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netsim, now
support multi-layer networks. These are networks with a common common
node set but different edge set (e.g., home-based and community-based
contact layers). An example implementation can be found at the EpiModel
Gallery.get_cumulative_degree function with an interface
similar to get_partners. This function helps look up
cumulative degree over a time period (e.g., number of partners over the
past year) for a specified set of nodes.get_network and set_network
functions created for more consistent access to the network objects
within netsim_dat class objects.update_cumulative_edgelist is now called
unconditionally and governed by the cumulative.edgelist
control.control.net setting
cumulative.edgelist == FALSE causes an error.netsim data objects now properly classed as
netsim_dat.icm data objects now properly classed as
icm_dat, consistent with netsim objects.ergm objects to
address backwards incompatible data structures for ergm
package v4.5.0.ergm.ego package estimation is now
supported. This is accomplished by passing an egor class
object instead of a network class object as the
nw argument to netest.end.horizon control setting to
control.net. This allows one to remove a set of modules
within network epidemic models at a given time step. This end horizon is
needed for cost-effectiveness analyses and related models that require
tracking person time in the absence of disease transmision..traceback.on.error and
.dump.frames.on.error controls to print the
traceback on error even on multicore settings and
dump.frames for remote debugging.get_attr_history would crash when
attribute history of posit_ids argument was
integer(0).saveout.net:
missing elements on some simulations now produce a warning instead of an
error. Additionally, elements passed to save.other that are
not present in the final object are skipped silently instead of
producing an error.networkLite class (sparse
network representations needed for epidemic modeling) from EpiModel and
placed into its own package on CRAN:
https://CRAN.R-project.org/package=networkLite.cumulative.edgelist and
truncate.el.cuml controls get default values in
netsim_validate_control (FALSE and
0). Better messages and warnings are sent when trying to
access an uncreated cumulative edgelist.netdx now calculates additional summary statistics to
quantify variability within and across simulations for model
diagnostics. See the help page for the associated print function for
futher details: help("print.netdx").get_transmat adds a deduplicate argument
to randomly select one transmitting act in the case that multiple
potential transmissions occur within a time step to the newly infected
person.get_sims not properly subsetting
el.cuml and _last_unique_id.netsim.tracker.net module was removed as an optional
extension module, and this functionality is now default for all network
models (built-in and extension models). See the Working with
Attributes and Summary Statistics Vignette for more details.transmat) storage by
using padded_vector instead of repeated rbind
calls. The result of get_transmat(netsim_object) is
unchanged.unflatten_params in
generate_random_params instead of bespoke code.netdx and netsim
objects.use_scenario function. See the Working with Model
Parameters vignette for details.trim_netest function has been added to reduce
netest object sizes in common use cases.networkLite class now supports some additional
functionalities.netsim with
tergmLite = FALSE now use tergm simulation to
produce a networkDynamic class object, similar to the
duration > 1 time step case.netdx now supports heterogeneous dissolution model
diagnostics. See the example in help("netdx").plot.netsim now supports
type = "duration","dissolution" for homogeneous
(“edges-only”) dissolution models.param.net via a data.frame. See the
Working with Model Parameters vignette for
details.fuzzynodematch was added, to support
modeling of more generalized notions of homophily.help("control.net).absdiffby and
absdiffnodemix are now usable again (due to enabling symbol
search).sim_nets_t1 when
initializing the network with the non-nested edges dissolution
approximation approach in netest.network class internals have been removed
from net.utils.R to make the code function properly with
networkLites.update_dissolution now correctly handles duration 1
models.get_edgelists and get_cumulative_edgelists
now throw informative errors when the network refers to
non-existing networks. get_partners and
get_cumulative_edgelists_df will throw errors as well as
they call those functions internally.netsim with
ncores > 1updater.net module was removed as an optional
module but its functionalities are now the default behavior for all
network models (built-in and custom).param.updater.list and
control.updater.list in param.net and
control.net respectively were renamed
.param.updater.list and .control.updater.list.
