Mathematical Modeling of Infectious Disease Dynamics
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.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.updater.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).Minor updates for CRAN submission.
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).