Package 'malariasimulation'

Title: An individual based model for malaria
Description: Specifies the latest and greatest malaria model.
Authors: Giovanni Charles [aut, cre], Peter Winskill [aut], Hillary Topazian [aut], Joseph Challenger [aut], Richard Fitzjohn [aut], Richard Sheppard [aut], Tom Brewer [aut], Kelly McCain [aut], Lydia Haile [aut], Imperial College of Science, Technology and Medicine [cph]
Maintainer: Giovanni Charles <[email protected]>
License: MIT + file LICENSE
Version: 2.0.0
Built: 2024-11-02 05:54:29 UTC
Source: https://github.com/mrc-ide/malariasimulation

Help Index

Preset parameters for the AL drug

Description

From SI of Commun. 5:5606 doi: 10.1038/ncomms6606 (2014)

Usage

AL_params

Format

An object of class numeric of length 4.

Details

Use a vector of preset parameters for the AL drug (artemether-lumefantrine)

Default parameters, from L to R, are: drug_efficacy: 0.95, drug_rel_c: 0.05094, drug_prophylaxis_shape: 11.3, drug_prophylaxis_scale: 10.6

Preset parameters for the An. arabiensis vector

Description

Preset parameters for the An. arabiensis vector

Usage

arab_params

Format

An object of class list of length 7.

Details

Default parameters: species: "arab" blood_meal_rates: 0.3333333 foraging_time: .69 Q0: 0.71 phi_bednets: 0.8 phi_indoors: 0.86 mum: 0.132

parameters from: https://www.pnas.org/content/pnas/early/2019/07/02/1820646116.full.pdf

Calculate the vector carrying capacity

Description

taken from "Modelling the impact of vector control interventions on Anopheles gambiae population dynamics"

Usage

calculate_carrying_capacity(parameters, m, species)

Arguments

parameters

model parameters
m

number of adult mosquitoes
species

index of the species to calculate for

Class: Correlation parameters

Description

Class: Correlation parameters

Class: Correlation parameters

Details

This class implements functionality that allows interventions to be correlated, positively or negatively. By default, interventions are applied independently and an individual's probability of receiving two interventions (either two separate interventions or two rounds of the same one) is the product of the probability of receiving each one.

By setting a positive correlation between two interventions, we can make it so that the individuals that receive intervention A are more likely to receive intervention B. Conversely, a negative correlation will make it such that individuals that receive intervention A are less likely to also receive intervention B.

Broadly speaking, the implementation works by assigning at startup a weight to each individual and intervention pair, reflecting how likely an individual is to receive that intervention. Those weights are derived stochastically from the configured correlation parameters.

For a detailed breakdown of the calculations, see Protocol S2 of Griffin et al. (2010). Derive the mvnorm from the configured correlations.

If a restored_mvnorm is specified, its columns (corresponding to restored interventions) will be re-used as is. Missing columns (for new interventions) are derived in accordance with the restored data.

Methods

Public methods

Method new()

initialise correlation parameters

Usage
CorrelationParameters$new(population, interventions)
Arguments
population

popularion size

interventions

character vector with the name of enabled interventions

Method inter_round_rho()

Add rho between rounds

Usage
CorrelationParameters$inter_round_rho(int, rho)
Arguments
int

string representing the intervention to update

rho

value between 0 and 1 representing the correlation between rounds of the intervention

Method inter_intervention_rho()

Add rho between interventions

Usage
CorrelationParameters$inter_intervention_rho(int_1, int_2, rho)
Arguments
int_1

string representing the first intervention

int_2

string representing the second intervention (intechangable with int_1)

rho

value between -1 and 1 representing the correlation between rounds of the intervention

Method sigma()

Standard deviation of each intervention between rounds

Usage
CorrelationParameters$sigma()

Method mvnorm()

multivariate norm draws for these parameters

Usage
CorrelationParameters$mvnorm()

Method save_state()

Save the correlation state.

Usage
CorrelationParameters$save_state()

Method restore_state()

Restore the correlation state.

Only the randomly drawn weights are restored. The object needs to be initialized with the same rhos.

Usage
CorrelationParameters$restore_state(timestep, state)
Arguments
timestep

the timestep at which simulation is resumed. This parameter's value is ignored, it only exists to conform to a uniform interface.

state

a previously saved correlation state, as returned by the save_state method.

