod_init$IMVNotGetDie1,
IMVNotGetDie2_0 = mod_init$IMVNotGetDie2,
IRec1_0 = mod_init$IRec1,
IRec2_0 = mod_init$IRec2,
R1_0 = mod_init$R1,
R2_0 = mod_init$R2,
D_0 = mod_init$D,
gamma_E = gamma_E,
gamma_IMild = gamma_IMild,
gamma_ICase = gamma_ICase,
gamma_get_ox_survive = gamma_get_ox_survive,
gamma_get_ox_die = gamma_get_ox_die,
gamma_not_get_ox_survive = gamma_not_get_ox_survive,
gamma_not_get_ox_die = gamma_not_get_ox_die,
gamma_get_mv_survive = gamma_get_mv_survive,
gamma_get_mv_die = gamma_get_mv_die,
gamma_not_get_mv_survive = gamma_not_get_mv_survive,
gamma_not_get_mv_die = gamma_not_get_mv_die,
gamma_rec = gamma_rec,
gamma_R = gamma_R,
prob_hosp = prob_hosp,
prob_severe = prob_severe,
prob_non_severe_death_treatment = prob_non_severe_death_treatment,
prob_non_severe_death_no_treatment = prob_non_severe_death_no_treatment,
prob_severe_death_treatment = prob_severe_death_treatment,
prob_severe_death_no_treatment = prob_severe_death_no_treatment,
p_dist = p_dist,
mix_mat_set = matrices_set,
hosp_beds = hosp_bed_capacity,
ICU_beds = ICU_bed_capacity,
beta_set = beta_set,
tt_hosp_beds = round(tt_hosp_beds/dt),
tt_ICU_beds = round(tt_ICU_beds/dt),
tt_matrix = round(tt_contact_matrix/dt),
tt_beta = round(tt_R0/dt),
tt_dur_get_mv_survive = round(tt_dur_get_mv_survive/dt),
tt_dur_get_ox_survive = round(tt_dur_get_ox_survive/dt),
tt_dur_get_mv_die = round(tt_dur_get_mv_die/dt),
tt_dur_get_ox_die = round(tt_dur_get_ox_die/dt),
dt = dt,
population = population,
contact_matrix_set = contact_matrix_set,
dur_E = dur_E,
dur_IMild = dur_IMild,
dur_ICase = dur_ICase,
dur_get_ox_survive = dur_get_ox_survive,
dur_get_ox_die = dur_get_ox_die,
dur_not_get_ox_survive = dur_not_get_ox_survive,
dur_not_get_ox_die = dur_not_get_ox_die,
dur_get_mv_survive = dur_get_mv_survive,
dur_get_mv_die = dur_get_mv_die,
dur_not_get_mv_survive = dur_not_get_mv_survive,
dur_not_get_mv_die = dur_not_get_mv_die,
dur_rec = dur_rec,
dur_R = dur_R)
class(pars) <- c("explicit_SEEIR_parameters", "squire_parameters")
return(pars)
}
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