param.icm: Epidemic Parameters for Stochastic Individual Contact Models

Description Usage Arguments Details Act Balancing New Modules See Also

View source: R/param.R

Description

Sets the epidemic parameters for stochastic individual contact models simulated with icm.

Usage

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param.icm(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 the 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 persons 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 may be parameterized as a rate per group 1 person time (with group 1 persons representing females), and with the a.rate.g2 rate set as described below.

ds.rate

Departure or exit rate for susceptible. For two-group models, it is the rate for the group 1 susceptible only.

di.rate

Departure or exit rate for infected. For two-group models, it is the rate for the group 1 infected only.

dr.rate

Departure or exit rate for recovered. For two-group models, it is the rate for the group 1 recovered 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.

di.rate.g2

Departure or exit rate for group 2 infected.

dr.rate.g2

Departure or exit rate for group 2 recovered. 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.icm sets the epidemic parameters for the stochastic individual contact models simulated with the icm function. Models may use the base types, for which these parameters are used, or new process modules which may use these parameters (but not necessarily). A detailed description of ICM parameterization for base models is found in the Basic ICMs tutorial.

For base models, the model specification will be chosen as a result of the model parameters entered here and the control settings in control.icm. One-group and two-group models are available, where the former assumes a homogenous mixing in the population and the latter assumes a purely heterogenous 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.

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 heterogenous mixing, the product of one group size and act rate must equal the product of the other group size and act rate: N_1 α_1 = N_2 α_2, where N_i is the group size and α_i the group-specific act rates 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.

New Modules

To build original models outside of the base models, new process modules may be constructed to replace the existing modules or to supplement the existing set. These are passed into the control settings in control.icm. New modules may use either the existing model parameters named here, an original set of parameters, or a combination of both. The ... allows the user to pass an arbitrary set of original model parameters into param.icm. Whereas there are strict checks with default modules for parameter validity, these checks are the user's responsibility with new modules.

See Also

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


EpiModel documentation built on Nov. 22, 2018, 1:04 a.m.