Method clone()

The objects of this class are cloneable with this method.

Usage
CorrelationParameters$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

create a PEV profile

Description

creates a data structure for holding pre-erythrocytic vaccine profile parameters. Parameters are validated on creation.

Usage

create_pev_profile(vmax, alpha, beta, cs, rho, ds, dl)

Arguments

vmax

maximum efficacy of the vaccine
alpha

shape parameter for the vaccine efficacy model
beta

scale parameter for the vaccine efficacy model
cs

peak parameters for the antibody model (vector of mean and std. dev)
rho

delay parameters for the antibody model (vector of mean and std. dev)
ds

delay parameters for the antibody model, short-term waning (vector of mean and std. dev)
dl

delay parameters for the antibody model, long-term waning (vector of mean and std. dev)

Create progress process

Description

Create progress process

Usage

create_progress_process(timesteps)

Arguments

timesteps

Simulation timesteps

Value

Progress bar process function

Preset parameters for the DHA-PQP drug

Description

From SI of Commun. 5:5606 doi: 10.1038/ncomms6606 (2014)

Usage

DHA_PQP_params

Format

An object of class numeric of length 4.

Details

Use a vector of preset parameters for the DHA-PQP drug (dihydroartemisinin-piperaquine)

Default parameters, from L to R, are: drug_efficacy: 0.95, drug_rel_c: 0.09434, drug_prophylaxis_shape: 4.4, drug_prophylaxis_scale: 28.1

Calculate the birthrate for a population in equilibrium

Description

Calculate the birthrate for a population in equilibrium

Usage

find_birthrates(pops, age_high, deathrates)

Arguments

pops

a vector of populations
age_high

a vector of age groups
deathrates

vector of deathrates for each age group

Preset parameters for the An. funestus vector

Description

Preset parameters for the An. funestus vector

Usage

fun_params

Format

An object of class list of length 7.

Details

Default parameters: species: "fun" blood_meal_rates: 0.3333333 foraging_time: .69 Q0: 0.94 phi_bednets: 0.78 phi_indoors: 0.87 mum: 0.112

parameters from: https://www.pnas.org/content/pnas/early/2019/07/02/1820646116.full.pdf

Preset parameters for the An. gambiae s.s vector

Description

Preset parameters for the An. gambiae s.s vector

Usage

gamb_params

Format

An object of class list of length 7.

Details

Default parameters: species: "gamb" blood_meal_rates: 0.3333333 foraging_time: .69 Q0: 0.92 phi_bednets: 0.85 phi_indoors: 0.90 mum: 0.132

parameters from: https://www.pnas.org/content/pnas/early/2019/07/02/1820646116.full.pdf

Retrieve resistance parameters

Description

Retrieve the resistance parameters associated with the drug each individual receiving clinical treatment has been administered in the current time step.

Usage

get_antimalarial_resistance_parameters(parameters, drugs, timestep)

Arguments

parameters

the model parameters
drugs

vector of integers representing the drugs administered to each individual receiving treatment
timestep

the current time step

Get default correlation parameters

Description

returns a CorrelationParameters object for you edit. By default, all correlations are set to 0

Usage

get_correlation_parameters(parameters)

Arguments

parameters

model parameters

Examples

# get the default model parameters
parameters <- get_parameters()

# Set some vaccination strategy
parameters <- set_mass_pev(
  parameters,
  profile = rtss_profile,
  timesteps = 100,
  coverages = .9,
  min_wait = 0,
  min_ages = 100,
  max_ages = 1000,
  booster_spacing = numeric(0),
  booster_coverage = numeric(0),
  booster_profile = NULL
)

# Set some smc strategy
parameters <- set_drugs(parameters, list(SP_AQ_params))
parameters <- set_smc(
  parameters,
  drug = 1,
  timesteps = 100,
  coverages = .9,
  min_age = 100,
  max_age = 1000
)

# Correlate the vaccination and smc targets
correlations <- get_correlation_parameters(parameters)
correlations$inter_intervention_rho('pev', 'smc', 1)

# Correlate the rounds of smc
correlations$inter_round_rho('smc', 1)

# You can now pass the correlation parameters to the run_simulation function

Get initialised carrying capacity for each species

Description

Get initialised carrying capacity for each species

Usage

get_init_carrying_capacity(parameters)

Arguments

parameters

the model parameters

Value

a vector of carrying initialised carrying capacity estimates for each vector species

Get model parameters

Description

get_parameters creates a named list of parameters for use in the model. These parameters are passed to process functions. These parameters are explained in "The US President's Malaria Initiative, Plasmodium falciparum transmission and mortality: A modelling study."

