R/parameters.R
In mrc-ide/malariasimulation: An individual based model for malaria
Defines functions
set_parameter_draw
parameterise_total_M
parameterise_mosquito_equilibrium
get_parameters
Documented in
get_parameters
parameterise_mosquito_equilibrium
parameterise_total_M
set_parameter_draw
#' @title Get model parameters
#' @description
#' get_parameters creates a named list of parameters for use in the model. These
#' parameters are passed to process functions.
#'
#' The default parameters, which are for Plasmodium falciparum, are explained in
#' "The US President's Malaria Initiative, Plasmodium falciparum transmission
#' and mortality: A modelling study."
#'
#' Plasmodium vivax specific parameters are explained in
#' "Mathematical modelling of the impact of expanding levels of malaria control
#' interventions on Plasmodium vivax." by White, Michael T., et al.
#'
#' @param overrides a named list of parameter values to use instead of defaults
#' @param parasite Plasmodium parasite species ("falciparum" or "vivax"); default = "falciparum"
#'
#' The parameters are defined below.
#'
#' parasite parameter
#' * parasite - parasite species (falciparum or vivax); default = "falciparum"
#'
#' initial state proportions:
#'
#' * s_proportion - the proportion of `human_population` that begin as susceptible; default = 0.420433246
#' * d_proportion - the proportion of `human_population` that begin with
#' clinical disease; default = 0.007215064
#' * a_proportion - the proportion of `human_population` that begin as
#' asymptomatic; default = 0.439323667
#' * u_proportion - the proportion of `human_population` that begin as
#' subpatents; default = 0.133028023
#' * t_proportion - the proportion of `human_population` that begin treated; default = 0
#'
#' human fixed state transitions:
#'
#' * dd - the delay for humans to move from state D to A; default = 5
#' * dt - the delay for humans to move from state Tr to S; default = 5
#' * da - the delay for humans to move from state A to U; default = 195
#' * du - the delay for humans to move from state U to S (p.f only); default = 110
#'
#' duration of pcr detectable infections: du (p.v only):
#'
#' * dpcr_max - Maximum duration of PCR-detectable infections: default = 53.69
#' * dpcr_min - Minimum duration of PCR-detectable infections: default = 10
#' * kpcr - Shape parameter: default = 4.021
#' * apcr50 - Scale parameter: default = 9.8
#'
#' human demography parameters:
#'
#' * human_population - the initial number of humans to model; default = 100
#' * average_age - the average age of humans (in timesteps), this is only used
#' if custom_demography is FALSE; default = 7665
#' * custom_demography - population demography given; default = FALSE
#'
#' initial immunity values:
#'
#' * init_ib - the initial pre-erythrocitic immunity (p.f only); default = 0
#' * init_iaa - the initial acquired anti-parasite immunity (p.v only): default = 0
#' * init_iam - the initial anti-parasite immunity at birth (p.v only); default = 0
#' * init_ica - the initial acquired immunity from clinical disease; default = 0
#' * init_icm - the initial clinical immunity at birth; default = 0
#' * init_iva - the initial acquired immunity from severe disease (p.f only); default = 0
#' * init_ivm - the initial severe immunity from severe disease at birth (p.f only); default = 0
#' * init_id - the initial acquired immunity to lm detectability (p.f only); default = 0
#'
#' immunity decay rates:
#'
#' * rb - decay rate for acquired pre-erythrocytic immunity (p.f only); default = 3650
#' * ra - decay rate for acquired anti-parasite immunity (p.v only); default = 3650
#' * rc - decay rate for acquired immunity to clinical disease; default = 10950
#' * rva - decay rate for acquired immunity to severe disease (p.f only); default = 10950
#' * rm - decay rate for maternal immunity to clinical disease (or p.v: maternal clinical and anti-parasite immunities); default = 67.6952
#' * rvm - decay rate for maternal immunity to severe disease (p.f only); default = 76.8365
#' * rid - decay rate for acquired immunity to lm-detectability (p.f only); default = 3650
#'
#' immunity boost grace periods:
#'
#' * ub - period in which pre-erythrocytic immunity cannot be boosted (p.f only); default = 7.2
#' * ua - period in which anti-parasite immunity cannot be boosted (p.v only); default = 44.09
#' * uc - period in which clinical immunity cannot be boosted; default = 6.06
#' * uv - period in which severe immunity cannot be boosted (p.f only); default = 11.4321
#' * ud - period in which immunity to detectability cannot be boosted (p.f only); default = 9.44512
#'
#' maternal immunity parameters:
#'
#' * pcm - new-born clinical immunity (or p.v: clinical and anti-parasite immunities) relative to mother's; default = 0.774368
#' * pvm - new-born severe immunity relative to mother's (p.f only); default = 0.195768
#'
#' unique biting rate:
#'
#' * a0 - age dependent biting parameter; default = 2920
#' * rho - age dependent biting parameter; default = 0.85
#' * sigma_squared - heterogeneity parameter; default = 1.67
#' * n_heterogeneity_groups - number discretised groups for heterogeneity, used
#' for sampling mothers; default = 5
#'
#' probability of pre-erythrocytic infection (p.f only):
#'
#' * b0 - maximum probability due to no immunity; default = 0.59
#' * b1 - maximum reduction due to immunity; default = 0.5
#' * ib0 - scale parameter; default = 43.9
#' * kb - shape parameter; default = 2.16
#'
#' probability of pre-erythrocytic infection (p.v only):
#' * b - probability of pre-erythrocytic infection: default = 0.25
#'
#' probability of detection by light-microscopy when asymptomatic (p.f only):
#'
#' * fd0 - time-scale at which immunity changes with age; default = 0.007055
#' * ad - scale parameter relating age to immunity; default = 7993.5
#' * gammad - shape parameter relating age to immunity; default = 4.8183
#' * d1 - minimum probability due to immunity; default = 0.160527
#' * id0 - scale parameter; default = 1.577533
#' * kd - shape parameter; default = 0.476614
#'
#' probability of light-microscopy detectable infections due to anti-parasite immunity (p.v only):
#'
#' * philm_max - maximum probability due to no immunity; default = 0.9329
#' * philm_min - maximum reduction due to immunity; default = 0.0131
#' * alm50 - scale parameter; default = 17.3
#' * klm - shape parameter; default = 3.202
#'
#' probability of clinical infection:
#'
#' * phi0 - maximum probability due to no immunity; default = 0.792
#' * phi1 - maximum reduction due to immunity; default = 0.00074
#' * ic0 - scale parameter; default = 18.02366
#' * kc - shape parameter; default = 2.36949
#'
#' probability of severe infection (p.f only):
#'
#' * theta0 - maximum probability due to no immunity; default = 0.0749886
#' * theta1 - maximum reduction due to immunity; default = 0.0001191
#' * iv0 - scale parameter; default = 1.09629
#' * kv - shape parameter; default = 2.00048
#' * fv0 - age dependent modifier; default = 0.141195
#' * av - age dependent modifier; default = 2493.41
#' * gammav - age dependent modifier; default = 2.91282
#'
#' infectivity towards mosquitoes:
#'
#' * cd - infectivity of clinically diseased humans towards mosquitoes; default = 0.068
#' * ca - infectivity of asymptomatic humans towards mosquitoes (p.v only); default = 0.1
#' * gamma1 - parameter for infectivity of asymptomatic humans; default = 1.82425
#' * cu - infectivity of subpatent infection; default = 0.0062
#' * ct - infectivity of treated infection; default = 0.021896
#'
#' mosquito fixed state transitions (including mortality):
