NEW FEATURES

• Export a genericget_discordant_edgelist where the attribute used to assess discordance as well as the values for each group can be specified.
• Exportparam.net_from_table andparam.net_to_table helper functions to convert parameter list and parameter data.frames used byparam.net.
• Allow saving the cumulative edge-list at the end of simulation using thesave.cumulative.edgelist control argument.
• Restarting a simulation now only requires savingdat$run. This removes the need to keep track of all the elements required at the end of a simulation. This requires the EpiModel user to put all elements indat$run.
• Exportget_forward_reachable andget_backward_reachable functions that works similarly to but more efficiently thantsna::tPath for multiple nodes and using cumulative edgelists.
• Exportoverwrite_attrs, a helper function to overwrite the attributes of the nodes with adata.frame at the start of the simulation. (see?overwrite_attrs).
• as.data.frame for model classesnetsim andicm now assign theepi.data.frame class in addition todata.frame.
• Add theplot.epi.data.frame method to plotepi.data.frame similar toplot.netsim(type = "epi").
• Exportas.epi.data.frame that assign theepi.data.frame class and validate that the inputdata.frame is correctly formatted.

OTHER

• Speed upraw.records andattr.history withcollections::queue instead ofbase::list.
• Addsave.diss.stats to the checked control values. Prevents undefined values when usingcontrol.net wrappers.
• Moveel.cuml,_last_unique_id, and_last_timestep andattr todat$run and update the tests; part of the restructuring of thedat object.
• Removedat$epi$sim.num(.g2) and replace it withdat$run$num(.g2) (single value). These values keep track of the current size of the network and are only needed during model runs.
• Speed up cumulative edge-list calculation by splitting current and historic edges.
• RemovedeleteAttr function deprecated since EpiModel v2.4.0.
• All function acceptingposit_ids as argument must now pass exclusively a numeric vector. Logical vectors are not accepted anymore as they were making the code heavier and were error prone.
• ergm.ego is now a suggestion to shorten the dependency chain. It needs to be installed separately to usenetest with anegor object.

NEW FEATURES

• Stochastic network models, simulated withnetsim, 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 theEpiModel Gallery.
• Add aget_cumulative_degree function with an interface similar toget_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.
• Genericget_network andset_network functions created for more consistent access to the network objects withinnetsim_dat class objects.

OTHER

• update_cumulative_edgelist is now called unconditionally and governed by thecumulative.edgelist control.
• Attempting to access a cumulative edgelist when thecontrol.net settingcumulative.edgelist == FALSE causes an error.
• netsim data objects now properly classed asnetsim_dat.
• icm data objects now properly classed asicm_dat, consistent withnetsim objects.
• Update network simulation handling ofergm objects to address backwards incompatible data structures forergm package v4.5.0.

NEW FEATURES

• Estimation with theergm.ego package estimation is now supported. This is accomplished by passing anegor class object instead of anetwork class object as thenw argument tonetest.
• Added anend.horizon control setting tocontrol.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.
• Added.traceback.on.error and.dump.frames.on.error controls to print thetraceback on error even on multicore settings anddump.frames for remote debugging.

BUG FIXES

• Fixed an error whereget_attr_history would crash when attribute history ofposit_ids argument wasinteger(0).
• Changed in the internal behavior ofsaveout.net: missing elements on some simulations now produce a warning instead of an error. Additionally, elements passed tosave.other that are not present in the final object are skipped silently instead of producing an error.

OTHER

• Removed functionality for thenetworkLite 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.

NEW FEATURES

• 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 adeduplicate argument to randomly select one transmitting act in the case that multiple potential transmissions occur within a time step to the newly infected person.

BUG FIXES

• Fixget_sims not properly subsettingel.cuml and_last_unique_id.
• Fix parallel memory leak innetsim.
• Rework the network resimulation module to allow for working with observed network data. See thisEpiModel Gallery Example.
• Fix error message for tergmLite/resimulate.network collision

OTHER

• Thetracker.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 theWorking with Attributes and Summary Statistics Vignette for more details.
• Speed up the transmission matrix (transmat) storage by usingpadded_vector instead of repeatedrbind calls. The result ofget_transmat(netsim_object) is unchanged.
• Useunflatten_params ingenerate_random_params instead of bespoke code.
• Standardize and speed up the summary calculations and plotting functionality fornetdx andnetsim objects.
• Streamline unit tests for testing on CRAN.

