Description Usage Arguments Details The attr.rules Argument New Modules See Also
Sets the controls for stochastic network models simulated with
netsim
.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 | 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(),
...
)
|
type |
Disease type to be modeled, with the choice of |
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
simulation is restarted with |
start |
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 |
nsims |
The total number of disease simulations. |
ncores |
Number of processor cores to run multiple simulations
on, using the |
resimulate.network |
If |
tergmLite |
Logical indicating usage of either |
cumulative.edgelist |
If |
truncate.el.cuml |
Number of time steps of the cumulative edgelist to
retain. See help file for |
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). |
epi.by |
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. |
initialize.FUN |
Module to initialize the model at time 1, with the
default function of |
resim_nets.FUN |
Module to resimulate the network at each time step,
with the default function of |
infection.FUN |
Module to simulate disease infection, with the default
function of |
recovery.FUN |
Module to simulate disease recovery, with the default
function of |
departures.FUN |
Module to simulate departure or exit, with the default
function of |
arrivals.FUN |
Module to simulate arrivals or entries, with the default
function of |
nwupdate.FUN |
Module to handle updating of network structure and nodal
attributes due to exogenous epidemic model processes, with the default
function of |
prevalence.FUN |
Module to calculate disease prevalence at each time
step, with the default function of |
verbose.FUN |
Module to print simulation progress to screen, with the
default function of |
module.order |
A character vector of module names that lists modules the
order in which they should be evaluated within each time step. If
|
save.nwstats |
If |
nwstats.formula |
A right-hand sided ERGM formula that includes network statistics of interest, with the default to the formation formula terms. |
save.transmat |
If |
save.network |
If |
save.other |
A vector of elements on the |
verbose |
If |
verbose.int |
Time step interval for printing progress to console, where
0 prints completion status of entire simulation and positive integer
|
skip.check |
If |
raw.output |
If |
tergmLite.track.duration |
logical; to track duration information
( |
set.control.ergm |
Control arguments passed to |
set.control.stergm |
Control arguments passed to |
... |
Additional control settings passed to model. |
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.
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
.
Use param.net
to specify model parameters and
init.net
to specify the initial conditions. Run the
parameterized model with netsim
.
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