#'
#' * del - the delay for mosquitoes to move from state E to L; default = 6.64
#' * dl - the delay for mosquitoes to move from state L to P; default = 3.72
#' * dpl - the delay mosquitoes to move from state P to Sm; default = 0.643
#' * me - early stage larval mortality rate; default = 0.0338
#' * ml - late stage larval mortality rate; default = 0.0348
#' * mup - the rate at which pupal mosquitoes die; default = 0.249
#' * mum - the rate at which developed mosquitoes die; default (An. gambiae) = .132
#'
#' vector biology:
#' species specific values are vectors
#' please set species parameters using the convenience function
#' \code{\link{set_species}}
#'
#' * beta - the average number of eggs laid per female mosquito per day; default = 21.2
#' * total_M - the initial number of adult mosquitos in the simulation; default = 1000
#' * init_foim - the FOIM used to calculate the equilibrium state for mosquitoes; default = 0
#' * species - names of the species in the simulation; default = "gamb"
#' * species_proportions - the relative proportions of each species; default = 1
#' * blood_meal_rates - the blood meal rates for each species; default = 1/3
#' * Q0 - proportion of blood meals taken on humans; default = 0.92
#' * foraging_time - time spent taking blood meals; default = 0.69
#'
#' seasonality and carrying capacity parameters:
#' please set flexible carrying capacity using the convenience function
#' \code{\link{set_carrying_capacity}}
#'
#' * model_seasonality - boolean switch TRUE iff the simulation models seasonal rainfall; default = FALSE
#' * g0 - rainfall fourier parameter; default = 2
#' * g - rainfall fourier parameter; default = 0.3, 0.6, 0.9
#' * h - rainfall fourier parameters; default = 0.1, 0.4, 0.7
#' * gamma - effect of density dependence on late instars relative to early
#' instars; default = 13.25
#' * rainfall_floor - the minimum rainfall value (must be above 0); default 0.001
#' * carrying_capacity; default = FALSE
#' * carrying_capacity_timesteps; default = NULL
#' * carrying_capacity_values; default = NULL#'
#'
#' parasite incubation periods:
#'
#' * de - duration of the human latent period of infection; default = 12
#' * delay_gam - lag from parasites to infectious gametocytes; default = 12.5
#' * dem - extrinsic incubation period in mosquito population model; default = 10
#'
#' hypnozoite batch parameters (p.v only):
#'
#' * f - hypnozoite batch relapse rate; default = 0.02439024
#' * gammal - hypnozoite batch clearance rate; default = 0.002610966
#' * init_hyp - initial hypnozoite batch number; default = 0
#' * kmax - maximum number of hypnozoite batches for use in the equilibrium solution; default = 10
#'
#' treatment parameters:
#' please set treatment parameters with the convenience functions
#' \code{\link{set_drugs}} and \code{\link{set_clinical_treatment}}
#'
#' * drug_efficacy - a vector of efficacies for available drugs; default = turned off
#' * drug_rel_c - a vector of relative onward infectiousness values for drugs; default = turned off
#' * drug_prophylaxis_shape - a vector of shape parameters for weibull curves to
#' model prophylaxis for each drug; default = turned off
#' * drug_prophylaxis_scale - a vector of scale parameters for weibull curves to
#' model prophylaxis for each drug; default = turned off
#' * drug_hypnozoite_efficacy - a vector of efficacies targeting hypnozoites; default = turned off
#' * drug_hypnozoite_prophylaxis_shape - a vector of shape parameters for weibull curves to model prophylaxis against hypnozoite batch formation (days); default = turned off
#' * drug_hypnozoite_prophylaxis_scale - a vector of scale parameters for weibull curves to model prophylaxis against hypnozoite batch formation (days); default = turned off
#' * clinical_treatment_drugs - a vector of drugs that are available for
#' clinically diseased (these values refer to the index in drug_* parameters); default = NULL, NULL, NULL
#' * clinical_treatment_coverage - a vector of coverage values for each drug; default = NULL, NULL, NULL
#'
#' MDA, SMC and PMC parameters:
#' please set these parameters with the convenience functions
#' \code{\link{set_mda}}, \code{\link{set_smc}} and \code{\link{set_pmc}},
#' with \code{\link{peak_season_offset}}
#'
#' bednet, irs and mosquito feeding cycle parameters:
#' please set vector control strategies using \code{\link{set_bednets}} and \code{\link{set_spraying}}
#'
#' * bednets - boolean for if bednets are enabled; default = FALSE
#' * phi_bednets - proportion of bites taken in bed; default = 0.85
#' * k0 - proportion of females bloodfed with no net; default = 0.699
#' * spraying - boolean for if indoor spraying is enabled; default = FALSE
#' * phi_indoors - proportion of bites taken indoors; default = 0.90
#'
#'
#' PEV parameters:
#' please set vaccine strategies with the convenience functions
#' \code{\link{set_pev_epi}} and \code{\link{set_mass_pev}}
#'
#' * pev_doses - the dosing schedule before the vaccine takes effect; default =
#' c(0, 1.5 * 30, 3 * 30)
#' default = 365
#'
#' TBV parameters:
#' please set TBV parameters with the convenience functions in
#' \code{\link{set_tbv}}
#'
#' * tbv_mt - effect on treated infectiousness; default = 35
#' * tbv_md - effect on diseased infectiousness; default = 46.7
#' * tbv_ma - effect on asymptomatic infectiousness; default = 3.6
#' * tbv_mu - effect on subpatent infectiousness; default = 0.8
#' * tbv_k - scale parameter for effect on infectiousness; default = 0.9
#' * tbv_tau - peak antibody parameter; default = 22
#' * tbv_rho - antibody component parameter; default = 0.7
#' * tbv_ds - antibody short-term delay parameter; default = 45
#' * tbv_dl - antibody long-term delay parameter; default = 591
#' * tbv_tra_mu - transmission reduction parameter; default = 12.63
#' * tbv_gamma1 - transmission reduction parameter; default = 2.5
#' * tbv_gamma2 - transmission reduction parameter; default = 0.06
#'
#' Antimalarial resistance parameters:
#' please set antimalarial resistance parameters with the convenience functions in
#' \code{\link{set_antimalarial_resistance}}
#'
#' * antimalarial_resistance - boolean for if antimalarial resistance is enabled; default = FALSE
#' * antimalarial_resistance_drug - vector of drugs for which resistance can be parameterised; default = NULL
#' * antimalarial_resistance_timesteps - vector of time steps on which resistance updates occur; default = NULL
#' * artemisinin_resistant_proportion - vector of proportions of infections resistant to the artemisinin component of a given drug; default = NULL
#' * partner_drug_resistance_proportion - vector of proportions of infections resistant to the parter drug component of a given drug; default = NULL
#' * slow_parasite_clearance_probability - vector of probabilities of slow parasite clearance for a given drug; default = NULL
#' * early_treatment_failure_probability - vector of probabilities of early treatment failure for a given drug; default = NULL
#' * late_clinical_failure_probability - vector of probabilities of late clinical failure for a given drug; default = NULL
#' * late_parasitological_failure_probability - vector of probabilities of late parasitological failure for a given drug; default = NULL
#' * reinfection_during_prophylaxis_probability - vector of probabilities of reinfection during prophylaxis for a given drug; default = NULL
#' * dt_slow_parasite_clearance - the delay for humans experiencing slow parasite clearance to move from state Tr to S; default = NULL
#'
#' rendering:
#' All values are in timesteps and all ranges are inclusive.