NEW FEATURES

• Network models can now use predefined scenarios with theuse_scenario function. See theWorking with Model Parameters vignette for details.
• Thetrim_netest function has been added to reducenetest object sizes in common use cases.
• ThenetworkLite class now supports some additional functionalities.
• Duration = 1 time step models innetsim withtergmLite = FALSE now usetergm simulation to produce anetworkDynamic class object, similar to the duration > 1 time step case.
• netdx now supports heterogeneous dissolution model diagnostics. See the example inhelp("netdx").
• plot.netsim now supportstype = "duration","dissolution" for homogeneous ("edges-only") dissolution models.
• Network model parameters can now be supplied toparam.net via adata.frame. See theWorking with Model Parameters vignette for details.
• A new termfuzzynodematch was added, to support modeling of more generalized notions of homophily.
• Network models can now be checkpointed to automate saving, recovering, and restarting simulations after interruption, as might occur with large-scale simulation jobs on high-performance computing (HPC) systems. Seehelp("control.net).

BUG FIXES

• EpiModel's custom termsabsdiffby andabsdiffnodemix are now usable again (due to enabling symbol search).
• The correct formula is now used insim_nets_t1 when initializing the network with the non-nested edges dissolution approximation approach innetest.
• References tonetwork class internals have been removed fromnet.utils.R to make the code function properly withnetworkLites.
• update_dissolution now correctly handles duration 1 models.
• get_edgelists andget_cumulative_edgelists now throw informative errors when thenetwork refers to non-existing networks.get_partners andget_cumulative_edgelists_df will throw errors as well as they call those functions internally.

OTHER

• Theupdater.net module was removed as an optional module but its functionalities are now the default behavior for all network models (built-in and custom).
• The parametersparam.updater.list andcontrol.updater.list inparam.net andcontrol.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.
• Dissolution models using thenodefactor term have been deprecated.
• stergm controls have been deprecated in favor oftergm controls.
• Formula-style simulations are used consistently for bothergm andtergm simulation, requiring control arguments of classcontrol.simulate.formula andcontrol.simulate.formula.tergm.
• ndtv is added to "Suggests" (again) andplot.transmat now accepts thetransmissionTimeline in thestyle argument (again).
• Systematic review and improvement of documentation across the package.
• netest andnetdx now have default control arguments following R's default argument mechanism.
• Simulation names are now attached tonetsim object fields produced via thesave.other mechanism.
• Imputed durational corrections for onset-censored edges are now sampled from a geometric distribution rather than simply using the mean of that distribution.

NEW FEATURES

• Improved optional moduleupdater.net allowing it to update the model controls as well as the parameters. See the vignette, "Working with model parameters."
• General updates to the names and content of the included vignettes.

BUG FIXES

• Fix dissolution model statistics calculations fornetsim in the case with a model with an "end horizon" (when the network is not resimulated at the end of the time series).
• Fix duplicate printing issues acrossprint.netsim,print.param.net, andprint.control.net.
• Fix use ofall.equal in unit tests as requested by CRAN.
• Change defaults of newly introduced cumulative edgelist functionality to not store it (improves speed).
• Allowset_attr forposit_ids to return unchangeddat object.

OTHER

• We have changed the names of arguments from the functionget_partners newly introduced in EpiModel v2.2.0:max.age is renamed totruncate for consistency with the other cumulative edgelist functions;only.active is renamedonly.active.nodes to clarify that this argument subsets bynodes and not bypartnerships.

