run_simulation.RdRun 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
run_simulation(timesteps, parameters = NULL, correlations = NULL)dataframe of results