#' Please set rendered age groups using the convenience function
#'
#' * age_group_rendering_min_ages - the minimum ages for population size outputs; default = turned off
#' * age_group_rendering_max_ages - the corresponding max ages; default = turned off
#' * incidence_rendering_min_ages - the minimum ages for incidence
#' outputs (includes asymptomatic microscopy +); default = turned off
#' * incidence_rendering_max_ages - the corresponding max ages; default = turned off
#' * clinical_incidence_rendering_min_ages - the minimum ages for clinical incidence outputs (symptomatic); default = 0
#' * clinical_incidence_rendering_max_ages - the corresponding max ages; default = 1825
#' * severe_incidence_rendering_min_ages - the minimum ages for severe incidence
#' outputs; default = turned off
#' * severe_incidence_rendering_max_ages - the corresponding max ages; default = turned off
#' * prevalence_rendering_min_ages - the minimum ages for clinical prevalence
#' outputs; default = 730
#' * prevalence_rendering_max_ages - the corresponding max ages; default = 3650
#' * n_with_hypnozoites_rendering_min_ages - the minimum ages for number with hypnozoites outputs (p.v only); default = numeric(0)
#' * n_with_hypnozoites_rendering_max_ages - the corresponding max ages; default = numeric(0)
#'
#' Age structured mean immunity (/hyponozoite) rendering:
#'
#' * ib_rendering_min_ages - the minimum ages for blood immunity outputs (p.f only); default = numeric(0)
#' * ib_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * id_rendering_min_ages - the minimum ages for acquired detectability immunity (p.f); default = numeric(0)
#' * id_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * iaa_rendering_min_ages - the minimum ages for antiparasite immunity (p.v only); default = numeric(0)
#' * iam_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * ica_rendering_min_ages - the minimum ages for acquired clinical immunity outputs; default = numeric(0)
#' * ica_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * iva_rendering_min_ages - the minimum ages for acquired severe immunity outputs (p.f only); default = numeric(0)
#' * iva_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * idm_rendering_min_ages - the minimum ages for maternal antiparasite immunity outputs (p.v only); default = numeric(0)
#' * idm_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * icm_rendering_min_ages - the minimum ages for maternal clinical immunity outputs; default = numeric(0)
#' * icm_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * ivm_rendering_min_ages - the minimum ages for maternal severe immunity outputs (p.f only); default = numeric(0)
#' * ivm_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * hypnozoites_rendering_min_ages - the minimum ages average hypnozoite batches outputs (p.v only); default = numeric(0)
#' * hypnozoites_rendering_max_ages - the corresponding max ages; default = numeric(0)
#'
#' mixing:
#'
#' * rdt_intercept - the y intercept for the log logit relationship betweeen rdt
#' and PCR prevalence; default = -0.968
#' * rdt_coeff - the coefficient for the log logit relationship betweeen rdt
#' and PCR prevalence; default = 1.186
#'
#' miscellaneous:
#'
#' * mosquito_limit - the maximum number of mosquitoes to allow for in the
#' simulation; default = 1.00E+05
#' * individual_mosquitoes - boolean whether adult mosquitoes are modeled
#' individually or compartmentally; default = TRUE
#' * human_population_timesteps - the timesteps at which the population should
#' change; default = 0
#' * r_tol - the relative tolerance for the ode solver; default = 1e-4
#' * a_tol - the absolute tolerance for the ode solver; default = 1e-4
#' * ode_max_steps - the max number of steps for the solver; default = 1e6
#' * enable_heterogeneity - boolean whether to include heterogeneity in biting
#' rates; default = TRUE
#'
#' @export
get_parameters <- function(overrides = list(), parasite = "falciparum") {
if(!parasite %in% c("falciparum","vivax")){stop("parasite must be 'falciparum' or 'vivax'")}
parameters <- c(
# human fixed state transitions
# initial immunities
# immunity decay rates
# immunity boost grace periods
# maternal immunity parameters
# probability of pre-erythrocytic infection/blood immunity
# probability of asymptomatic detection (p.f only)
# probability of light-microscopy detectable infection (due to anti-parasite immunity, p.v only)
# probability of clinical infection
# probability of severe infection (p.f only)
# infectivity towards mosquitos
# parasite incubation periods
# hypnozoite parameters (p.v only)
malariasimulation::parasite_parameters[[parasite]],
list(
# parasite
parasite = parasite,
# initial state proportions
s_proportion = 0.420433246,
d_proportion = 0.007215064,
a_proportion = 0.439323667,
u_proportion = 0.133028023,
t_proportion = 0,
# human demography parameters
human_population = 100,
average_age = 7663,
custom_demography = FALSE,
# unique biting rate
a0 = 8 * 365,
rho = .85,
sigma_squared = 1.67,
n_heterogeneity_groups = 5,
enable_heterogeneity = TRUE,
# mosquito fixed state transitions (inc. mortality)
del = 6.64,
dl = 3.72,
dpl = .643,
me = .0338,
ml = .0348,
mup = .249,
mum = .132,
# species-specific vector biology (default is An. gambiae s.s)
species = 'gamb',
species_proportions = 1,
blood_meal_rates = 1/3,
Q0 = .92,
foraging_time = .69,
beta = 21.2,
total_M = 1000,
init_foim= 0,
# carrying capacity parameters
g0 = 2,
g = c(.3, .6, .9),
h = c(.1, .4, .7),
gamma = 13.25,
model_seasonality = FALSE,
rainfall_floor = 0.001,
# flexible carrying capacity
carrying_capacity = FALSE,
carrying_capacity_timesteps = NULL,
carrying_capacity_values = NULL,
# treatment parameters
drug_efficacy = numeric(0),
drug_rel_c = numeric(0),
drug_prophylaxis_shape = numeric(0),
drug_prophylaxis_scale = numeric(0),
drug_hypnozoite_efficacy = numeric(0),
drug_hypnozoite_prophylaxis_shape = numeric(0),
drug_hypnozoite_prophylaxis_scale = numeric(0),
clinical_treatment_drugs = list(),
clinical_treatment_timesteps = list(),
clinical_treatment_coverages = list(),
# MDA
mda = FALSE,
