param.dcm: Epidemic Parameters for Deterministic Compartmental Models

In EpiModel: Mathematical Modeling of Infectious Disease Dynamics

Epidemic Parameters for Deterministic Compartmental Models

Description

Sets the epidemic parameters for deterministic compartmental models simulated with dcm.

Usage

param.dcm(
  inf.prob,
  inter.eff,
  inter.start,
  act.rate,
  rec.rate,
  a.rate,
  ds.rate,
  di.rate,
  dr.rate,
  inf.prob.g2,
  act.rate.g2,
  rec.rate.g2,
  a.rate.g2,
  ds.rate.g2,
  di.rate.g2,
  dr.rate.g2,
  balance,
  ...
)

Arguments

inf.prob	Probability of infection per transmissible act between a susceptible and an infected person. In two-group models, this is the probability of infection for the group 1 members.
inter.eff	Efficacy of an intervention which affects the per-act probability of infection. Efficacy is defined as 1 - the relative hazard of infection given exposure to the intervention, compared to no exposure.
inter.start	Time step at which the intervention starts, between 1 and the number of time steps specified in the model. This will default to 1 if inter.eff is defined but this parameter is not.
act.rate	Average number of transmissible acts per person per unit time. For two-group models, this is the number of acts per group 1 person per unit time; a balance between the acts in groups 1 and 2 is necessary, and set using the balance parameter (see details).
rec.rate	Average rate of recovery with immunity (in SIR models) or re-susceptibility (in SIS models). The recovery rate is the reciprocal of the disease duration. For two-group models, this is the recovery rate for group 1 persons only. This parameter is only used for SIR and SIS models.
a.rate	Arrival or entry rate. For one-group models, the arrival rate is the rate of new arrivals per person per unit time. For two-group models, the arrival rate is parameterized as a rate per group 1 person per unit time, with the a.rate.g2 rate set as described below.
ds.rate	Departure or exit rate for susceptible persons. For two-group models, it is the rate for the group 1 susceptible persons only.
di.rate	Departure or exit rate for infected persons. For two-group models, it is the rate for the group 1 infected persons only.
dr.rate	Departure or exit rate for recovered persons. For two-group models, it is the rate for the group 1 recovered persons only. This parameter is only used for SIR models.
inf.prob.g2	Probability of infection per transmissible act between a susceptible group 2 person and an infected group 1 person. It is the probability of infection to group 2 members.
act.rate.g2	Average number of transmissible acts per group 2 person per unit time; a balance between the acts in groups 1 and 2 is necessary, and set using the balance parameter (see details).
rec.rate.g2	Average rate of recovery with immunity (in SIR models) or re-susceptibility (in SIS models) for group 2 persons. This parameter is only used for two-group SIR and SIS models.
a.rate.g2	Arrival or entry rate for group 2. This may either be specified numerically as the rate of new arrivals per group 2 persons per unit time, or as NA in which case the group 1 rate, a.rate, governs the group 2 rate. The latter is used when, for example, the first group is conceptualized as female, and the female population size determines the arrival rate. Such arrivals are evenly allocated between the two groups.
ds.rate.g2	Departure or exit rate for group 2 susceptible persons.
di.rate.g2	Departure or exit rate for group 2 infected persons.
dr.rate.g2	Departure or exit rate for group 2 recovered persons. This parameter is only used for SIR model types.
balance	For two-group models, balance the act.rate to the rate set for group 1 (with balance="g1") or group 2 (with balance="g2"). See details.
...	Additional arguments passed to model.

Details

param.dcm sets the epidemic parameters for deterministic compartmental models solved with the dcm function. The models may use the base types, for which these parameters are used, or original model specifications for which these parameters may be used (but not necessarily). A detailed description of DCM parameterization for base models is found in the Basic DCMs tutorial.

For base models, the model specification will be selected as a function of the model parameters entered here and the control settings in control.dcm. One-group and two-group models are available, where the former assumes a homogeneous mixing in the population and the latter assumes some form of heterogeneous mixing between two distinct partitions in the population (e.g., men and women). Specifying any group two parameters (those with a .g2) implies the simulation of a two-group model. All the parameters for a desired model type must be specified, even if they are zero.

Value

An EpiModel object of class param.dcm.

Act Balancing

In two-group models, a balance between the number of acts for group 1 members and those for group 2 members must be maintained. With purely heterogeneous mixing, the product of one group size and act rate must equal the product of the other group size and act rate: N_1 \alpha_1 = N_2 \alpha_2, where N_i is the group size and \alpha_i the group-specific act rate at time t. The balance parameter here specifies which group's act rate should control the others with respect to balancing. See the Basic DCMs tutorial for further details.

Sensitivity Analyses

dcm has been designed to easily run DCM sensitivity analyses, where a series of models varying one or more of the model parameters is run. This is possible by setting any parameter as a vector of length greater than one. See the Basic DCMs tutorial.

New Model Types

To build original model specifications outside of the base models, start by consulting the New DCMs with EpiModel tutorial. Briefly, an original model may use either the existing model parameters named here, an original set of parameters, or a combination of both. The ... argument allows the user to pass an arbitrary set of new model parameters into param.dcm. Whereas there are strict checks for base models that the model parameters are valid, parameter validity is the user's responsibility with these original models.

See Also

Use init.dcm to specify the initial conditions and control.dcm to specify the control settings. Run the parameterized model with dcm.

EpiModel documentation built on July 9, 2023, 5:21 p.m.