% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/net.inputs.R
\name{param.net}
\alias{param.net}
\title{Epidemic Parameters for Stochastic Network Models}
\usage{
param.net(
  inf.prob,
  inter.eff,
  inter.start,
  act.rate,
  rec.rate,
  a.rate,
  ds.rate,
  di.rate,
  dr.rate,
  inf.prob.g2,
  rec.rate.g2,
  a.rate.g2,
  ds.rate.g2,
  di.rate.g2,
  dr.rate.g2,
  ...
)
}
\arguments{
\item{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 to the group 1 nodes. This may also be a
vector of probabilities, with each element corresponding to the
probability in that time step of infection (see Time-Varying
Parameters below).}

\item{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.}

\item{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 \code{inter.eff} is defined but this parameter is not.}

\item{act.rate}{Average number of transmissible acts \emph{per partnership}
per unit time (see \code{act.rate} Parameter below). This may also be
a vector of rates, with each element corresponding to the rate in
that time step of infection (see Time-Varying Parameters below).}

\item{rec.rate}{Average rate of recovery with immunity (in \code{SIR} models)
or re-susceptibility (in \code{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 \code{SIR} and \code{SIS} models. This may also be a vector
of rates, with each element corresponding to the rate in that time
step of infection (see Time-Varying Parameters below).}

\item{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 \code{a.rate.g2} rate set as described
below.}

\item{ds.rate}{Departure or exit rate for susceptible persons. For two-group
models, it is the rate for group 1 susceptible persons only.}

\item{di.rate}{Departure or exit rate for infected persons. For two-group
models, it is the rate for group 1 infected persons only.}

\item{dr.rate}{Departure or exit rate for recovered persons. For two-group
models, it is the rate for group 1 recovered persons only. This
parameter is only used for \code{SIR} models.}

\item{inf.prob.g2}{Probability of transmission given a transmissible act
between a susceptible group 2 person and an infected group 1 person.
It is the probability of transmission to group 2 members.}

\item{rec.rate.g2}{Average rate of recovery with immunity (in \code{SIR}
models) or re-susceptibility (in \code{SIS} models) for group 2
persons. This parameter is only used for two-group \code{SIR} and
\code{SIS} models.}

\item{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 person
per unit time, or as \code{NA}, in which case the group 1 rate,
\code{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.}

\item{ds.rate.g2}{Departure or exit rate for group 2 susceptible persons.}

\item{di.rate.g2}{Departure or exit rate for group 2 infected persons.}

\item{dr.rate.g2}{Departure or exit rate for group 2 recovered persons. This
parameter is only used for \code{SIR} model types.}

\item{...}{Additional arguments passed to model.}
}
\value{
An \code{EpiModel} object of class \code{param.net}.
}
\description{
Sets the epidemic parameters for stochastic network models
simulated with \code{\link{netsim}}.
}
\details{
\code{param.net} sets the epidemic parameters for the stochastic network
models simulated with the \code{\link{netsim}} 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 network model parameterization for base models is found in
the \href{https://epimodel.github.io/sismid/}{Network Modeling for Epidemics}
tutorials.

For base models, the model specification will be chosen as a result of
the model parameters entered here and the control settings in
\code{\link{control.net}}. One-group and two-group models are available,
where the latter assumes a heterogeneous mixing between two distinct
partitions in the population (e.g., men and women). Specifying any two-group
parameters (those with a \code{.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.
}
\section{The \code{act.rate} Parameter}{

A key difference between these network models and DCM/ICM classes is the
treatment of transmission events. With DCM and ICM, contacts or partnerships
are mathematically instantaneous events: they have no duration in time, and
thus no changes may occur within them over time. In contrast, network models
allow for partnership durations defined by the dynamic network model,
summarized in the model dissolution coefficients calculated in
\code{\link{dissolution_coefs}}. Therefore, the \code{act.rate} parameter has
a different interpretation here, where it is the number of transmissible acts
\emph{per partnership} per unit time.
}

