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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.
icmclasses now allow creation of a
single data frame with epidemic outcomes across multiple simulations, where
previous only single individual simulations would be output. This is specified
sim = "all"parameter when
out = "vals". See the help page for
examples. This "tidy" data format allows for easier integration with external
plotting and analysis approaches, including ggplot2.
geom_bandsis a new "geom" for use by
ggplot2to facilitate plotting of
simulation intervals given a specified lower and upper quantile set. Examples
of plotting ICM simulations are provided, and the same principle applies for
network models. As a result of this,
ggplot2was added as a depend.
truncate_simsis a new utility function that takes truncates the time series
icmclass object at a specified time step. This truncation
will remove all epidemic output before that time step, and reset the control
settings to start at that time step. This is useful in our modeling workflows
when we need to remove a pre-intervention burnin period from the model
init.netallows you to pass in a vector of backwards-looking infection times
for those initally infected at t_1 through the
Combined with the
status.vectorparameter, this provides users maximal control
over who is infected and for how long as initial conditions.
- Fixed bug in DCM Shiny app related to plotting prevalence vs count outcomes.
- Removed unneeded and unused input parameters from
- Fixed issue where SIS/SIR models with vital dynamics, and a low mortality rate
relative to the recovery rate (which is typical) would get very long initial
infection times assigned at t_1.
- Changed the title (actually, it's a subtitle) in the DESCRIPTION to: "Mathematical
Modeling of Infectious Disease Dynamics".
- Deprecated the
users to specify a random number of initially infected. Support for this got
too complex for a little (or never) used argument, and users interested in
randomly setting the initial number infected may control this more flexibly
- This version of EpiModel has been used to prepare the examples in the manuscript
"EpiModel: An R Package for Mathematical Modeling of Infectious Disease over
Networks", currently in press (2017-06-01) at the Journal of Statistical
gridargument to plot functions to overlay a grid on line plots.
- Fix bug in
plot.netdxexamples in help file.
- Reset the
verbosedefault for network models to
TRUE(reverts change in
v1.3.0 specifically for network models).
legargument name (to add default legends to plots) to
this is backwards-incompatible because of fuzzy matching with other function
leg; prior model code must be updated.
- Change default transparency level to 0.5 (if unspecified).
nstepsmay now be a vector of time steps or, as before, an
integer containing the number of time steps within a DCM simulation. For example,
control.dcm(..., nsteps = seq(1980, 2015, 1/12), ...)for solve for monthly
outputs from a range of dates from 1980 to 2015.
mutate_epifor adding new variables to a epidemic simulation object now works
for all three model classes.
- Outputs from
controlfunctions are now dual-classed as
lists as well as their native classes.
- When passing a
control.dcm, printing the
no longer yields a warning and instead prints the function name.
- Update handling of transparent colors within
transcoto use the base
- Derivatives tracking a "flow" or the size of a transition between compartments
for DCM simulations (e.g., disease incidence) often output
NAfor the final
value, creating issues with analyzing those data. Those
NAs are replaced with
the penultimate value of that vector.
- Simplify printing of
netsimobjects to list "Variables"
together instead of dividing them into compartments, flows, and other.
- Change the
popfracdefault for plotting
FALSE. This avoids any problems when prevalences are already stored within
the model simulation.
- Change the
verbosedefault for control functions to
- Print simulation number and prevalence value for static network plots in
min, or `max.
- Add new line at end of
- Tighten the default ylim ranges for
- Include error check for duration < 1 in
- Update documentation in a number of places.
- Add new
mutate_epifunction inspired by the
dplyrpackage, to add
post-hoc summary statistic calculations to completed network simulations.
See the function help file for examples.
- Added a speedy
get_degreefunction that returns a vector of current
network degree for each person in a network.
- Updated internal plot functions that calculate prevalences.
- Disable verbose output if running network models in parallel.
- Allow network simulations of 1 time step (mainly used for debugging and
- Updates to
as.phylo.transmatto fix issues with vertex exit times and to
now accept multiple seed vertices if multiple seeds are detected, returning
a list of phylo objects of class
multiPhylofollowing the convention of
- Corrected an error governing the birth rate of 2-group, open-population
deterministic compartmental models (DCMs).
- Updated license to GPL-3.
- Added multicore functionality to simulating stochastic network models with
only supports single-node frameworks currently, using the
doParallelpackage. Run models
in parallel by using the
- Modifications to the
as.phylo.transmatfunction to construct the phylo tree with all
network vertices as phylo-tips and all transmissions as phylo nodes.
- General code cleanup and improvement of package tests to increase coverage about 90%.