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@smjenness smjenness released this Aug 5, 2020 · 4 commits to master since this release

Minor updates for CRAN submission.

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@smjenness smjenness released this Jul 20, 2020 · 44 commits to master since this release

Minor updates for CRAN resubmission.

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@smjenness smjenness released this Jul 20, 2020 · 50 commits to master since this release

  • 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/.
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@smjenness smjenness released this May 8, 2020 · 611 commits to master since this release

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.
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@smjenness smjenness released this Dec 29, 2019 · 631 commits to master since this release

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.
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@smjenness smjenness released this Aug 29, 2019 · 650 commits to master since this release

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.
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@smjenness smjenness released this Dec 18, 2018 · 686 commits to master since this release

BUG FIXES

  • Fix logical evaluations in get_sims and unit tests in plot.transmat found
    during CRAN submission for v1.7.1.
Assets 2

@smjenness smjenness released this Dec 17, 2018 · 692 commits to master since this release

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.
Assets 2

@smjenness smjenness released this Nov 21, 2018 · 734 commits to master since this release

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.
Assets 2

@smjenness smjenness released this Apr 10, 2018 · 885 commits to master since this release

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.
Assets 2
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