The leading dot indicates that these are built-in EpiModel elements not
to be confused with the user-defined ones.nodefactor term have been
deprecated.stergm controls have been deprecated in favor of
tergm controls.ergm and tergm simulation, requiring control
arguments of class control.simulate.formula and
control.simulate.formula.tergm.ndtv is added to “Suggests” (again) and
plot.transmat now accepts the
transmissionTimeline in the style argument
(again).netest and netdx now have default control
arguments following R’s default argument mechanism.netsim object
fields produced via the save.other mechanism.updater.net allowing it to
update the model controls as well as the parameters. See the vignette,
“Working with model parameters.”netsim in the case with a model with an “end horizon” (when
the network is not resimulated at the end of the time series).print.netsim,
print.param.net, and print.control.net.all.equal in unit tests as requested by
CRAN.set_attr for posit_ids to return
unchanged dat object.get_partners newly introduced in EpiModel v2.2.0:
max.age is renamed to truncate for consistency
with the other cumulative edgelist functions; only.active
is renamed only.active.nodes to clarify that this argument
subsets by nodes and not by partnerships.create_dat_object helper function was added to
standardize the creation of the core dat object within
initialize.net.netsim simulations is now
stored in the dat object and accessible with
get_current_timestep. This eliminates the need to
explicitly pass at as a function argument, although that is
still allowed.get_param_set function that extracts
from a netsim object the set of parameters used by each
simulation. See the help page: help("get_param_set").netsim simulation. See the vignette, “Working
with attributes and summary statistics.”netsim simulation. This allows users
to avoid updating the prevalence.net module. See the
vignette, “Working with attributes and summary statistics.”netsim
simulations (i.e., time-varying parameters). See the vignette, “Working
with model parameters.”plot on a netsim object, the
arguments in the ellipsis (...) are now correctly passed to
the base::plot call.group attribute,
netsim will now output a more explicit error if the values
used are not only 1 and 2.netdx when edapprox == FALSE that were causing
the plotting functions to misbehave.set_transmat function removing
the assumption that dat$stats$transmat was to exist only if
at != 2 (thanks to @thednainus).netdx and netsim.netsim modules with
type == NULL, some built-in modules no longer stop because
they required type to be a string.Error, Warning or
Message in netsim printing twice.saveout.net, resulting in the unique ids to start a 1 again
when restarting a model from a previous simulation.statnet organization on Github.netsim class objects
(epidemic simulations) are now available when tergmLite is
used. Previously these network statistics were only available when
tergmLite = FALSE but updates to the
networkLite class in tergmLite made this
possible. These network stats are output with save.nwstats
and nwstats.formula arguments in
control.net.help("param.net").initialize.net, so that the user-facing code in that
function is more readable, and the more complex code is put in
sim_nets_t1.duration = 1 in
dissolution_coefs).update_params function to add new parameters
to an existing list of network parameters specified in
param.net. This aids in workflows that distinguish fixed
parameters versus varying parameters that may change across scenarios or
simulations.generate_random_params for examples.append_core_attr function in the initialization and
arrival modules in any extension models. This includes a standardized
implementation of persistent, unique IDs as an attribute that remains
constant for nodes even with open population models.dt < 1, fix NA
output for any .flow variables.netdx, with updated numerical summaries in
print.netdx and visuals in plot.netdx. Because
relational ages are left-censored for any edges that existed at time
zero, this led to a misleading diagnostic that ages were lower than the
targeted durations. Imputation of a start time for those edges was
added, with the option in plot.netdx to visualize with
imputed start times (default = TRUE) or not.statnet.common::trim_env(), used in
netest.netest “edges dissolution
approximation” for efficient estimation of a temporal ERGM via a
cross-sectional ERGM estimation with adjustment of formation model
coefficients (see netest help page). This new approach
further reduces bias in the approximation method, plus now allows for
non-nested dissolution models (i.e., dissolution formula does not need
to be a subset of the formation formula).netsim so
that epidemic modules with errors or warnings are clearly identified in
the console.save.transmat
in control.net independently of using tergmLite methods
(previously use of tergmLite did not allow for saving these data).infstat parameter to the internal
discord_edgelist function used in the infection module, to
allow for arbitrary specification of which disease statuses are
considered infectious for the purpose of dyad discordance.plot.netsim with
type = 'network' with vertex.cex
parameter.plot.netdx when plot legend set to
FALSE.print.netsim that does not error when
displaying new epidemic modules for extension models.netsim for networks with duration of 1 (i.e., one-time
contacts handled with cross-sectional ERGMs).dissolution_coefs.netdx if a static ERGM