Usage

get_parameters(overrides = list())

Arguments

overrides

a named list of parameter values to use instead of defaults The parameters are defined below.

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; default = 110

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_icm - the immunity from clinical disease at birth; default = 0

  • init_ivm - the immunity from severe disease at birth; default = 0

  • init_ib - the initial pre-erythrocitic immunity; default = 0

  • init_ica - the initial acquired immunity from clinical disease; default = 0

  • init_iva - the initial acquired immunity from severe disease; default = 0

  • init_id - the initial acquired immunity to detectability; default = 0

immunity decay rates:

  • rm - decay rate for maternal immunity to clinical disease; default = 67.6952

  • rvm - decay rate for maternal immunity to severe disease; default = 76.8365

  • rb - decay rate for acquired pre-erythrocytic immunity; default = 3650

  • rc - decay rate for acquired immunity to clinical disease; default = 10950

  • rva - decay rate for acquired immunity to severe disease; default = 10950

  • rid - decay rate for acquired immunity to detectability; default = 3650

immunity boost grace periods:

  • ub - period in which pre-erythrocytic immunity cannot be boosted; default = 7.2

  • uc - period in which clinical immunity cannot be boosted; default = 6.06

  • uv - period in which severe immunity cannot be boosted; default = 11.4321

  • ud - period in which immunity to detectability cannot be boosted; default = 9.44512

maternal immunity parameters:

  • pcm - new-born clinical immunity relative to mother's; default = 0.774368

  • pvm - new-born severe immunity relative to mother's; 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:

  • 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 detection by light-microscopy when asymptomatic:

  • 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 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:

  • 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

  • gamma1 - parameter for infectivity of asymptomatic humans; default = 1.82425

  • cu - infectivity of sub-patent 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 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 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

treatment parameters: please set treatment parameters with the convenience functions set_drugs and 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

  • 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 set_mda, set_smc and set_pmc, with peak_season_offset

bednet, irs and mosquito feeding cycle parameters: please set vector control strategies using set_bednets and 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 set_pev_epi and 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 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 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

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

Parameter draws

Description

1000 draws from the joint posterior fit from

Usage

parameter_draws

Format

parameter_draws

A list of lists of length 1000, each level contains a list of drawn parameters

Source

https://www.nature.com/articles/ncomms4136

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"

Usage

parameterise_mosquito_equilibrium(parameters, EIR)

Arguments

parameters

the parameters to modify
EIR

to work from

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.

Usage

parameterise_total_M(parameters, total_M)

Arguments

parameters

the parameters to modify
total_M

the initial adult mosquitoes in the simulation

Calculate the yearly offset (in timesteps) for the peak mosquito season

Description

Calculate the yearly offset (in timesteps) for the peak mosquito season

Usage

peak_season_offset(parameters)

Arguments

parameters

to work from

R21 booster vaccine profile

Description

Parameters for a booster dose of R21 for use with the set_mass_pev and set_pev_epi functions (Schmit + Topazian et al. 2022 Lancet ID)

Usage

r21_booster_profile

Format

An object of class list of length 7.

R21 vaccine profile

Description

Parameters for a primary dose of R21 for use with the set_mass_pev and set_pev_epi functions (Schmit + Topazian et al. 2022 Lancet ID)

Usage

r21_profile

Format

An object of class list of length 7.

RTS,S booster vaccine profile

Description

Parameters for a booster dose of RTS,S for use with the set_mass_pev and set_pev_epi functions (White MT et al. 2015 Lancet ID)

Usage

rtss_booster_profile

Format

An object of class list of length 7.