mda_drug = 0,
mda_timesteps = NULL,
mda_coverages = NULL,
mda_min_ages = -1,
mda_max_ages = -1,
smc = FALSE,
smc_drug = 0,
smc_timesteps = NULL,
smc_coverages = NULL,
smc_min_ages = -1,
smc_max_ages = -1,
# PMC
pmc = FALSE,
pmc_drug = 0,
pmc_timesteps = NULL,
pmc_coverages = NULL,
pcs_ages = -1,
# bed nets
bednets = FALSE,
phi_bednets = .85,
k0 = .699,
# indoor spraying
spraying = FALSE,
phi_indoors = .90,
# pev
pev = FALSE,
pev_doses = c(0, 1.5 * 30, 3 * 30),
# tbv
tbv = FALSE,
tbv_mt = 35,
tbv_md = 46.7,
tbv_ma = 3.6,
tbv_mu = 0.8,
tbv_k = 0.9,
tbv_tau = 22,
tbv_rho = .7,
tbv_ds = 45,
tbv_dl = 591,
tbv_tra_mu = 12.63,
tbv_gamma1 = 2.5,
tbv_gamma2 = .06,
tbv_timesteps = NULL,
tbv_coverages = NULL,
tbv_ages = NULL,
# antimalarial resistance
antimalarial_resistance = FALSE,
antimalarial_resistance_drug = NULL,
antimalarial_resistance_timesteps = NULL,
artemisinin_resistance_proportion = NULL,
partner_drug_resistance_proportion = NULL,
slow_parasite_clearance_probability = NULL,
early_treatment_failure_probability = NULL,
late_clinical_failure_probability = NULL,
late_parasitological_failure_probability = NULL,
reinfection_during_prophylaxis_probability = NULL,
dt_slow_parasite_clearance = NULL,
# rendering
age_group_rendering_min_ages = numeric(0),
age_group_rendering_max_ages = numeric(0),
incidence_rendering_min_ages = numeric(0),
incidence_rendering_max_ages = numeric(0),
clinical_incidence_rendering_min_ages = numeric(0),
clinical_incidence_rendering_max_ages = numeric(0),
severe_incidence_rendering_min_ages = numeric(0),
severe_incidence_rendering_max_ages = numeric(0),
prevalence_rendering_min_ages = 2 * 365,
prevalence_rendering_max_ages = 10 * 365,
n_with_hypnozoites_rendering_min_ages = numeric(0),
n_with_hypnozoites_rendering_max_ages = numeric(0),
# age structured average immunity (/hypnozoite) rendering
ib_rendering_min_ages = numeric(0),
ib_rendering_max_ages = numeric(0),
id_rendering_min_ages = numeric(0),
id_rendering_max_ages = numeric(0),
ica_rendering_min_ages = numeric(0),
ica_rendering_max_ages = numeric(0),
iva_rendering_min_ages = numeric(0),
iva_rendering_max_ages = numeric(0),
idm_rendering_min_ages = numeric(0),
idm_rendering_max_ages = numeric(0),
icm_rendering_min_ages = numeric(0),
icm_rendering_max_ages = numeric(0),
ivm_rendering_min_ages = numeric(0),
ivm_rendering_max_ages = numeric(0),
hypnozoites_rendering_min_ages = numeric(0),
hypnozoites_rendering_max_ages = numeric(0),
# mixing
rdt_intercept = -0.968,
rdt_coeff = 1.186,
# misc
mosquito_limit = 100 * 1000,
individual_mosquitoes = FALSE,
human_population_timesteps = 0,
r_tol = 1e-4,
a_tol = 1e-4,
ode_max_steps = 1e6,
progress_bar = FALSE
)
)
# Override parameters with any client specified ones
if (!is.list(overrides)) {
stop('overrides must be a list')
}
for (name in names(overrides)) {
if (!(name %in% names(parameters))) {
stop(paste('unknown parameter', name, sep=' '))
}
parameters[[name]] <- overrides[[name]]
}
props <- c(
parameters$s_proportion,
parameters$d_proportion,
parameters$a_proportion,
parameters$u_proportion,
parameters$t_proportion
)
if (!approx_sum(props, 1)) {
stop("Starting proportions do not sum to 1")
}
parameters
}
#' @title Parameterise total_M and carrying capacity for mosquitos from EIR
#'
#' @description NOTE: the inital EIR is likely to change unless the rest of the
#' model is in equilibrium. NOTE: please set seasonality first, since the mosquito_limit
#' will estimate an upper bound from the peak season.
#'
#' max_total_M is calculated using the equilibrium solution from "Modelling the
#' impact of vector control interventions on Anopheles gambiae population
#' dynamics"
#'
#' @param parameters the parameters to modify
#' @param EIR to work from
#' @export
parameterise_mosquito_equilibrium <- function(parameters, EIR) {
parameterise_total_M(parameters, equilibrium_total_M(parameters, EIR))
}
#' @title Parameterise total_M
#'
#' @description Sets total_M and an upper bound for the number of mosquitoes in
#' the simulation. NOTE: please set seasonality first, since the mosquito_limit
#' will estimate an upper bound from the peak season.
#'
#' @param parameters the parameters to modify
#' @param total_M the initial adult mosquitoes in the simulation
#' @export
parameterise_total_M <- function(parameters, total_M) {
parameters$total_M <- total_M
if (!parameters$individual_mosquitoes) {
return(parameters)
}
max_total_M <- 0
for (i in seq_along(parameters$species)) {
species_M <- total_M * parameters$species_proportions[[i]]
K0 <- calculate_carrying_capacity(parameters, species_M, i)
R_bar <- calculate_R_bar(parameters)
max_K <- max(vnapply(seq(365), function(t) {
carrying_capacity(
t,
parameters$model_seasonality,
parameters$g0,
parameters$g,
parameters$h,
K0,
R_bar,
parameters$rainfall_floor
)
}))
omega <- calculate_omega(parameters, i)
mum <- weighted.mean(parameters$mum, parameters$species_proportions)
max_total_M <- max_total_M + max_K * (
1 / (
2 * parameters$dl * mum * (
1 + parameters$dpl * parameters$mup
)
)
) * (
1 / (
parameters$gamma * (omega + 1)
)
) * (
omega / (parameters$ml * parameters$del) - (
1 / (parameters$ml * parameters$dl)
) - 1
)
}
parameters$mosquito_limit <- ceiling(max_total_M * 5) #Allow for random fluctuations
parameters
}
#' Use parameter draw from the join posterior
#'
#' Overrides default (median) model parameters with a single draw from the fitted
#' joint posterior. Must be called prior to set_equilibrium.
#'
#' @param parameters the model parameters
#' @param draw the draw to use. Must be an integer between 1 and 1000
#'
#' @export
set_parameter_draw <- function(parameters, draw){
if(parameters$parasite == "falciparum"){
parameter_draws <- parameter_draws_pf
} else if (parameters$parasite == "vivax"){
parameter_draws <- parameter_draws_pv
}
if(draw > 1000 || draw < 1){
stop("draw must be an integer between 1 and 1000")
}
parameter_draw <- parameter_draws[[draw]]
for (name in names(parameter_draw)) {
parameters[[name]] <- parameter_draw[[name]]
}
return(parameters)
}
mrc-ide/malariasimulation documentation built on Feb. 18, 2025, 8:43 a.m.
