statnet / EpiModel

Minor updates for CRAN resubmission.

• This release introduces a major update to the EpiModel package infrastructure and application programming interface for both built-in models (primarily used for teaching purposes) and extension models (primarily used for research purposes). The major substantive changes are summarized in a EpiModel 1.x to EpiModel 2.0 migration guide on our primary website: https://epimodel.org/.

BUG FIXES

• Improve error handling for inputs to dissolution_coefs.
• Skip dissolution diagnostics in netdx if a static ERGM is passed.

NOTE

• This will be the last version of EpiModel 1.0 before major revisions to the
  package infrastructure and API to be released in EpiModel 2.0.

NEW FEATURES

• Add foundation updates to support the tergmLite package (to be released).
• Print network statistic diagnostics stored in netsim object with
  print.netsim(x, formation.stats = TRUE).

BUG FIXES

• Fix issue plot.netsim default colors when number of variables exceeds 3.

OTHER

• Add example for differential homophily in a TERGM dissolution model in
  dissolution_coefs documentation.

NEW FEATURES

• Add a skip.dissolution argument to netdx to skip dissolution diagnostics
  for computational efficiency.

BUG FIXES

• Fixes output formatting of network stats saved during netsim runs.
• Correctly errors when running dynamic network diagnostics with netdx on a
  cross-sectional ergm.
• Remove old unused utility functions.
• Enforce depend on ergm >= 3.10 package.

BUG FIXES

• Fix logical evaluations in get_sims and unit tests in plot.transmat found
  during CRAN submission for v1.7.1.

NEW FEATURES

• Two helper functions, get_args and apportion_lr, ported over from
  EpiModelHIV.
• Two custom ERGM terms, absdiffby and absdiffnodemix, ported over from
  EpiModelHIV.

BUG FIXES

• Fix linked functions in embedded Shiny apps broken in v1.7.0.
• Update handling of parameter and module name changes related to births/deaths
  to arrivals/departures renames in v1.7.0.
• Reduce complexity of verbose output so that it can generalize across EpiModel
  extension packages.
• Fix bug in as.data.frame.dcm when dt control setting < 1.

NEW FEATURES

• Add 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.
• Change the default handling of 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.
• New as.data.frame.netdx function extracts the timed edgelists directly from
  a netdx object.
• The get_nwstats function now extracts data frames of network statistics from
  both netdx and netsim objects.

BUG FIXES

• Improve functionality and error handling of get_sims.
• Fix problems with color handling of network statistics plots in plot.netdx
  and plot.netsim.
• Enforce maximum number ncores argument in netdx to prevent over
  parallelization of simulations.
• Removed the redundant storage of the timed edgelist data in netdx objects.
• Fix errors in calculation of population sizes in verbose module that prints
  simulation output to the console.

OTHER

• Add warning for input parameter with a name act.rate.m2 for network models
  in param.net, as this is an unused parameter for built-in models.
• Updated parameters and documentation throughout EpiModel for vital dynamics
  parameters and processes to reflect a more general method of demographic
  in-flows and out-flows from the population. Previous terms were births and
  deaths; new terms are arrivals and departures. The default parameter for
  births was previously 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.
• Adapted y-axis limit calculation for all stochastic plots to depend on dynamic
  range of data displayed instead of full data range.
• Changed the default plot type for static diagnostics in 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.

NEW FEATURES

• 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.

BUG FIXES

• Fix mutate_epi output when new variable is a constant.

OTHER

• Move ggplot2 from depend to import.
• References added for publication of Journal of Statistical Software methods
  paper on EpiModel: Jenness SM, Goodreau SM, Morris M. EpiModel: An R Package
  for Mathematical Modeling of Infectious Disease over Networks. Journal of
  Statistical Software. 2018; 84(8): 1-47. DOI: 10.18637/jss.v084.i08.