is passed.tergmLite package
(to be released).netsim
object with print.netsim(x, formation.stats = TRUE).plot.netsim default colors when number of
variables exceeds 3.dissolution_coefs documentation.skip.dissolution argument to netdx
to skip dissolution diagnostics for computational efficiency.netsim runs.netdx on a cross-sectional ergm.get_sims and unit tests in
plot.transmat found during CRAN submission for v1.7.1.get_args and
apportion_lr, ported over from EpiModelHIV.absdiffby and
absdiffnodemix, ported over from EpiModelHIV.as.data.frame.dcm when dt
control setting < 1.keep.tnetwork parameter to netdx to
allow for retaining the full networkDynamic object during
dynamic network simulations. Relatedly, add support for
get_network to extract those networks from
netdx objects.as.data.frame function
for processing model output for all three model classes (DCM, ICM, and
Network Models) to generate a stacked data frame of all simulations
(instead of row means across simulations). This is a breaking
change that may require updating old code.as.data.frame.netdx function extracts the timed
edgelists directly from a netdx object.get_nwstats function now extracts data frames of
network statistics from both netdx and netsim
objects.get_sims.plot.netdx and plot.netsim.ncores argument in
netdx to prevent over parallelization of simulations.netdx objects.act.rate.m2
for network models in param.net, as this is an unused
parameter for built-in models.b.rate; it is
now a.rate. Inputs of a b.rate parameter yield
a message and will automatically set a.rate to the
b.rate value. This is a breaking change that may
require updating old code.netdx (when dynamic is set to
FALSE) to smoothed rolling averages instead of the full
MCMC trace. The trace plots may be turned back on with
sim.lines = TRUE.netdx now includes a new argument,
sequential, for static diagnostics that mirrors the same
argument from ergm::simulate.ergm to simulate from MCMC
chains based on previous draws versus new draws.mutate_epi output when new variable is a
constant.ggplot2 from depend to import.identical
function causing some to fail under alternative BLAS/LAPACK
implementations.as.data.frame methods for netsim and
icm classes now allow creation of a single data frame with
epidemic outcomes across multiple simulations, where previous only
single individual simulations would be output. This is specified with
the sim = "all" parameter when out = "vals".
See the help page for examples. This “tidy” data format allows for
easier integration with external plotting and analysis approaches,
including ggplot2.geom_bands is a new “geom” for use by
ggplot2 to facilitate plotting of simulation intervals
given a specified lower and upper quantile set. Examples of plotting ICM
simulations are provided, and the same principle applies for network
models. As a result of this, ggplot2 was added as a
depend.truncate_sims is a new utility function that takes
truncates the time series of a netsim or icm
class object at a specified time step. This truncation will remove all
epidemic output before that time step, and reset the control settings to
start at that time step. This is useful in our modeling workflows when
we need to remove a pre-intervention burnin period from the model
simulations.init.net allows you to pass in a vector of
backwards-looking infection times for those initally infected at t_1
through the infTime.vector parameter. Combined with the
status.vector parameter, this provides users maximal
control over who is infected and for how long as initial
conditions.discord_edgelist function.status.rand argument for
init.net and init.icm that allowed users to
specify a random number of initially infected. Support for this got too
complex for a little (or never) used argument, and users interested in
randomly setting the initial number infected may control this more
flexibly with the status.vector parameter.grid argument to plot functions to overlay a grid
on line plots.plot.netdx examples in help file.verbose default for network models to
TRUE (reverts change in v1.3.0 specifically for network
models).leg argument name (to add default legends to
plots) to legend. Note this is backwards-incompatible
because of fuzzy matching with other function arguments starting
leg; prior model code must be updated.control.dcm, nsteps may now be a vector
of time steps or, as before, an integer containing the number of time
steps within a DCM simulation. For example,
control.dcm(..., nsteps = seq(1980, 2015, 1/12), ...) for
solve for monthly outputs from a range of dates from 1980 to 2015.mutate_epi for adding new variables to a epidemic
simulation object now works for all three model classes.param, init, and
control functions are now dual-classed as lists as well as
their native classes.new.mod into control.dcm,
printing the control.dcm object no longer yields a warning
and instead prints the function name.transco to
use the base adjustcolor function.NA for the final value, creating issues with analyzing
those data. Those NAs are replaced with the penultimate
value of that vector.dcm, icm, and
netsim objects to list “Variables” together instead of
dividing them into compartments, flows, and other.popfrac default for plotting
dcm, icm, and netsim objects to
FALSE. This avoids any problems when prevalences are
already stored within the model simulation.verbose default for control functions to