RTS,S vaccine profile

Description

Parameters for a primary dose of RTS,S for use with the set_mass_pev and set_pev_epi functions (White MT et al. 2015 Lancet ID)

Usage

rtss_profile

Format

An object of class list of length 7.

Run a metapopulation model

Description

Run a metapopulation model

Usage

run_metapop_simulation(
  timesteps,
  parameters,
  correlations = NULL,
  mixing_tt,
  export_mixing,
  import_mixing,
  p_captured_tt,
  p_captured,
  p_success
)

Arguments

timesteps

the number of timesteps to run the simulation for (in days)
parameters

a list of model parameter lists for each population
correlations

a list of correlation parameters for each population (default: NULL)
mixing_tt

a vector of time steps for each mixing matrix
export_mixing

a list of matrices of coefficients for exportation of infectivity. Rows = origin sites, columns = destinations. Each matrix element describes the mixing pattern from destination to origin. Each matrix element must be between 0 and 1. Each matrix is activated at the corresponding timestep in mixing_tt
import_mixing

a list of matrices of coefficients for importation of infectivity.
p_captured_tt

a vector of time steps for each p_captured matrix
p_captured

a list of matrices representing the probability that travel between sites is intervened by a test and treat border check. Dimensions are the same as for export_mixing
p_success

the probability that an individual who has tested positive (through an RDT) successfully clears their infection through treatment

Value

a list of dataframe of model outputs as in run_simulation

Run the simulation in a resumable way

Description

this function accepts an initial simulation state as an argument, and returns the final state after running all of its timesteps. This allows one run to be resumed, possibly having changed some of the parameters.

Usage

run_resumable_simulation(
  timesteps,
  parameters = NULL,
  correlations = NULL,
  initial_state = NULL,
  restore_random_state = FALSE
)

Arguments

timesteps

the timestep at which to stop the simulation
parameters

a named list of parameters to use
correlations

correlation parameters
initial_state

the state from which the simulation is resumed
restore_random_state

if TRUE, restore the random number generator's state from the checkpoint.

Value

a list with two entries, one for the dataframe of results and one for the final simulation state.

Run the simulation

Description

Run the simulation for some time given some parameters. This currently returns a dataframe with the number of individuals in each state at each timestep.

The resulting dataframe contains the following columns:

  • timestep: the timestep for the row

  • infectivity: the infectivity from humans towards mosquitoes

  • FOIM: the force of infection towards mosquitoes (per species)

  • mu: the death rate of adult mosquitoes (per species)

  • EIR: the Entomological Inoculation Rate (per timestep, per species, over the whole population)

  • n_bitten: number of humans bitten by an infectious mosquito

  • n_treated: number of humans treated for clinical or severe malaria this timestep

  • n_infections: number of humans who get an asymptomatic, clinical or severe malaria this timestep

  • natural_deaths: number of humans who die from aging

  • S_count: number of humans who are Susceptible

  • A_count: number of humans who are Asymptomatic

  • D_count: number of humans who have the clinical malaria

  • U_count: number of subpatent infections in humans

  • Tr_count: number of detectable infections being treated in humans

  • ica_mean: the mean acquired immunity to clinical infection over the population of humans

  • icm_mean: the mean maternal immunity to clinical infection over the population of humans

  • ib_mean: the mean blood immunity to all infection over the population of humans

  • id_mean: the mean immunity from detection through microscopy over the population of humans

  • n: number of humans between an inclusive age range at this timestep. This defaults to n_730_3650. Other age ranges can be set with prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.

  • n_detect_lm (or pcr): number of humans with an infection detectable by microscopy (or pcr) between an inclusive age range at this timestep. This defaults to n_detect_730_3650. Other age ranges can be set with prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.

  • p_detect_lm (or pcr): the sum of probabilities of detection by microscopy (or pcr) between an inclusive age range at this timestep. This defaults to p_detect_730_3650. Other age ranges can be set with prevalence_rendering_min_ages and prevalence_rendering_max_ages parameters.

  • n_inc: number of new infections for humans between an inclusive age range at this timestep. incidence columns can be set with incidence_rendering_min_ages and incidence_rendering_max_ages parameters.

  • p_inc: sum of probabilities of infection for humans between an inclusive age range at this timestep. incidence columns can be set with incidence_rendering_min_ages and incidence_rendering_max_ages parameters.