\section{Time-Varying Parameters}{

The \code{inf.prob}, \code{act.rate}, \code{rec.rate} arguments (and their
\code{.g2} companions) may be specified as time-varying parameters by passing
in a vector of probabilities or rates, respectively. The value in each
position on the vector then corresponds to the probability or rate at that
discrete time step for the infected partner. For example, an \code{inf.prob}
of \code{c(0.5, 0.5, 0.1)} would simulate a 0.5 transmission probability for
the first two time steps of a person's infection, followed by a 0.1 for the
third time step. If the infected person has not recovered or exited the
population by the fourth time step, the third element in the vector will
carry forward until one of those events occurs or the simulation ends. For
further examples, see the
\href{https://epimodel.github.io/sismid/}{Network Modeling for Epidemics} tutorials.
}

\section{Random Parameters}{

In addition to deterministic parameters in either fixed or time-varying
varieties above, one may also include a generator for random parameters.
These might include a vector of potential parameter values or a statistical
distribution definition; in either case, one draw from the generator would
be completed per individual simulation. This is possible by passing a list
named \code{random.params} into \code{param.net}, with each element of
\code{random.params} a named generator function. See the help page and
examples in \code{\link{generate_random_params}}. A simple factory function
for sampling is provided with \code{\link{param_random}} but any function
will do.
}

\section{Using a Parameter data.frame}{

It is possible to set input parameters using a specifically formatted
\code{data.frame} object. The first 3 columns of this \code{data.frame} must
be:
\itemize{
\item \code{param}: The name of the parameter. If this is a non-scalar
parameter (a vector of length > 1), end the parameter name with the
position on the vector (e.g., \code{"p_1"}, \code{"p_2"}, ...).
\item \code{value}: the value for the parameter (or the value of the
parameter in the Nth position if non-scalar).
\item \code{type}: a character string containing either \code{"numeric"},
\code{"logical"}, or \code{"character"} to define the parameter object
class.
}

In addition to these 3 columns, the \code{data.frame} can contain any number
of other columns, such as \code{details} or \code{source} columns to document
parameter meta-data. However, these extra columns will not be used by
EpiModel.

This data.frame is then passed in to \code{param.net} under a
\code{data.frame.parameters} argument. Further details and examples are
provided in the "Working with Model Parameters in EpiModel" vignette.
}

\section{Parameters with 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
\code{\link{control.net}}. New modules may use either the existing model
parameters named here, an original set of parameters, or a combination of
both. The \code{...} allows the user to pass an arbitrary set of original
model parameters into \code{param.net}. Whereas there are strict checks with
default modules for parameter validity, this becomes a user
responsibility when using new modules.
}

\examples{
## Example SIR model parameterization with fixed and random parameters
# Network model estimation
nw <- network_initialize(n = 100)
formation <- ~edges
target.stats <- 50
coef.diss <- dissolution_coefs(dissolution = ~offset(edges), duration = 20)
est <- netest(nw, formation, target.stats, coef.diss, verbose = FALSE)

# Random epidemic parameter list (here act.rate values are sampled uniformly
# with helper function param_random, and inf.prob follows a general Beta
# distribution with the parameters shown below)
my_randoms <- list(
  act.rate = param_random(1:3),
  inf.prob = function() rbeta(1, 1, 2)
)

# Parameters, initial conditions, and control settings
param <- param.net(rec.rate = 0.02, random.params = my_randoms)

# Printing parameters shows both fixed and and random parameter functions
param

# Set initial conditions and controls
init <- init.net(i.num = 10, r.num = 0)
control <- control.net(type = "SIR", nsteps = 10, nsims = 3, verbose = FALSE)

# Simulate the model
sim <- netsim(est, param, init, control)

# Printing the sim object shows the randomly drawn values for each simulation
sim

# Parameter sets can be extracted with:
get_param_set(sim)

}
\seealso{
Use \code{\link{init.net}} to specify the initial conditions and
\code{\link{control.net}} to specify the control settings. Run the
parameterized model with \code{\link{netsim}}.
}
\keyword{parameterization}