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Defines functions set_parameter_draw parameterise_total_M parameterise_mosquito_equilibrium get_parameters
Documented in get_parameters parameterise_mosquito_equilibrium parameterise_total_M set_parameter_draw
#' @title Get model parameters
#' @description
#' get_parameters creates a named list of parameters for use in the model. These
#' parameters are passed to process functions.
#'
#' The default parameters, which are for Plasmodium falciparum, are explained in
#' "The US President's Malaria Initiative, Plasmodium falciparum transmission
#' and mortality: A modelling study."
#'
#' Plasmodium vivax specific parameters are explained in
#' "Mathematical modelling of the impact of expanding levels of malaria control
#' interventions on Plasmodium vivax." by White, Michael T., et al.
#'
#' @param overrides a named list of parameter values to use instead of defaults
#' @param parasite Plasmodium parasite species ("falciparum" or "vivax"); default = "falciparum"
#'
#' The parameters are defined below.
#'
#' parasite parameter
#' * parasite - parasite species (falciparum or vivax); default = "falciparum"
#'
#' initial state proportions:
#'
#' * s_proportion - the proportion of `human_population` that begin as susceptible; default = 0.420433246
#' * d_proportion - the proportion of `human_population` that begin with
#' clinical disease; default = 0.007215064
#' * a_proportion - the proportion of `human_population` that begin as
#' asymptomatic; default = 0.439323667
#' * u_proportion - the proportion of `human_population` that begin as
#' subpatents; default = 0.133028023
#' * t_proportion - the proportion of `human_population` that begin treated; default = 0
#'
#' human fixed state transitions:
#'
#' * dd - the delay for humans to move from state D to A; default = 5
#' * dt - the delay for humans to move from state Tr to S; default = 5
#' * da - the delay for humans to move from state A to U; default = 195
#' * du - the delay for humans to move from state U to S (p.f only); default = 110
#'
#' duration of pcr detectable infections: du (p.v only):
#'
#' * dpcr_max - Maximum duration of PCR-detectable infections: default = 53.69
#' * dpcr_min - Minimum duration of PCR-detectable infections: default = 10
#' * kpcr - Shape parameter: default = 4.021
#' * apcr50 - Scale parameter: default = 9.8
#'
#' human demography parameters:
#'
#' * human_population - the initial number of humans to model; default = 100
#' * average_age - the average age of humans (in timesteps), this is only used
#' if custom_demography is FALSE; default = 7665
#' * custom_demography - population demography given; default = FALSE
#'
#' initial immunity values:
#'
#' * init_ib - the initial pre-erythrocitic immunity (p.f only); default = 0
#' * init_iaa - the initial acquired anti-parasite immunity (p.v only): default = 0
#' * init_iam - the initial anti-parasite immunity at birth (p.v only); default = 0
#' * init_ica - the initial acquired immunity from clinical disease; default = 0
#' * init_icm - the initial clinical immunity at birth; default = 0
#' * init_iva - the initial acquired immunity from severe disease (p.f only); default = 0
#' * init_ivm - the initial severe immunity from severe disease at birth (p.f only); default = 0
#' * init_id - the initial acquired immunity to lm detectability (p.f only); default = 0
#'
#' immunity decay rates:
#'
#' * rb - decay rate for acquired pre-erythrocytic immunity (p.f only); default = 3650
#' * ra - decay rate for acquired anti-parasite immunity (p.v only); default = 3650
#' * rc - decay rate for acquired immunity to clinical disease; default = 10950
#' * rva - decay rate for acquired immunity to severe disease (p.f only); default = 10950
#' * rm - decay rate for maternal immunity to clinical disease (or p.v: maternal clinical and anti-parasite immunities); default = 67.6952
#' * rvm - decay rate for maternal immunity to severe disease (p.f only); default = 76.8365
#' * rid - decay rate for acquired immunity to lm-detectability (p.f only); default = 3650
#'
#' immunity boost grace periods:
#'
#' * ub - period in which pre-erythrocytic immunity cannot be boosted (p.f only); default = 7.2
#' * ua - period in which anti-parasite immunity cannot be boosted (p.v only); default = 44.09
#' * uc - period in which clinical immunity cannot be boosted; default = 6.06
#' * uv - period in which severe immunity cannot be boosted (p.f only); default = 11.4321
#' * ud - period in which immunity to detectability cannot be boosted (p.f only); default = 9.44512
#'
#' maternal immunity parameters:
#'
#' * pcm - new-born clinical immunity (or p.v: clinical and anti-parasite immunities) relative to mother's; default = 0.774368
#' * pvm - new-born severe immunity relative to mother's (p.f only); default = 0.195768
#'
#' unique biting rate:
#'
#' * a0 - age dependent biting parameter; default = 2920
#' * rho - age dependent biting parameter; default = 0.85
#' * sigma_squared - heterogeneity parameter; default = 1.67
#' * n_heterogeneity_groups - number discretised groups for heterogeneity, used
#' for sampling mothers; default = 5
#'
#' probability of pre-erythrocytic infection (p.f only):
#'
#' * b0 - maximum probability due to no immunity; default = 0.59
#' * b1 - maximum reduction due to immunity; default = 0.5
#' * ib0 - scale parameter; default = 43.9
#' * kb - shape parameter; default = 2.16
#'
#' probability of pre-erythrocytic infection (p.v only):
#' * b - probability of pre-erythrocytic infection: default = 0.25
#'
#' probability of detection by light-microscopy when asymptomatic (p.f only):
#'
#' * fd0 - time-scale at which immunity changes with age; default = 0.007055
#' * ad - scale parameter relating age to immunity; default = 7993.5
#' * gammad - shape parameter relating age to immunity; default = 4.8183
#' * d1 - minimum probability due to immunity; default = 0.160527
#' * id0 - scale parameter; default = 1.577533
#' * kd - shape parameter; default = 0.476614
#'
#' probability of light-microscopy detectable infections due to anti-parasite immunity (p.v only):
#'
#' * philm_max - maximum probability due to no immunity; default = 0.9329
#' * philm_min - maximum reduction due to immunity; default = 0.0131
#' * alm50 - scale parameter; default = 17.3
#' * klm - shape parameter; default = 3.202
#'
#' probability of clinical infection:
#'
#' * phi0 - maximum probability due to no immunity; default = 0.792
#' * phi1 - maximum reduction due to immunity; default = 0.00074
#' * ic0 - scale parameter; default = 18.02366
#' * kc - shape parameter; default = 2.36949
#'
#' probability of severe infection (p.f only):
#'
#' * theta0 - maximum probability due to no immunity; default = 0.0749886
#' * theta1 - maximum reduction due to immunity; default = 0.0001191
#' * iv0 - scale parameter; default = 1.09629
#' * kv - shape parameter; default = 2.00048
#' * fv0 - age dependent modifier; default = 0.141195
#' * av - age dependent modifier; default = 2493.41
#' * gammav - age dependent modifier; default = 2.91282
#'
#' infectivity towards mosquitoes:
#'
#' * cd - infectivity of clinically diseased humans towards mosquitoes; default = 0.068
#' * ca - infectivity of asymptomatic humans towards mosquitoes (p.v only); default = 0.1
#' * gamma1 - parameter for infectivity of asymptomatic humans; default = 1.82425
#' * cu - infectivity of subpatent infection; default = 0.0062
#' * ct - infectivity of treated infection; default = 0.021896
#'
#' mosquito fixed state transitions (including mortality):
#'