  • n_inc_clinical: number of new clinical infections for humans between an inclusive age range at this timestep. clinical incidence columns can be set with clinical_incidence_rendering_min_ages and clinical_incidence_rendering_max_ages parameters.

  • p_inc_clinical: sub of probabilities of clinical infection for humans between an inclusive age range at this timestep. clinical incidence columns can be set with clinical_incidence_rendering_min_ages and clinical_incidence_rendering_max_ages parameters.

  • n_inc_severe: number of new severe infections for humans between an inclusive age range at this timestep. severe incidence columns can be set with severe_incidence_rendering_min_ages and severe_incidence_rendering_max_ages parameters.

  • p_inc_severe: the sum of probabilities of severe infection for humans between an inclusive age range at this timestep. severe incidence columns can be set with severe_incidence_rendering_min_ages and severe_incidence_rendering_max_ages parameters.

  • E_count: number of mosquitoes in the early larval stage (per species)

  • L_count: number of mosquitoes in the late larval stage (per species)

  • P_count: number of mosquitoes in the pupal stage (per species)

  • Sm_count: number of adult female mosquitoes who are Susceptible (per species)

  • Pm_count: number of adult female mosquitoes who are incubating (per species)

  • Im_count: number of adult female mosquitoes who are infectious (per species)

  • rate_D_A: rate that humans transition from clinical disease to asymptomatic

  • rate_A_U: rate that humans transition from asymptomatic to subpatent

  • rate_U_S: rate that humans transition from subpatent to susceptible

  • net_usage: the number people protected by a bed net

  • mosquito_deaths: number of adult female mosquitoes who die this timestep

  • n_drug_efficacy_failures: number of clinically treated individuals whose treatment failed due to drug efficacy

  • n_early_treatment_failure: number of clinically treated individuals who experienced early treatment failure

  • n_successfully_treated: number of clinically treated individuals who are treated successfully (includes individuals who experience slow parasite clearance)

  • n_slow_parasite_clearance: number of clinically treated individuals who experienced slow parasite clearance

Usage

run_simulation(timesteps, parameters = NULL, correlations = NULL)

Arguments

timesteps

the number of timesteps to run the simulation for (in days)
parameters

a named list of parameters to use
correlations

correlation parameters

Value

dataframe of results

Run the simulation with repetitions

Description

Run the simulation with repetitions

Usage

run_simulation_with_repetitions(
  timesteps,
  repetitions,
  overrides = list(),
  parallel = FALSE
)

Arguments

timesteps

the number of timesteps to run the simulation for
repetitions

n times to run the simulation
overrides

a named list of parameters to use instead of defaults
parallel

execute runs in parallel

Parameterise antimalarial resistance

Description

Parameterise antimalarial resistance

Usage

set_antimalarial_resistance(
  parameters,
  drug,
  timesteps,
  artemisinin_resistance_proportion,
  partner_drug_resistance_proportion,
  slow_parasite_clearance_probability,
  early_treatment_failure_probability,
  late_clinical_failure_probability,
  late_parasitological_failure_probability,
  reinfection_during_prophylaxis_probability,
  slow_parasite_clearance_time
)

Arguments

parameters

the model parameters
drug

the index of the drug which resistance is being set, as set by the set_drugs() function, in the parameter list
timesteps

vector of time steps for each update to resistance proportion and resistance outcome probability
artemisinin_resistance_proportion

vector of updates to the proportions of infections that are artemisinin resistant at time t
partner_drug_resistance_proportion

vector of updates to the proportions of infections that are partner-drug resistant at time t
slow_parasite_clearance_probability

vector of updates to the proportion of artemisinin-resistant infections that result in early treatment failure
early_treatment_failure_probability

vector of updates to the proportion of artemisinin-resistant infections that result in slow parasite clearance
late_clinical_failure_probability

vector of updates to the proportion of partner-drug-resistant infections that result in late clinical failure
late_parasitological_failure_probability

vector of updates to the proportion of partner-drug-resistant infections that result in late parasitological failure
reinfection_during_prophylaxis_probability

vector of updates to the proportion of partner-drug-resistant infections that result in reinfection during prophylaxis
slow_parasite_clearance_time

single value representing the mean time individual's experiencing slow parasite clearance reside in the treated state

Parameterise a bed net strategy

Description

The model will distribute bed nets at timesteps to a random sample of the entire human population. The sample size will be a proportion of the human population taken from the corresponding coverages. The sample can contain humans who already have bed nets.

