run_simulation: Run the simulation

In mrc-ide/malariasimulation: An individual based model for malaria

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

mrc-ide/malariasimulation documentation built on Oct. 14, 2024, 7:33 p.m.