FALSE.print.netsim when sims is
mean, min, or `max.print.coefdiss output.plot.netsimdissolution_coefs.mutate_epi function inspired by the
dplyr package, to add post-hoc summary statistic
calculations to completed network simulations. See the function help
file for examples.get_degree function that returns a
vector of current network degree for each person in a network.as.phylo.transmat to fix issues with vertex
exit times and to now accept multiple seed vertices if multiple seeds
are detected, returning a list of phylo objects of class
multiPhylo following the convention of
ape::read.tree.netsim. This only supports single-node
frameworks currently, using the doParallel package. Run
models in parallel by using the ncores parameter in
control.net.as.phylo.transmat function to
construct the phylo tree with all network vertices as phylo-tips and all
transmissions as phylo nodes.plot.netsim now correctly functions for diagnostic
plots (type = "formation") when summary statistics contain
variable names with numeric values as suffixes.edapprox = FALSE in
the netest function).netest when models were fit with the full STERGM
method.depend parameter to TRUE
in control.net when user passes in any new birth or death
modules.ape package and a transmission
timeline from the ndtv package. See the help files for the
as.phylo.transmat and plot.transmat
functions.epiweb(class = "net"). It is also hosted online at
shinyapps.get_sims function is used to extract individual
simulations from larger netsim objects. This function has
been updated to include a var argument that allows for
automatic calculation of which simulation is closest to the mean across
all simulations for extraction.as.data.frame
method for icm and netsim classes. This will
provide a data frame of output corresponding to defined quantiles across
all simulations contained within a model object.plot.netsim in cases where there are NA values
in the epidemiological output.control.net when
type is missing, and automatically sets type
to "SI". This will impact extensions to EpiModel in the
case when the default transmission module is replaced.netdx on calculating summary statistics
from models with multiple structural zeros for target statistics.status.rand, which controls
whether the number initially infected in stochastic epidemic models, to
FALSE. This will ensure that exactly the number specified
in init.icm and init.net are matched in each
simulation.netsim_parallel function from the
package. See the EpiModelHPC extension package at https://github.com/EpiModel/EpiModelHPC for running
network simulations in parallel.check_bip_degdist now uses more tolerant checks of
equality when comparing bipartite mode statistics.dcm function.netest to improve performance of fitting models.births.FUN, from the dynamic workflow by setting
the argument value for that module to NULL in the
control.net inputs.calc_eql function now returns test statistics
invisibly.plot.netsim is now a separate method for epidemic plots (it
was previously a function call to plot.icm), with function
arguments and default settings more consistent across plotting
functions. There may be minor backwards incompatibility for some
epidemic plots. Network statistic plots in plot.netdx and
plot.netsim now use the same methods and share the same
defaults. The defaults for these plots will be to plot smoothed quantile
bands (the IQR) and means of simulations without the individual
simulation lines. Any individual elements may be toggled on or off as
before.param.icm and
param.net classes.dissolution argument to netest.
This argument specified the right- hand sided dissolution formula for
temporal ERGMs. It was removed because this formula was already
specified in the dissolution_coefs function, the output of
which is passed to netest, thereby removing the
duplication.as.data.frame methods for stochastic models remove
NA from individual simulations when calculating row
means.verbose parameter in netest now
correctly controls the model fitting output level in the underlying
ergm and stergm functions.merge.netsim now correctly checks elements of two
objects to be merged when the classes of those elements may be of length
greater than 1.... argument to epiweb to pass
additional arguments to shiny::runApp.graphics, grDevices,
stats, and utils packages as required by
CRAN.netsim_parallel
function has been deprecated. This functionality has been replaced with
model simulation functions within the EpiModelHPC extension
package: https://github.com/EpiModel/EpiModelHPCepiweb.calc_eql, calculates whether a model of
any class in EpiModel has reached an equilibrium state over a defined
time series. Equilibrium is defined as the absolute value of the
difference of the maximum prevalence and minimum prevalence over a
specified time series falling below a specified threshold. For
stochastic models, these values are calcualted based on the mean of the
individual time series simulations.netest now includes a new argument,
nonconv.error, that will send the function to an error
state if the ERGM did not coverge after the specified number of
interations. The default is to allow for a nonconverged model fit to be
returned. Requiring an error may be helpful when running a number of
models in batch mode.dcm function, there was an error in the calculation of
flows (e.g., disease incidence or number of deaths per unit time) when
the models were integrated with methods other than the “Euler” solution.