All of the sample "use" their bed nets on the timestep after they are distributed. Incomplete usage is not part of this model.

If a human in the sample already has a bed net, their bed net will be replaced by a new one.

Bed nets will be randomly removed each timestep with a rate of 1 - exp(-1/retention)

The structure for the bed net model is documented in the S.I. of 10.1038/s41467-018-07357-w

Usage

set_bednets(parameters, timesteps, coverages, retention, dn0, rn, rnm, gamman)

Arguments

parameters

a list of parameters to modify
timesteps

the timesteps at which to distribute bed nets
coverages

the proportion of the human population who receive bed nets
retention

the average number of timesteps a net is kept for
dn0

a matrix of death probabilities for each species over time. With nrows=length(timesteps), ncols=length(species)
rn

a matrix of repelling probabilities for each species over time With nrows=length(timesteps), ncols=length(species)
rnm

a matrix of minimum repelling probabilities for each species over time With nrows=length(timesteps), ncols=length(species)
gamman

a vector of bednet half-lives for each distribution timestep

Parameterise custom baseline carrying capacity

Description

Allows the user to set a completely flexible and custom carrying capacity for each species

Usage

set_carrying_capacity(parameters, timesteps, carrying_capacity_scalers)

Arguments

parameters

the model parameters
timesteps

vector of timesteps for each rescale change
carrying_capacity_scalers

matrix of scaling factors to scale the baseline carrying capacity for each species with nrows = length(timesteps), ncols = length(species)

Parameterise clinical treatment

Description

Parameterise clinical treatment

Usage

set_clinical_treatment(parameters, drug, timesteps, coverages)

Arguments

parameters

the model parameters
drug

the index of the drug to set as a treatment
timesteps

vector of timesteps for each coverage change
coverages

vector of coverages for this drug

Parameterise variable deathrates

Description

Parameterise variable deathrates

Usage

set_demography(parameters, agegroups, timesteps, deathrates)

Arguments

parameters

the model parameters
agegroups

vector of agegroups (in timesteps)
timesteps

vector of timesteps for each change in demography
deathrates

matrix of deathrates per age group per timestep. Rows are timesteps from the timesteps param. Columns are the age groups from the agegroups param.

Parameterise drugs to use in the model

Description

Parameterise drugs to use in the model

Usage

set_drugs(parameters, drugs)

Arguments

parameters

the model parameters
drugs

a list of drug parameters, can be set using presets

Parameterise age grouped output rendering

Description

Parameterise age grouped output rendering

Usage

set_epi_outputs(
  parameters,
  age_group = NULL,
  incidence = NULL,
  clinical_incidence = NULL,
  severe_incidence = NULL,
  prevalence = NULL,
  ica = NULL,
  icm = NULL,
  iva = NULL,
  ivm = NULL,
  id = NULL,
  ib = NULL
)

Arguments

parameters

the model parameters
age_group

age breaks for population size outputs; default = NULL
incidence

age breaks for incidence outputs (D+Tr+A); default = NULL
clinical_incidence

age breaks for clinical incidence outputs (symptomatic); default = c(0, 1825)
severe_incidence

age breaks for severe incidence outputs; default = NULL
prevalence

age breaks for clinical prevalence outputs (pcr and lm detectable infections); default = c(730, 3650)
ica

age breaks for average acquired clinical immunity; default = NULL
icm

age breaks for average maternal clinical immunity; default = NULL
iva

age breaks for average acquired severe immunity; default = NULL
ivm

age breaks for average maternal severe immunity; default = NULL
id

age breaks for average immunity to detectability; default = NULL
ib

age breaks for average blood immunity; default = NULL

Details

this function produces contiguous age groups, inclusive of the lower age limit and exclusive of the upper age limit: e.g., c(0, 10, 100) will produce two age groups: 0-9 and 10-99 in days.

