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,
...
)An EpiModel object of class param.dcm.
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 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
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). 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 is parameterized as a rate per group 1
person per unit time, with the a.rate.g2 rate set as described
below.
Departure or exit rate for susceptible persons. For two-group models, it is the rate for the group 1 susceptible persons only.
Departure or exit rate for infected persons. For two-group models, it is the rate for the group 1 infected persons only.
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.
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 persons.
Departure or exit rate for group 2 infected persons.
Departure or exit rate for group 2 recovered persons. 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 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.
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.
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).
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.
Use init.dcm to specify the initial conditions and
control.dcm to specify the control settings. Run the
parameterized model with dcm.