Sets the controls for stochastic network models simulated with
netsim.
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,
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.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.stergm = control.simulate.network(),
...
)Disease type to be modeled, with the choice of "SI" for
Susceptible-Infected diseases, "SIR" for
Susceptible-Infected-Recovered diseases, and "SIS" for
Susceptible-Infected-Susceptible diseases.
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
simulation is restarted with start argument, this number must
be at least one greater than that argument's value.
For models with network resimulation , time point to start up
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 nsteps.
The total number of disease simulations.
Number of processor cores to run multiple simulations
on, using the foreach and doParallel implementations.
If 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).
Logical indicating usage of either tergm
(tergmLite = FALSE), or tergmLite
(tergmLite = TRUE). Default of FALSE.
If 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.
Number of time steps of the cumulative edgelist to
retain. See help file for update_cumulative_edgelist for
options.
A list containing the rules for setting the attributes of incoming nodes, with one list element per attribute to be set (see details below).
A character vector of length 1 containing a nodal attribute for which subgroup epidemic prevalences should be calculated. This nodal attribute must be contained in the network model formation formula, otherwise it is ignored.
Module to initialize the model at time 1, with the
default function of initialize.net.
Module to resimulate the network at each time step,
with the default function of resim_nets.
Module to simulate disease infection, with the default
function of infection.net.
Module to simulate disease recovery, with the default
function of recovery.net.
Module to simulate departure or exit, with the default
function of departures.net.
Module to simulate arrivals or entries, with the default
function of arrivals.net.
Module to handle updating of network structure and nodal
attributes due to exogenous epidemic model processes, with the default
function of nwupdate.net.
Module to calculate disease prevalence at each time
step, with the default function of prevalence.net.
Module to print simulation progress to screen, with the
default function of verbose.net.
A character vector of module names that lists modules the
order in which they should be evaluated within each time step. If
NULL, the modules will be evaluated as follows: first any
new modules supplied through ... in the order in which they are
listed, then the built-in modules in their order of the function
listing. The initialize.FUN will always be run first and the
verbose.FUN always last.
If TRUE, save network statistics in a data frame.
The statistics to be saved are specified in the nwstats.formula
argument.
A right-hand sided ERGM formula that includes network statistics of interest, with the default to the formation formula terms.
If TRUE, complete transmission matrix is saved at
simulation end. Default of TRUE.
If TRUE, networkDynamic/network object is
saved at simulation end. Implicit reset to FALSE if
tergmLite = TRUE (because network history not saved with tL).
A vector of elements on the dat master data list
to save out after each simulation. One example for base models is
the attribute list, "attr", at the final time step.
If TRUE, print model progress to the console.
Time step interval for printing progress to console, where
0 prints completion status of entire simulation and positive integer
x prints progress after each x time steps. The default
is to print progress after each time step.
If 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 FALSE is recommended when running models with new
modules specified.
If TRUE, netsim will output a list of nestsim
data (one per simulation) instead of a formatted netsim object.
logical; to track duration information
(time and lasttoggle) for tergm models in
tergmLite simulations. If TRUE, the time and
lasttoggle values are initialized from the network attributes
of the networks passed to init_tergmLite, with time
defaulting to 0 and lasttoggle defaulting to all
lasttoggle times unspecified (effectively -INT_MAX/2).
Control arguments passed to ergm's
.simulate_formula.network.
Control arguments passed to tergm's
simulate.network. See the help file for netdx
for details and examples on specifying this parameter.
Additional control settings passed to model.
The 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:
"current": new nodes will be assigned this attribute in proportion to the distribution of that attribute among existing nodes at that current time step.
"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 netest).
<Value>: all new nodes will be assigned this specific value, with no variation.
For example, the rules list
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 "current" for all attributes except status,
in which case it is "s" (that is, all incoming nodes are susceptible).
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
.FUN arguments. For each module, there is a default function used in
the simulation. The default infection module, for example, is contained in
the 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 ... argument. Consult
the New Network Models tutorials.
One may remove existing modules, such as arrivals.FUN, from the
workflow by setting the parameter value for that argument to NULL.
control.net sets the required control settings for any network model
solved with the 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
Basic Network Models tutorials.
For all base models, the type argument is a necessary parameter
and it has no default.
Use param.net to specify model parameters and
init.net to specify the initial conditions. Run the
parameterized model with netsim.