Set equilibrium

Description

This will update the IBM parameters to match the equilibrium parameters and set up the initial human and mosquito population to acheive init_EIR

Usage

set_equilibrium(parameters, init_EIR, eq_params = NULL)

Arguments

parameters

model parameters to update
init_EIR

the desired initial EIR (infectious bites per person per day over the entire human population)
eq_params

parameters from the malariaEquilibrium package, if null. The default malariaEquilibrium parameters will be used

Parameterise a vaccine mass distribution strategy

Description

distribute pre-erythrocytic vaccine to a population in an age range. Efficacy will take effect after the last dose

Usage

set_mass_pev(
  parameters,
  profile,
  timesteps,
  coverages,
  min_ages,
  max_ages,
  min_wait,
  booster_spacing,
  booster_coverage,
  booster_profile
)

Arguments

parameters

a list of parameters to modify
profile

a list of details for the vaccine profile, create with create_pev_profile
timesteps

a vector of timesteps for each round of vaccinations
coverages

the coverage for each round of vaccinations
min_ages

for the target population, inclusive (in timesteps)
max_ages

for the target population, inclusive (in timesteps)
min_wait

the minimum acceptable time since the last vaccination (in timesteps); When using both set_mass_pev and set_pev_epi, this represents the minimum time between an individual being vaccinated under one scheme and vaccinated under another.
booster_spacing

the timesteps (following the final primary dose) at which booster vaccinations are administered
booster_coverage

a matrix of coverages (timesteps x boosters) specifying the proportion the previously vaccinated population to continue receiving booster doses. The rows of the matrix must be the same size as timesteps. The columns of the matrix must be the same size as booster_spacing.
booster_profile

list of lists representing each booster profile, the outer list must be the same length as booster_spacing. Create vaccine profiles with create_pev_profile

Parameterise a Mass Drug Administration

Description

Parameterise a Mass Drug Administration

Usage

set_mda(parameters, drug, timesteps, coverages, min_ages, max_ages)

Arguments

parameters

a list of parameters to modify
drug

the index of the drug to administer
timesteps

a vector of timesteps for each round of mda
coverages

a vector of the proportion of the target population who receive each round
min_ages

a vector of minimum ages of the target population for each round exclusive (in timesteps)
max_ages

a vector of maximum ages of the target population for each round exclusive (in timesteps)

Use parameter draw from the join posterior

Description

Overrides default (median) model parameters with a single draw from the fitted joint posterior. Must be called prior to set_equilibrium.

Usage

set_parameter_draw(parameters, draw)

Arguments

parameters

the model parameters
draw

the draw to use. Must be an integer between 1 and 1000

Parameterise a pre-erythrocytic vaccine with an EPI strategy

Description

distribute vaccine when an individual becomes a certain age. Efficacy will take effect after the last dose

Usage

set_pev_epi(
  parameters,
  profile,
  coverages,
  timesteps,
  age,
  min_wait,
  booster_spacing,
  booster_coverage,
  booster_profile,
  seasonal_boosters = FALSE
)

Arguments

parameters

a list of parameters to modify
profile

a list of details for the vaccine profile, create with create_pev_profile
coverages

a vector of coverages for the primary doses
timesteps

a vector of timesteps for each change in coverage
age

the age when an individual will receive the first dose of the vaccine (in timesteps)
min_wait

the minimum acceptable time since the last vaccination (in timesteps); When seasonal_boosters = TRUE, this represents the minimum time between an individual receiving the final dose and the first booster. When using both set_mass_pev and set_pev_epi, this represents the minimum time between an individual being vaccinated under one scheme and vaccinated under another.
booster_spacing

the timesteps (following the final primary dose) at which booster vaccinations are administered
booster_coverage

a matrix of coverages (timesteps x boosters) specifying the proportion the previously vaccinated population to continue receiving booster doses. The rows of the matrix must be the same size as timesteps. The columns of the matrix must be the same size as booster_spacing.
booster_profile

list of lists representing each booster profile, the outer list must be the same length as booster_spacing. Create vaccine profiles with create_pev_profile
seasonal_boosters

logical, if TRUE the first booster timestep is relative to the start of the year, otherwise they are relative to the last primary dose

Parameterise a perennial malaria chemoprevention (PMC, formerly IPIi)

