% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/net.inputs.R
\name{control.net}
\alias{control.net}
\title{Control Settings for Stochastic Network Models}
\usage{
control.net(
  type,
  nsteps,
  start = 1,
  nsims = 1,
  ncores = 1,
  resimulate.network = FALSE,
  tergmLite = FALSE,
  cumulative.edgelist = FALSE,
  truncate.el.cuml = 0,
  attr.rules,
  epi.by,
  initialize.FUN = initialize.net,
  resim_nets.FUN = resim_nets,
  summary_nets.FUN = summary_nets,
  infection.FUN = NULL,
  recovery.FUN = NULL,
  departures.FUN = NULL,
  arrivals.FUN = NULL,
  nwupdate.FUN = nwupdate.net,
  prevalence.FUN = prevalence.net,
  verbose.FUN = verbose.net,
  module.order = NULL,
  save.nwstats = TRUE,
  nwstats.formula = "formation",
  save.transmat = TRUE,
  save.network,
  save.run = FALSE,
  save.cumulative.edgelist = FALSE,
  save.other,
  verbose = TRUE,
  verbose.int = 1,
  skip.check = FALSE,
  raw.output = FALSE,
  tergmLite.track.duration = FALSE,
  set.control.ergm = control.simulate.formula(MCMC.burnin = 2e+05),
  set.control.tergm = control.simulate.formula.tergm(MCMC.maxchanges = Inf),
  save.diss.stats = TRUE,
  dat.updates = NULL,
  ...
)
}
\arguments{
\item{type}{Disease type to be modeled, with the choice of \code{"SI"} for Susceptible-Infected
diseases, \code{"SIR"} for Susceptible-Infected-Recovered diseases, and \code{"SIS"} for
Susceptible-Infected-Susceptible diseases.}

\item{nsteps}{Number of time steps to simulate the model over. This must be a positive integer
that is equal to the final step of a simulation. If a simulation is restarted with \code{start}
argument, this number must be at least one greater than that argument's value.}

\item{start}{For models with network resimulation, time point to start up the simulation. For
restarted simulations, this must be one greater than the final time step in the prior
simulation and must be less than the value in \code{nsteps}.}

\item{nsims}{The total number of disease simulations.}

\item{ncores}{Number of processor cores to run multiple simulations on, using the \code{foreach} and
\code{doParallel} implementations.}

\item{resimulate.network}{If \code{TRUE}, resimulate the network at each time step. This is required
when the epidemic or demographic processes impact the network structure (e.g., vital
dynamics).}

\item{tergmLite}{Logical indicating usage of either \code{tergm} (\code{tergmLite = FALSE}), or \code{tergmLite}
(\code{tergmLite = TRUE}). Default of \code{FALSE}.}

\item{cumulative.edgelist}{If \code{TRUE}, calculates a cumulative edgelist within the network
simulation module. This is used when tergmLite is used and the entire networkDynamic
object is not used.}

\item{truncate.el.cuml}{Number of time steps of the cumulative edgelist to retain. See help for
\code{\link{update_cumulative_edgelist}} for options.}

\item{attr.rules}{A list containing the  rules for setting the attributes of incoming nodes, with
one list element per attribute to be set (see details below).}

\item{epi.by}{A character vector of length 1 containing a nodal attribute for which subgroup
stratified prevalence summary statistics are calculated. This nodal attribute must be
contained in the network model formation formula, otherwise it is ignored.}

\item{initialize.FUN}{Module to initialize the model at time 1, with the default function of
\code{\link{initialize.net}}.}

\item{resim_nets.FUN}{Module to resimulate the network at each time step, with the default
function of \code{\link{resim_nets}}.}

\item{summary_nets.FUN}{Module to extract summary statistics of the network
at each time step, with the default function of \code{\link{summary_nets}}.}

\item{infection.FUN}{Module to simulate disease infection, with the default function of
\code{\link{infection.net}}.}

\item{recovery.FUN}{Module to simulate disease recovery, with the default function of
\code{\link{recovery.net}}.}

\item{departures.FUN}{Module to simulate departure or exit, with the default function of
\code{\link{departures.net}}.}

\item{arrivals.FUN}{Module to simulate arrivals or entries, with the default function of
\code{\link{arrivals.net}}.}

\item{nwupdate.FUN}{Module to handle updating of network structure and nodal attributes due to
exogenous epidemic model processes, with the default function of \code{\link{nwupdate.net}}.}