Flows are now calculated correctly for all numerical integration methods
supported via the deSolve package.netest will now check to ensure that the formation and
dissolution models are in allignment (terms specified in the same order)
and that dissolution model is of proper forms (see v1.1.4 notes).dissolution_coefs
for examples.use.pids in control.net.
See help(“persistent.ids”) in the networkDynamic package
for more background.births.net module that set the default
entrTime and exitTime attributes twice for
bipartite models (#205).xlab
and ylab (#206).get_sims extraction now outputs correct data when
object contains single simulation.skip.check argument for control.net is
even more flexible, to allow for passing different class elements into
netsim with original models.param.error argument for merge.netsim
that allows bypassing the stop error if the parameters and control
settings from the two merged objects are not identical.control.net has new module.order argument
to provide control of the order in which modules are evaluated within
each time step. The default ordering is maintained as explained in the
updated help file.netsim_parallel now returns the correct object if used
for single simulations or on single cores.plot.icm removes NA values from the data when
calculating ylim and the quantile bands.netest now implements an improved “Edges Dissolution
Approximation” via the edapprox argument.control.dcm option dede, which
if true allows for delayed differential equations to be passed into a
new model solved with dcm.netdx to simulate static diagnostics
from an ERGM, rather than the temporal diagnostics (still the default).
This will help better diagnose poor dynamic model fit when using the
edges dissolution approximation (#175).netdx, with the
method parameter, to plot boxplots of the simulations
against the target statistics. The default is still the line plots
(#191).netdx objects, similar to epidemic data plots: mean lines
and quantile bands. Additional arguments added to allow toggling of
these along with individual simulation lines and target lines.netdx is updated, along with a new
statistic for the percent deviation between the simulation means and
target statistics (#192).print.netsim (#183).get_sims will subset and extract entire
simulations from netsim objects with multiple simulations.
A vector of simulation numbers may be specified, or if set as “mean”,
the simulation with the infected prevalence closest to the means across
all simulations will be chosen.save.other parameter in control.net may now be
merged with merge.netsim (#185).plot for ICMs and network
models when the y argument is specified (#188).deSolve moved from import to depend
(#194).netdx, for the
proportion of edges that dissolve per time step, as another diagnostic
for the dissolution model (#53).plot.netsim now allow specifying
"mean", "min", or "max" to plot
the network at with the most average, maximum, and minumum disease
prevalence at the specified time step (#73).param.net function has been updated
with details (#65).param.sens, that allows
bypassing the default behavior of evaluating parameters with length
greater than 1 as sensitivity analyses. This should be used for
single-run models if passing in parameters with arbitrary form.plot.netsim fixed (#164).edges_correct,
now runs for any dependent network simulations, not just if built-in
vital dynamics modules are called (#141).verbose.icm
function (#71).save.other control setting in control.net are
now printed as output in print.netsim (#174).get_network, get_transmat, and
get_nwstats) which extract the network objects,
transmission matrices, and data frame of network statistics from a
completed netsim simulation. These functions also support
extraction of network model simulations with multiple networks (see API
note).netsim objects now has an
argument, network, for plotting network statistics and static networks
(type = "formation" and "network",
respectively) in simulations with multiple networks.mean.smooth. If TRUE, this uses a lowess
smoother on the outcome variables of interest. This is helpful in
visualization of low-count outcomes like disease incidence.netsim_parallel function. Note that this is experimental
and has not been tested extensively across platforms, so bug reports are
welcome. Two parallel methods are supported: doParallel for
multiple cores on a single node, and doMPI for multiple
cores across multiple nodes. The latter requires an MPI installation on
a linux-based cluster.netdx also accepts a new
ncores argument, which will run the diagnostic simulations
and calculations on those simulations in parallel on a specified number
of cores (single node only).skip.check, for the control settings
in both ICM and network model classes, which overrides the default error
checking of parameters, initial conditions, and control settings. This
should only be used for original models with new modules that may
unnecessarily trigger a check error.save.other, for the control settings
in network models, which is a character vector of other elements from
the main data list, dat, to save out in the
simulation.start, for the control settings in
network models, which is a starting time step to resume simulations. In
this case, the x argument in netsim is a
previously saved netsim object rather than a
netest object. The start argument should be
one integer higher than the nsteps in that earlier
netsim object. The nsteps argument should now
be the final steps for the simulation. Note that this requires
specifying save.other = "attr" in the control settings, as
well as saving the networks.netdx diagnostic simulations
for computationally intensive parts of the simulations.netest now provides an
output argument. When using the edges dissolution approximation
(edapprox = TRUE), one may set output to "sim"
to save a static simulation network instead of the ergm
object as an element of the netest output. This is mainly
for file size efficiency.(0, 1, 2) to character ("s", "i", "r").