NEW FEATURES

• Developed a general approach to tracking and querying historical and contacts, called a cumulative edgelist. This may be used, for example, to query the recent but non-current contacts of newly infected nodes. See the vignette, "Working with network objects".
• Acreate_dat_object helper function was added to standardize the creation of the coredat object withininitialize.net.
• The current timestep withinnetsim simulations is now stored in thedat object and accessible withget_current_timestep. This eliminates the need to explicitly passat as a function argument, although that is still allowed.
• Addition of theget_param_set function that extracts from anetsim object the set of parameters used by each simulation. See the help page:help("get_param_set").
• Developed a mechanism to store nodal attribute history over the course of anetsim simulation. See the vignette, "Working with attributes and summary statistics."
• Developed an optional module to define prevalence statistics (also called "epi stats") as functions to be passed to the model as control settings before eachnetsim simulation. This allows users to avoid updating theprevalence.net module. See the vignette, "Working with attributes and summary statistics."
• Developed an optional module allowing the update of the model parameters over timesteps withinnetsim simulations (i.e., time-varying parameters). See the vignette, "Working with model parameters."
• Improved the random parameterization programming interface to allow correlation between parameters in each simulation (e.g., the ability to pass in a multivariate parameter set for each simulation). See the vignette, "Working with model parameters."

BUG FIXES

• When callingplot on anetsim object, the arguments in the ellipsis (...) are now correctly passed to thebase::plot call.
• When trying to use the built-ingroup attribute,netsim will now output a more explicit error if the values used are not only1 and2.
• Fixed the names of the target formation statistics innetdx whenedapprox == FALSE that were causing the plotting functions to misbehave.
• Simplification of theset_transmat function removing the assumption thatdat$stats$transmat was to exist only ifat != 2 (thanks to@thednainus).
• More consistent formation and dissolution statistics print betweennetdx andnetsim.
• Removed duplication in the printing of the parameters when a parameter was defined both as fixed and as random.
• When using customnetsim modules withtype == NULL, some built-in modules no longer stop because they requiredtype to be a string.
• Fixed issue withError,Warning orMessage innetsim printing twice.
• Fixed problem with unique ID counter not saved bysaveout.net, resulting in the unique ids to start a 1 again when restarting a model from a previous simulation.

Other

• The new home for EpiModel on Github is:https://github.com/EpiModel/EpiModel. It was previously located on thestatnet organization on Github.

Contributors

NEW FEATURES

• Summary network statistics fornetsim class objects (epidemic simulations) are now available whentergmLite is used. Previously these network statistics were only available whentergmLite = FALSE but updates to thenetworkLite class intergmLite made this possible. These network stats are output withsave.nwstats andnwstats.formula arguments incontrol.net.
• Developed a general storage and printing mechanism for the recently developed random parameterization interface. See the help pagehelp("param.net").
• Cleaned up the handling of the initial network simulation ininitialize.net, so that the user-facing code in that function is more readable, and the more complex code is put insim_nets_t1.

BUG FIXES

• Addressed errors in handling cross-sectional network simulations embedded within a dynamic epidemic model (e.g., contacts that last the length of one time step, specified byduration = 1 indissolution_coefs).

Minor updates for CRAN submission.

NEW FEATURES

• Added newupdate_params function to add new parameters to an existing list of network parameters specified inparam.net. This aids in workflows that distinguish fixed parameters versus varying parameters that may change across scenarios or simulations.
• Added new general interface for random parameters in network models that allows randomly drawing a parameter value from a specified statistical distribution, where the distribution may either be a sampling of discrete values or a factory function for any of R's random statistical distribution functions. See help file forgenerate_random_params for examples.
• Implemented a standardized approach with helper functions for setting core attributes (those nodal attributes which should be present in any workflows) in network models. This functionality is specified withappend_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.

BUG FIXES

• With the use of a standardized core attribute framework that now correctly handles unique IDs in all models, now the transmission matrix objects output from any network model work consistently and correctly for both closed population and open population models.
• For DCM models withdt < 1, fixNA output for any.flow variables.
• Reduce complexity of some unit tests that were stochastically generating errors due to ERGM MCMC estimation problems.
• Fix problem with temporally extended status variables in network models (i.e., tracking of disease status history across time steps) by simplifying the general approach that works across built-in and extension model types.

OTHER

• Reimplemented the handling of relational age diagnostics innetdx, with updated numerical summaries inprint.netdx and visuals inplot.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 inplot.netdx to visualize with imputed start times (default = TRUE) or not.
• More consistent approach to trimming unneeded environmental data from ERGM objects implemented withstatnet.common::trim_env(), used innetest.
• Reimplemented thenetest "edges dissolution approximation" for efficient estimation of a temporal ERGM via a cross-sectional ERGM estimation with adjustment of formation model coefficients (seenetest 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).