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 NA
s 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.netsim
dissolution_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 http://statnet.shinyapps.io/epinet/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 http://github.com/statnet/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/statnet/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 master 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:
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://statnet.org/EpiModel/vignette/NewDCMs.html
Moved the package vignettes external to the package to reduce package size and build time. They are now available at the EpiModel homepage at: http://statnet.org/trac/wiki/EpiModel
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 at http://statnet.org/trac/wiki/EpiModel to get started.