\item{prevalence.FUN}{Module to calculate disease prevalence at each time step, with the default
function of \code{\link{prevalence.net}}.}

\item{verbose.FUN}{Module to print simulation progress to screen, with the default function of
\code{\link{verbose.net}}.}

\item{module.order}{A character vector of module names that lists modules in the order in which
they should be evaluated within each time step. If \code{NULL}, the modules will be evaluated
as follows: first any new modules supplied through \code{...} in the order in which they are
listed, then the built-in modules in the order in which they are listed as arguments
above. \code{initialize.FUN} will always be run first and \code{verbose.FUN} will always be run last.}

\item{save.nwstats}{If \code{TRUE}, save network statistics in a data frame. The statistics to be
saved are specified in the \code{nwstats.formula} argument.}

\item{nwstats.formula}{A right-hand sided ERGM formula that includes network statistics of
interest, with the default to the formation formula terms. Supports \code{\link{multilayer}}
specification.}

\item{save.transmat}{If \code{TRUE}, complete transmission matrix is saved at simulation end.}

\item{save.network}{If \code{TRUE}, networkDynamic or networkLite object is saved at simulation end.}

\item{save.run}{If \code{TRUE}, the \code{run} sublist of \code{dat} is saved, allowing a
simulation to restart from this output.}

\item{save.cumulative.edgelist}{If \code{TRUE}, the \code{cumulative.edgelist} is saved at simulation end.}

\item{save.other}{A character vector of elements on the \code{netsim_dat} main data list to save out
after each simulation. One example for base models is the attribute list, \code{"attr"}, at
the final time step.}

\item{verbose}{If \code{TRUE}, print model progress to the console.}

\item{verbose.int}{Time step interval for printing progress to console, where \code{0} prints
completion status of entire simulation and positive integer \code{x} prints progress after
every \code{x} time steps. The default is to print progress after each time step.}

\item{skip.check}{If \code{TRUE}, skips the default error checking for the structure and consistency
of the parameter values, initial conditions, and control settings before running base
epidemic models. Setting this to \code{FALSE} is recommended when running models with new
modules specified.}

\item{raw.output}{If \code{TRUE}, \code{netsim} will output a list of raw data (one per simulation) instead
of a cleaned and formatted \code{netsim} object.}

\item{tergmLite.track.duration}{If \code{TRUE}, track duration information for models in \code{tergmLite}
simulations. Supports \code{\link{multilayer}} specification.}

\item{set.control.ergm}{Control arguments passed to \code{ergm::simulate_formula.network}. In \code{netsim},
this is only used when initializing the network with \code{edapprox = TRUE}. All other
simulations in \code{netsim} use \code{tergm}. Supports \code{\link{multilayer}} specification.}

\item{set.control.tergm}{Control arguments passed to \code{tergm::simulate_formula.network}. See the
help file for \code{\link{netdx}} for details and examples on specifying this parameter. Supports
\code{\link{multilayer}} specification.}

\item{save.diss.stats}{If \code{TRUE}, \code{netsim} will compute and save duration and dissolution
statistics for plotting and printing, provided \code{save.network} is \code{TRUE}, \code{tergmLite} is
\code{FALSE}, and the dissolution model is homogeneous.}

\item{dat.updates}{Either \code{NULL}, a single function taking arguments \code{dat},
\code{at}, and \code{network}, or a list of functions of length one greater
than the number of networks being simulated, with each function in
the list taking arguments \code{dat} and \code{at}. Here \code{dat} is the main
\code{netsim_dat} class object, \code{at} is the current timestep, and \code{network}
is an index indicating the current position within the sequence of
network (re)simulations on each time step. If a single function is
passed, it will be called before the first network is simulated and
after each network is simulated, with \code{network = 0L} before the first
network is simulated and with \code{network = i} after the \code{i}th network
is simulated. If a list of functions is passed, the first function
will be called before the first network is simulated, and the
\code{i + 1}th function will be called after the \code{i}th network is
simulated. (Note that \code{at = 0L} is used for initial cross-sectional
simulations in \code{\link{sim_nets_t1}}.) The function(s) should return the
\code{netsim_dat} object with any updates needed to correctly represent the
network states for calls to \code{simulate} and/or \code{summary}. This can be
useful if nodal attributes appearing in one network model depend on
nodal degrees in a different network.}