#' * del - the delay for mosquitoes to move from state E to L; default = 6.64
#' * dl - the delay for mosquitoes to move from state L to P; default = 3.72
#' * dpl - the delay mosquitoes to move from state P to Sm; default = 0.643
#' * me - early stage larval mortality rate; default = 0.0338
#' * ml - late stage larval mortality rate; default = 0.0348
#' * mup - the rate at which pupal mosquitoes die; default = 0.249
#' * mum - the rate at which developed mosquitoes die; default (An. gambiae) = .132
#'
#' vector biology:
#' species specific values are vectors
#' please set species parameters using the convenience function
#' \code{\link{set_species}}
#'
#' * beta - the average number of eggs laid per female mosquito per day; default = 21.2
#' * total_M - the initial number of adult mosquitos in the simulation; default = 1000
#' * init_foim - the FOIM used to calculate the equilibrium state for mosquitoes; default = 0
#' * species - names of the species in the simulation; default = "gamb"
#' * species_proportions - the relative proportions of each species; default = 1
#' * blood_meal_rates - the blood meal rates for each species; default = 1/3
#' * Q0 - proportion of blood meals taken on humans; default = 0.92
#' * foraging_time - time spent taking blood meals; default = 0.69
#'
#' seasonality and carrying capacity parameters:
#' please set flexible carrying capacity using the convenience function
#' \code{\link{set_carrying_capacity}}
#'
#' * model_seasonality - boolean switch TRUE iff the simulation models seasonal rainfall; default = FALSE
#' * g0 - rainfall fourier parameter; default = 2
#' * g - rainfall fourier parameter; default = 0.3, 0.6, 0.9
#' * h - rainfall fourier parameters; default = 0.1, 0.4, 0.7
#' * gamma - effect of density dependence on late instars relative to early
#' instars; default = 13.25
#' * rainfall_floor - the minimum rainfall value (must be above 0); default 0.001
#' * carrying_capacity; default = FALSE
#' * carrying_capacity_timesteps; default = NULL
#' * carrying_capacity_values; default = NULL#'
#'
#' parasite incubation periods:
#'
#' * de - duration of the human latent period of infection; default = 12
#' * delay_gam - lag from parasites to infectious gametocytes; default = 12.5
#' * dem - extrinsic incubation period in mosquito population model; default = 10
#'
#' hypnozoite batch parameters (p.v only):
#'
#' * f - hypnozoite batch relapse rate; default = 0.02439024
#' * gammal - hypnozoite batch clearance rate; default = 0.002610966
#' * init_hyp - initial hypnozoite batch number; default = 0
#' * kmax - maximum number of hypnozoite batches for use in the equilibrium solution; default = 10
#'
#' treatment parameters:
#' please set treatment parameters with the convenience functions
#' \code{\link{set_drugs}} and \code{\link{set_clinical_treatment}}
#'
#' * drug_efficacy - a vector of efficacies for available drugs; default = turned off
#' * drug_rel_c - a vector of relative onward infectiousness values for drugs; default = turned off
#' * drug_prophylaxis_shape - a vector of shape parameters for weibull curves to
#' model prophylaxis for each drug; default = turned off
#' * drug_prophylaxis_scale - a vector of scale parameters for weibull curves to
#' model prophylaxis for each drug; default = turned off
#' * drug_hypnozoite_efficacy - a vector of efficacies targeting hypnozoites; default = turned off
#' * drug_hypnozoite_prophylaxis_shape - a vector of shape parameters for weibull curves to model prophylaxis against hypnozoite batch formation (days); default = turned off
#' * drug_hypnozoite_prophylaxis_scale - a vector of scale parameters for weibull curves to model prophylaxis against hypnozoite batch formation (days); default = turned off
#' * clinical_treatment_drugs - a vector of drugs that are available for
#' clinically diseased (these values refer to the index in drug_* parameters); default = NULL, NULL, NULL
#' * clinical_treatment_coverage - a vector of coverage values for each drug; default = NULL, NULL, NULL
#'
#' MDA, SMC and PMC parameters:
#' please set these parameters with the convenience functions
#' \code{\link{set_mda}}, \code{\link{set_smc}} and \code{\link{set_pmc}},
#' with \code{\link{peak_season_offset}}
#'
#' bednet, irs and mosquito feeding cycle parameters:
#' please set vector control strategies using \code{\link{set_bednets}} and \code{\link{set_spraying}}
#'
#' * bednets - boolean for if bednets are enabled; default = FALSE
#' * phi_bednets - proportion of bites taken in bed; default = 0.85
#' * k0 - proportion of females bloodfed with no net; default = 0.699
#' * spraying - boolean for if indoor spraying is enabled; default = FALSE
#' * phi_indoors - proportion of bites taken indoors; default = 0.90
#'
#'
#' PEV parameters:
#' please set vaccine strategies with the convenience functions
#' \code{\link{set_pev_epi}} and \code{\link{set_mass_pev}}
#'
#' * pev_doses - the dosing schedule before the vaccine takes effect; default =
#' c(0, 1.5 * 30, 3 * 30)
#' default = 365
#'
#' TBV parameters:
#' please set TBV parameters with the convenience functions in
#' \code{\link{set_tbv}}
#'
#' * tbv_mt - effect on treated infectiousness; default = 35
#' * tbv_md - effect on diseased infectiousness; default = 46.7
#' * tbv_ma - effect on asymptomatic infectiousness; default = 3.6
#' * tbv_mu - effect on subpatent infectiousness; default = 0.8
#' * tbv_k - scale parameter for effect on infectiousness; default = 0.9
#' * tbv_tau - peak antibody parameter; default = 22
#' * tbv_rho - antibody component parameter; default = 0.7
#' * tbv_ds - antibody short-term delay parameter; default = 45
#' * tbv_dl - antibody long-term delay parameter; default = 591
#' * tbv_tra_mu - transmission reduction parameter; default = 12.63
#' * tbv_gamma1 - transmission reduction parameter; default = 2.5
#' * tbv_gamma2 - transmission reduction parameter; default = 0.06
#'
#' Antimalarial resistance parameters:
#' please set antimalarial resistance parameters with the convenience functions in
#' \code{\link{set_antimalarial_resistance}}
#'
#' * antimalarial_resistance - boolean for if antimalarial resistance is enabled; default = FALSE
#' * antimalarial_resistance_drug - vector of drugs for which resistance can be parameterised; default = NULL
#' * antimalarial_resistance_timesteps - vector of time steps on which resistance updates occur; default = NULL
#' * artemisinin_resistant_proportion - vector of proportions of infections resistant to the artemisinin component of a given drug; default = NULL
#' * partner_drug_resistance_proportion - vector of proportions of infections resistant to the parter drug component of a given drug; default = NULL
#' * slow_parasite_clearance_probability - vector of probabilities of slow parasite clearance for a given drug; default = NULL
#' * early_treatment_failure_probability - vector of probabilities of early treatment failure for a given drug; default = NULL
#' * late_clinical_failure_probability - vector of probabilities of late clinical failure for a given drug; default = NULL
#' * late_parasitological_failure_probability - vector of probabilities of late parasitological failure for a given drug; default = NULL
#' * reinfection_during_prophylaxis_probability - vector of probabilities of reinfection during prophylaxis for a given drug; default = NULL
#' * dt_slow_parasite_clearance - the delay for humans experiencing slow parasite clearance to move from state Tr to S; default = NULL
#'
#' rendering:
#' All values are in timesteps and all ranges are inclusive.
