Internal code for the Ebola model

Usage

.model_ebola_internal(
  initial_state,
  erlang_subcompartments,
  transmission_rate,
  infectiousness_rate,
  removal_rate,
  prop_community,
  etu_risk,
  funeral_risk,
  intervention,
  time_dependence,
  time_end,
  replicates,
  local_seeds
)

Arguments

erlang_subcompartments: A numeric, integer-like vector for the number of Erlang sub-compartments assumed for the exposed, infectious, and hospitalised compartments. Defaults to 2.
transmission_rate: A numeric vector for the rate at which individuals move from the susceptible to the exposed compartment upon contact with an infectious individual. Often denoted as \(\beta\), with \(\beta = R_0 / \text{infectious period}\). See Details for default values.
infectiousness_rate: A numeric vector for the rate at which individuals move from the exposed to the infectious compartment. Often denoted as \(\sigma\), with \(\sigma = 1.0 / \text{pre-infectious period}\). This value does not depend upon the number of infectious individuals in the population. See Details for default values.
removal_rate: A numeric vector for the rate at which infectious individuals transition from the infectious or hospitalised compartments to the funeral or removed compartments. This model does not distinguish between recoveries and deaths. Denoted in Getz and Dougherty as \(\gamma^I\) (see Details).
prop_community: A numeric vector for the proportion of infectious individuals who remain in the community and are not hospitalised for treatment. Defaults to 0.9.
etu_risk: A numeric vector for the relative risk of onward transmission of EVD from hospitalised individuals, with values between 0.0 and 1.0, where 0.0 indicates that hospitalisation completely prevents onward transmission, and 1.0 indicates that hospitalisation does not prevent onward transmission at all; values are relative to the baseline transmission rate \(\beta\). Defaults to 0.7.
funeral_risk: A numeric vector for the relative risk of onward transmission of EVD from funerals of individuals who died with EVD. Must be between 0.0 and 1.0, where 0.0 indicates that there is no onward transmission, and 1.0 indicates that funeral transmission is equivalent to the baseline transmission rate in the community \(\beta\). Defaults to 0.5.
intervention: An optional named list of <rate_intervention> objects representing optional pharmaceutical or non-pharmaceutical interventions applied to the model parameters listed above. May also be a list of such lists, in which case each set of interventions is treated as a separate scenario. See Details below.
time_dependence: An optional named list where each element is a function with the first two arguments being the current simulation time, and x, a value that is dependent on time (x represents a model parameter). List names must correspond to model parameters modified by the function. Alternatively, may be a list of such lists, in which case each set of functions is treated as a distinct scenario. See Details for more information, as well as the vignette on time- dependence vignette("time_dependence", package = "epidemics").
time_end: A numeric, integer-like vector for the maximum number of
replicates: A single number for replicates to run. Defaults to 100. timesteps over which to run the model, in days. Defaults to 100 days.

Details

NOTE that all arguments to this internal function must be scalars for infection parameters or single intervention or time-dependence sets for composable elements.