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 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.