#' Please set rendered age groups using the convenience function
#'
#' * age_group_rendering_min_ages - the minimum ages for population size outputs; default = turned off
#' * age_group_rendering_max_ages - the corresponding max ages; default = turned off
#' * incidence_rendering_min_ages - the minimum ages for incidence
#' outputs (includes asymptomatic microscopy +); default = turned off
#' * incidence_rendering_max_ages - the corresponding max ages; default = turned off
#' * clinical_incidence_rendering_min_ages - the minimum ages for clinical incidence outputs (symptomatic); default = 0
#' * clinical_incidence_rendering_max_ages - the corresponding max ages; default = 1825
#' * severe_incidence_rendering_min_ages - the minimum ages for severe incidence
#' outputs; default = turned off
#' * severe_incidence_rendering_max_ages - the corresponding max ages; default = turned off
#' * prevalence_rendering_min_ages - the minimum ages for clinical prevalence
#' outputs; default = 730
#' * prevalence_rendering_max_ages - the corresponding max ages; default = 3650
#' * n_with_hypnozoites_rendering_min_ages - the minimum ages for number with hypnozoites outputs (p.v only); default = numeric(0)
#' * n_with_hypnozoites_rendering_max_ages - the corresponding max ages; default = numeric(0)
#'
#' Age structured mean immunity (/hyponozoite) rendering:
#'
#' * ib_rendering_min_ages - the minimum ages for blood immunity outputs (p.f only); default = numeric(0)
#' * ib_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * id_rendering_min_ages - the minimum ages for acquired detectability immunity (p.f); default = numeric(0)
#' * id_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * iaa_rendering_min_ages - the minimum ages for antiparasite immunity (p.v only); default = numeric(0)
#' * iam_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * ica_rendering_min_ages - the minimum ages for acquired clinical immunity outputs; default = numeric(0)
#' * ica_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * iva_rendering_min_ages - the minimum ages for acquired severe immunity outputs (p.f only); default = numeric(0)
#' * iva_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * idm_rendering_min_ages - the minimum ages for maternal antiparasite immunity outputs (p.v only); default = numeric(0)
#' * idm_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * icm_rendering_min_ages - the minimum ages for maternal clinical immunity outputs; default = numeric(0)
#' * icm_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * ivm_rendering_min_ages - the minimum ages for maternal severe immunity outputs (p.f only); default = numeric(0)
#' * ivm_rendering_max_ages - the corresponding max ages; default = numeric(0)
#' * hypnozoites_rendering_min_ages - the minimum ages average hypnozoite batches outputs (p.v only); default = numeric(0)
#' * hypnozoites_rendering_max_ages - the corresponding max ages; default = numeric(0)
#'
#' mixing:
#'
#' * rdt_intercept - the y intercept for the log logit relationship betweeen rdt
#' and PCR prevalence; default = -0.968
#' * rdt_coeff - the coefficient for the log logit relationship betweeen rdt
#' and PCR prevalence; default = 1.186
#'
#' miscellaneous:
#'
#' * mosquito_limit - the maximum number of mosquitoes to allow for in the
#' simulation; default = 1.00E+05
#' * individual_mosquitoes - boolean whether adult mosquitoes are modeled
#' individually or compartmentally; default = TRUE
#' * human_population_timesteps - the timesteps at which the population should
#' change; default = 0
#' * r_tol - the relative tolerance for the ode solver; default = 1e-4
#' * a_tol - the absolute tolerance for the ode solver; default = 1e-4
#' * ode_max_steps - the max number of steps for the solver; default = 1e6
#' * enable_heterogeneity - boolean whether to include heterogeneity in biting
#' rates; default = TRUE
#'
#' @export
get_parameters <- function(overrides = list(), parasite = "falciparum") {
if(!parasite %in% c("falciparum","vivax")){stop("parasite must be 'falciparum' or 'vivax'")}
parameters <- c(
# human fixed state transitions
# initial immunities
# immunity decay rates
# immunity boost grace periods
# maternal immunity parameters
# probability of pre-erythrocytic infection/blood immunity
# probability of asymptomatic detection (p.f only)
# probability of light-microscopy detectable infection (due to anti-parasite immunity, p.v only)
# probability of clinical infection
# probability of severe infection (p.f only)
# infectivity towards mosquitos
# parasite incubation periods
# hypnozoite parameters (p.v only)
malariasimulation::parasite_parameters[[parasite]],
list(
# parasite
parasite = parasite,
# initial state proportions
s_proportion = 0.420433246,
d_proportion = 0.007215064,
a_proportion = 0.439323667,
u_proportion = 0.133028023,
t_proportion = 0,
# human demography parameters
human_population = 100,
average_age = 7663,
custom_demography = FALSE,
# unique biting rate
a0 = 8 * 365,
rho = .85,
sigma_squared = 1.67,
n_heterogeneity_groups = 5,
enable_heterogeneity = TRUE,
# mosquito fixed state transitions (inc. mortality)
del = 6.64,
dl = 3.72,
dpl = .643,
me = .0338,
ml = .0348,
mup = .249,
mum = .132,
# species-specific vector biology (default is An. gambiae s.s)
species = 'gamb',
species_proportions = 1,
blood_meal_rates = 1/3,
Q0 = .92,
foraging_time = .69,
beta = 21.2,
total_M = 1000,
init_foim= 0,
# carrying capacity parameters
g0 = 2,
g = c(.3, .6, .9),
h = c(.1, .4, .7),
gamma = 13.25,
model_seasonality = FALSE,
rainfall_floor = 0.001,
# flexible carrying capacity
carrying_capacity = FALSE,
carrying_capacity_timesteps = NULL,
carrying_capacity_values = NULL,
# treatment parameters
drug_efficacy = numeric(0),
drug_rel_c = numeric(0),
drug_prophylaxis_shape = numeric(0),
drug_prophylaxis_scale = numeric(0),
drug_hypnozoite_efficacy = numeric(0),
drug_hypnozoite_prophylaxis_shape = numeric(0),
drug_hypnozoite_prophylaxis_scale = numeric(0),
clinical_treatment_drugs = list(),
clinical_treatment_timesteps = list(),
clinical_treatment_coverages = list(),
