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- 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/.
- Improve error handling for inputs to
- Skip dissolution diagnostics in
netdxif a static ERGM is passed.
- 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.
- Add foundation updates to support the
tergmLitepackage (to be released).
- Print network statistic diagnostics stored in
print.netsim(x, formation.stats = TRUE).
- Fix issue
plot.netsimdefault colors when number of variables exceeds 3.
- Add example for differential homophily in a TERGM dissolution model in
- Add a
netdxto skip dissolution diagnostics
for computational efficiency.
- Fixes output formatting of network stats saved during
- Correctly errors when running dynamic network diagnostics with
- Remove old unused utility functions.
- Enforce depend on ergm >= 3.10 package.
- Two helper functions,
apportion_lr, ported over from
- Two custom ERGM terms,
absdiffnodemix, ported over from
- 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
- Fix bug in
dtcontrol setting < 1.
netdxto allow for retaining the full
networkDynamicobject during dynamic network simulations. Relatedly, add
get_networkto extract those networks from
- Change the default handling of
as.data.framefunction 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.netdxfunction extracts the timed edgelists directly from
get_nwstatsfunction now extracts data frames of network statistics from
- Improve functionality and error handling of
- Fix problems with color handling of network statistics plots in
- Enforce maximum number
netdxto prevent over
parallelization of simulations.
- Removed the redundant storage of the timed edgelist data in
- Fix errors in calculation of population sizes in verbose module that prints
simulation output to the console.
- Add warning for input parameter with a name
act.rate.m2for network models
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
parameter yield a message and will automatically set
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
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.
netdxnow includes a new argument,
sequential, for static diagnostics
that mirrors the same argument from
ergm::simulate.ergmto simulate from
MCMC chains based on previous draws versus new draws.
mutate_epioutput when new variable is a constant.
ggplot2from 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.