This changes little when running the integrated models, and has greater
implications for the API when editing modules. But one change for
integrated models is that the status vector passed into the initial
conditions functions must now be in this new format. This also impacts
the expansion of EpiModel for original models.zeromarg argument has been removed from
plot.netsim for static network plots
(type = "network") to reduce potential issues with setting
default margins on plots. Now they must explicitly be set with standard
par options.all to dat to prevent function
name conflicts. Additionally, all summary output is now stored within
dat$epi, whereas the previous location was
all$out.edges_correct and
verbose.net. The former performs the adjustment to the
edges coefficient for network models with population size changes, in
order to preserve the mean degree; for mass action epidemic models, for
example, one would not want this adjustment, so the module should be set
to NULL in control.net. The latter performs the printing of
simulation results to the console. Both functions are now listed in the
modules help file accessed by: help(modules.net).param,
init, and control functions altogether for
original ICM and network models, because the definition of new and
replacement modules occurs within the control functions themselves. The
existing control functions should be used as a template if one is
considering replacing these parameterization functions.control.net) by setting the argument for
that module to NULL. This may be replaced in the future by
a user-defined ordered vector of modules.x argument in netsim may now be a list of
netest objects. This would be used only if supplying new
simulation modules that know how to process that data structure. The
motivation for this is to allow original models with multiple networks
simulated (e.g., a main partnership network and a casual partnership
network).epiweb function). These apps now benefit
from the more stable parameterization functions.print method for the param.net
class to handle parameters that are lists or data frames.merge.netsim now ignores any differences in the
environment of the nwstats.formula control, previously
preventing proper merging of some network model simulations.Model parameterization for all model classes has been substantially revised to improve organization and ability for expansion. Whereas previous models required input of parameters directly into the main functions (now: dcm, icm, and netsim), now the parameters are input into three parameter-processing functions: param, init, and control. The param function sets the core epidemic parameters, the init function sets the initial conditions, and the control function specifies other model settings. These functions are class-specific, so each function has a .dcm, .icm, or .net suffix.
Modeling functions have been renamed for clarity and consistency:
dcm is now used for deterministic compartmental models (replaces epiDCM)
icm is now used for stochastic individual contact models (replaces epiICM)
netest is now used for network model estimation (replaces epiNet.est)
netsim is now used for network model simulation (replaces epiNet.simTrans)
Network models with independence between epidemic/demographic processes and network structures (independent models) were previously first simulated with epiNet.simNet, and then those pre-simulated networks were input to epiNet.simTrans. Now the network model simulation is all handled within the simulation function, netsim.
Network model diagnostics have been moved from within the network estimation process (netest) to their own function: netdx. The parameter names for running, printing, and plotting the results of these diagnostics have been updated for consistency. See ?netdx and related functions.
Internal model functions have been significantly revised to improve efficiency.
The dcm function can handle model functions, parameter sets, and initial conditions of arbitrary complexity. See the HTML vignette on this topic at: http://www.epimodel.org/
Moved the package vignettes external to the package to reduce package size and build time.
The EpiModel package provides functions for building, solving, and plotting mathematical models of infectious disease.
See the main package help function ?EpiModel-package, and the EpiModel tutorials online.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.