\item{...}{Additional control settings passed to model.}
}
\value{
An EpiModel object of class \code{control.net}.
}
\description{
Sets the controls for stochastic network models simulated with
\code{\link{netsim}}.
}
\details{
\code{control.net} sets the required control settings for any network model solved with the \code{\link{netsim}}
function. Controls are required for both base model types and when passing original process
modules. For an overview of control settings for base models, consult the
\href{https://epimodel.github.io/sismid/}{Network Modeling for Epidemics} course materials For
all base models, the \code{type} argument is a necessary parameter and it has no default.
}
\section{The attr.rules Argument}{

The \code{attr.rules} parameter is used to specify the rules for how nodal attribute values for
incoming nodes should be set. These rules are only necessary for models in which there are
incoming nodes (i.e., arrivals). There are three rules available for each attribute value:
\itemize{
\item \strong{\code{current}}: new nodes will be assigned this attribute in proportion to the distribution of
that attribute among existing nodes at that current time step.
\item \strong{\code{t1}}: new nodes will be assigned this attribute in proportion to the distribution of that
attribute among nodes at time 1 (that is, the proportions set in the original network for
\code{\link{netest}}).
\item \strong{\code{Value}}: all new nodes will be assigned this specific value, with no variation.
For example, the rules list \code{attr.rules = list(race = "t1", sex = "current", status = "s")}
specifies how the race, sex, and status attributes should be set for incoming nodes. By default,
the rule is \code{"current"} for all attributes except status, in which case it is \code{"s"} (that is, all
incoming nodes are susceptible).
}
}

\section{Checkpointing Simulations}{

\code{netsim} has a built-in checkpoint system to prevent losing computation work if the function is
interrupted (SIGINT, power loss, time limit exceeded on a computation cluster). When enabled,
each simulation will be saved every \code{.checkpoint.steps} time steps. Then, if a checkpoint enabled
simulation is launched again with \code{netsim}, it will restart at the last checkpoint available in
the saved data.

To enable the checkpoint capabilities of \code{netsim}, two control arguments have to be set:
\code{.checkpoint.steps}, which is a positive number of time steps to be run between each file save;
and \code{.checkpoint.dir}, which is the path to a directory to save the checkpointed data. If
\code{.checkpoint.dir} directory does not exist, \code{netsim} will attempt to create it on the first
checkpoint save. With these two controls defined, one can simply re-run \code{netsim} with the same
arguments to restart a set of simulations that were interrupted.

Simulations are checkpointed individually: for example, if 3 simulations are run on a single core,
the first 2 are finished, then the interruption occurs during the third, \code{netsim} will only
restart the third one from the last checkpoint.

A \code{.checkpoint.compress} argument can be set to overwrite the \code{compress} argument in \code{saveRDS}
used to save the checkpointed data. The current default for \code{saveRDS} is \code{gunzip (gz)}, which
provides fast compression that usually works well on \code{netsim} objects.

By default, if \code{netsim} reaches the end of all simulations, the checkpoint data directory and its
content are removed before returning the \code{netsim} object. The \code{.checkpoint.keep} argument can be
set to \code{TRUE} to prevent this removal to inspect the raw simulation objects.
}

\section{New Modules}{

Base network models use a set of module functions that specify how the individual nodes in the
network are subjected to infection, recovery, demographics, and other processes. Core modules are
those listed in the \code{.FUN} arguments. For each module, there is a default function used in
the simulation. The default infection module, for example, is contained in the \code{\link{infection.net}}
function.

For original models, one may substitute replacement module functions for any of the default
functions. New modules may be added to the workflow at each time step by passing a module function
via the \code{...} argument. Consult the
\href{https://epimodel.github.io/sismid/9_extending/mod9-Intro.html}{Extending EpiModel}
section of the Network Modeling for Epidemics course materials.
One may remove existing modules, such as \code{arrivals.FUN}, from the workflow by setting
the parameter value for that argument to \code{NULL}.
}

\section{End Horizon}{

\code{netsim} implements an "End Horizon" mechanism, where a set of modules are
removed from the simulation at a specific time step. This is enabled through
the \code{end.horizon} parameter to \code{control.net}.

This parameter must receive a \code{list} with fields \code{at}, the time step at which
the end horizon occurs, and \code{modules}, a character vector with the names of
the modules to remove. (e.g `list(at = 208, modules = c("arrivals.FUN",
"infections.FUN")))
}

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