# MDA
mda = FALSE,
mda_drug = 0,
mda_timesteps = NULL,
mda_coverages = NULL,
mda_min_ages = -1,
mda_max_ages = -1,
smc = FALSE,
smc_drug = 0,
smc_timesteps = NULL,
smc_coverages = NULL,
smc_min_ages = -1,
smc_max_ages = -1,
# PMC
pmc = FALSE,
pmc_drug = 0,
pmc_timesteps = NULL,
pmc_coverages = NULL,
pcs_ages = -1,
# bed nets
bednets = FALSE,
phi_bednets = .85,
k0 = .699,
# indoor spraying
spraying = FALSE,
phi_indoors = .90,
# pev
pev = FALSE,
pev_doses = c(0, 1.5 * 30, 3 * 30),
# tbv
tbv = FALSE,
tbv_mt = 35,
tbv_md = 46.7,
tbv_ma = 3.6,
tbv_mu = 0.8,
tbv_k = 0.9,
tbv_tau = 22,
tbv_rho = .7,
tbv_ds = 45,
tbv_dl = 591,
tbv_tra_mu = 12.63,
tbv_gamma1 = 2.5,
tbv_gamma2 = .06,
tbv_timesteps = NULL,
tbv_coverages = NULL,
tbv_ages = NULL,
# antimalarial resistance
antimalarial_resistance = FALSE,
antimalarial_resistance_drug = NULL,
antimalarial_resistance_timesteps = NULL,
artemisinin_resistance_proportion = NULL,
partner_drug_resistance_proportion = NULL,
slow_parasite_clearance_probability = NULL,
early_treatment_failure_probability = NULL,
late_clinical_failure_probability = NULL,
late_parasitological_failure_probability = NULL,
reinfection_during_prophylaxis_probability = NULL,
dt_slow_parasite_clearance = NULL,
# rendering
age_group_rendering_min_ages = numeric(0),
age_group_rendering_max_ages = numeric(0),
incidence_rendering_min_ages = numeric(0),
incidence_rendering_max_ages = numeric(0),
clinical_incidence_rendering_min_ages = numeric(0),
clinical_incidence_rendering_max_ages = numeric(0),
severe_incidence_rendering_min_ages = numeric(0),
severe_incidence_rendering_max_ages = numeric(0),
prevalence_rendering_min_ages = 2 * 365,
prevalence_rendering_max_ages = 10 * 365,
n_with_hypnozoites_rendering_min_ages = numeric(0),
n_with_hypnozoites_rendering_max_ages = numeric(0),
# age structured average immunity (/hypnozoite) rendering
ib_rendering_min_ages = numeric(0),
ib_rendering_max_ages = numeric(0),
id_rendering_min_ages = numeric(0),
id_rendering_max_ages = numeric(0),
ica_rendering_min_ages = numeric(0),
ica_rendering_max_ages = numeric(0),
iva_rendering_min_ages = numeric(0),
iva_rendering_max_ages = numeric(0),
idm_rendering_min_ages = numeric(0),
idm_rendering_max_ages = numeric(0),
icm_rendering_min_ages = numeric(0),
icm_rendering_max_ages = numeric(0),
ivm_rendering_min_ages = numeric(0),
ivm_rendering_max_ages = numeric(0),
hypnozoites_rendering_min_ages = numeric(0),
hypnozoites_rendering_max_ages = numeric(0),
# mixing
rdt_intercept = -0.968,
rdt_coeff = 1.186,
# misc
mosquito_limit = 100 * 1000,
individual_mosquitoes = FALSE,
human_population_timesteps = 0,
r_tol = 1e-4,
a_tol = 1e-4,
ode_max_steps = 1e6,
progress_bar = FALSE
)
)
# Override parameters with any client specified ones
if (!is.list(overrides)) {
stop('overrides must be a list')
}
for (name in names(overrides)) {
if (!(name %in% names(parameters))) {
stop(paste('unknown parameter', name, sep=' '))
}
parameters[[name]] <- overrides[[name]]
}
props <- c(
parameters$s_proportion,
parameters$d_proportion,
parameters$a_proportion,
parameters$u_proportion,
parameters$t_proportion
)
if (!approx_sum(props, 1)) {
stop("Starting proportions do not sum to 1")
}
parameters
}
#' @title Parameterise total_M and carrying capacity for mosquitos from EIR
#'
#' @description NOTE: the inital EIR is likely to change unless the rest of the
#' model is in equilibrium. NOTE: please set seasonality first, since the mosquito_limit
#' will estimate an upper bound from the peak season.
#'
#' max_total_M is calculated using the equilibrium solution from "Modelling the
#' impact of vector control interventions on Anopheles gambiae population
#' dynamics"
#'
#' @param parameters the parameters to modify
#' @param EIR to work from
#' @export
parameterise_mosquito_equilibrium <- function(parameters, EIR) {
parameterise_total_M(parameters, equilibrium_total_M(parameters, EIR))
}
#' @title Parameterise total_M
#'
#' @description Sets total_M and an upper bound for the number of mosquitoes in
#' the simulation. NOTE: please set seasonality first, since the mosquito_limit
#' will estimate an upper bound from the peak season.
#'
#' @param parameters the parameters to modify
#' @param total_M the initial adult mosquitoes in the simulation
#' @export
parameterise_total_M <- function(parameters, total_M) {
parameters$total_M <- total_M
if (!parameters$individual_mosquitoes) {
return(parameters)
}
max_total_M <- 0
for (i in seq_along(parameters$species)) {
species_M <- total_M * parameters$species_proportions[[i]]
K0 <- calculate_carrying_capacity(parameters, species_M, i)
R_bar <- calculate_R_bar(parameters)
max_K <- max(vnapply(seq(365), function(t) {
carrying_capacity(
t,
parameters$model_seasonality,
parameters$g0,
parameters$g,
parameters$h,
K0,
R_bar,
parameters$rainfall_floor
)
}))
omega <- calculate_omega(parameters, i)
mum <- weighted.mean(parameters$mum, parameters$species_proportions)
max_total_M <- max_total_M + max_K * (
1 / (
2 * parameters$dl * mum * (
1 + parameters$dpl * parameters$mup
)
)
) * (
1 / (
parameters$gamma * (omega + 1)
)
) * (
omega / (parameters$ml * parameters$del) - (
1 / (parameters$ml * parameters$dl)
) - 1
)
}
parameters$mosquito_limit <- ceiling(max_total_M * 5) #Allow for random fluctuations
parameters
}
#' Use parameter draw from the join posterior
#'
#' Overrides default (median) model parameters with a single draw from the fitted
#' joint posterior. Must be called prior to set_equilibrium.
#'
#' @param parameters the model parameters
#' @param draw the draw to use. Must be an integer between 1 and 1000
#'
#' @export
set_parameter_draw <- function(parameters, draw){
if(parameters$parasite == "falciparum"){
parameter_draws <- parameter_draws_pf
} else if (parameters$parasite == "vivax"){
parameter_draws <- parameter_draws_pv
}
if(draw > 1000 || draw < 1){
stop("draw must be an integer between 1 and 1000")
}
parameter_draw <- parameter_draws[[draw]]
for (name in names(parameter_draw)) {
parameters[[name]] <- parameter_draw[[name]]
}
return(parameters)
}
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