Description

Parameterise a perennial malaria chemoprevention (PMC, formerly IPIi)

Usage

set_pmc(parameters, drug, timesteps, coverages, ages)

Arguments

parameters

a list of parameters to modify
drug

the index of the drug to administer
timesteps

a vector of timesteps for each change in coverage
coverages

a vector of proportions of the target population to receive the intervention
ages

a vector of ages at which PMC is administered (in timesteps)

Parameterise a Seasonal Malaria Chemoprevention

Description

Parameterise a Seasonal Malaria Chemoprevention

Usage

set_smc(parameters, drug, timesteps, coverages, min_ages, max_ages)

Arguments

parameters

a list of parameters to modify
drug

the index of the drug to administer
timesteps

a vector of timesteps for each round of smc
coverages

a vector of the proportion of the target population who receive each round
min_ages

a vector of minimum ages of the target population for each round exclusive (in timesteps)
max_ages

a vector of maximum ages of the target population for each round exclusive (in timesteps) drug

Parameterise the mosquito species to use in the model

Description

Parameterise the mosquito species to use in the model

Usage

set_species(parameters, species, proportions)

Arguments

parameters

the model parameters
species

a list of species presets
proportions

a vector of proportions for each species

Parameterise an indoor spraying strategy

Description

The model will apply indoor spraying at timesteps to a random sample of the entire human population. The sample size will be a proportion of the human population taken from the corresponding coverages. The sample can contain humans who have already benefited from spraying.

If a human in the sample lives in a sprayed house, the efficacy of the spraying will be returned to the maximum.

The structure for the indoor residual spraying model is documented in the S.I. of 10.1038/s41467-018-07357-w

Usage

set_spraying(
  parameters,
  timesteps,
  coverages,
  ls_theta,
  ls_gamma,
  ks_theta,
  ks_gamma,
  ms_theta,
  ms_gamma
)

Arguments

parameters

a list of parameters to modify
timesteps

the timesteps at which to spray
coverages

the proportion of the population who get indoor spraying
ls_theta

matrix of mortality parameters With nrows=length(timesteps), ncols=length(species)
ls_gamma

matrix of mortality parameters per timestep With nrows=length(timesteps), ncols=length(species)
ks_theta

matrix of feeding success parameters per timestep With nrows=length(timesteps), ncols=length(species)
ks_gamma

matrix of feeding success parameters per timestep With nrows=length(timesteps), ncols=length(species)
ms_theta

matrix of deterrence parameters per timestep With nrows=length(timesteps), ncols=length(species)
ms_gamma

matrix of deterrence parameters per timestep With nrows=length(timesteps), ncols=length(species)

Parameterise an TBV strategy

Description

Parameterise an TBV strategy

Usage

set_tbv(parameters, timesteps, coverages, ages)

Arguments

parameters

a list of parameters to modify
timesteps

a vector of timesteps for each round of vaccinations
coverages

the coverage for each round of vaccinations
ages

a vector of ages of the target population (in years)

Preset parameters for the SP-AQ drug

Description

Preset parameters for the SP-AQ drug

Usage

SP_AQ_params

Format

An object of class numeric of length 4.

Details

Use a vector of preset parameters for the SP-AQ drug (sulphadoxine-pyrimethamine and amodiaquine)

Default parameters, from L to R, are: drug_efficacy: 0.9, drug_rel_c: 0.32, drug_prophylaxis_shape: 4.3, drug_prophylaxis_scale: 38.1

Preset parameters for the An. stephensi vector

Description

Preset parameters for the An. stephensi vector

Usage

steph_params

Format

An object of class list of length 7.

Details

Default parameters: species: "steph" blood_meal_rates: 0.3333333 foraging_time: .69 Q0: 0.21 phi_bednets: 0.57 phi_indoors: 0.37 mum: 0.112

parameters reference: https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-022-02324-1 Values for phi are from: https://github.com/arranhamlet/stephensi_ETH_publication/blob/297352e244f8ed658e8bc3f32be42f011269c7f0/R/functions/cluster_hypercube_sampling_djibouti.R#L14-L21 values for Q0: are the average from: ttps://github.com/cwhittaker1000/stephenseasonality/blob/main/data/bionomic_species_all_LHC_100.csv