Sets the epidemic parameters for deterministic compartmental
models simulated with dcm.
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,
...
)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.
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.
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.
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).
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.
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.
Departure or exit rate for susceptible. For two-group models, it is the rate for the group 1 susceptible only.
Departure or exit rate for infected. For two-group models, it is the rate for the group 1 infected only.
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.
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.
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).
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.
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.
Departure or exit rate for group 2 susceptible.
Departure or exit rate for group 2 infected.
Departure or exit rate for group 2 recovered. This parameter is
only used for SIR model types.
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.
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: \(N_1 \alpha_1 = N_2 \alpha_2\), where
\(N_i\) is the group size and \(\alpha_i\) 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
for further details.
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
both the example below and the
Basic DCMs tutorial.
To build original model specifications outside of the base models, start
by consulting the Solving
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.
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 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.
Use init.dcm to specify the initial conditions and
control.dcm to specify the control settings. Run the
parameterized model with dcm.