@smjenness smjenness released this Apr 10, 2018 · 50 commits to master since this release

Assets 2

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.

@smjenness smjenness released this Jan 25, 2018 · 69 commits to master since this release

Assets 2

OTHER

  • Fixed minor issue with unit tests using identical function causing some to
    fail under alternative BLAS/LAPACK implementations.

@smjenness smjenness released this Jan 24, 2018 · 72 commits to master since this release

Assets 2

NEW FEATURES

  • as.data.frame methods for netsim and icm classes 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
    with the 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_bands is a new "geom" for use by ggplot2 to 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, ggplot2 was added as a depend.
  • truncate_sims is a new utility function that takes truncates the time series
    of a netsim or icm class 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
    simulations.
  • init.net allows you to pass in a vector of backwards-looking infection times
    for those initally infected at t_1 through the infTime.vector parameter.
    Combined with the status.vector parameter, this provides users maximal control
    over who is infected and for how long as initial conditions.

BUG FIXES

  • Fixed bug in DCM Shiny app related to plotting prevalence vs count outcomes.
  • Removed unneeded and unused input parameters from discord_edgelist function.
  • 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.

OTHER

  • Changed the title (actually, it's a subtitle) in the DESCRIPTION to: "Mathematical
    Modeling of Infectious Disease Dynamics".
  • Deprecated the status.rand argument for init.net and init.icm that allowed
    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
    with the status.vector parameter.

@smjenness smjenness released this May 31, 2017 · 131 commits to master since this release

Assets 2

NOTE

  • 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
    Software.

NEW FEATURES

  • Add grid argument to plot functions to overlay a grid on line plots.

BUG FIXES

  • Fix bug in plot.netdx examples in help file.

OTHER

  • Reset the verbose default for network models to TRUE (reverts change in
    v1.3.0 specifically for network models).
  • Rename leg argument name (to add default legends to plots) to legend. Note
    this is backwards-incompatible because of fuzzy matching with other function
    arguments starting leg; prior model code must be updated.
  • Change default transparency level to 0.5 (if unspecified).

@smjenness smjenness released this Mar 13, 2017 · 166 commits to master since this release

Assets 2

NEW FEATURES

  • In control.dcm, nsteps may 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_epi for adding new variables to a epidemic simulation object now works
    for all three model classes.

BUG FIXES

  • Outputs from param, init, and control functions are now dual-classed as
    lists as well as their native classes.
  • When passing a new.mod into control.dcm, printing the control.dcm object
    no longer yields a warning and instead prints the function name.

OTHER

  • Update handling of transparent colors within transco to use the base
    adjustcolor function.
  • Derivatives tracking a "flow" or the size of a transition between compartments
    for DCM simulations (e.g., disease incidence) often output NA for the final
    value, creating issues with analyzing those data. Those NAs are replaced with
    the penultimate value of that vector.
  • Simplify printing of dcm, icm, and netsim objects to list "Variables"
    together instead of dividing them into compartments, flows, and other.
  • Change the popfrac default for plotting dcm, icm, and netsim objects
    to FALSE. This avoids any problems when prevalences are already stored within
    the model simulation.
  • Change the verbose default for control functions to FALSE.

@smjenness smjenness released this Dec 16, 2016 · 191 commits to master since this release

Assets 2

NEW FEATURES

  • Print simulation number and prevalence value for static network plots in
    print.netsim when sims is mean, min, or `max.

BUG FIXES

  • Add new line at end of print.coefdiss output.
  • Tighten the default ylim ranges for plot.netsim

OTHER

  • Include error check for duration < 1 in dissolution_coefs.
  • Update documentation in a number of places.

@smjenness smjenness released this Jul 29, 2016 · 210 commits to master since this release

Assets 2

NEW FEATURES

  • Add new mutate_epi function inspired by the dplyr package, to add
    post-hoc summary statistic calculations to completed network simulations.
    See the function help file for examples.
  • Added a speedy get_degree function that returns a vector of current
    network degree for each person in a network.

BUG FIXES

  • Updated internal plot functions that calculate prevalences.
  • Disable verbose output if running network models in parallel.

OTHER

  • Allow network simulations of 1 time step (mainly used for debugging and
    testing).

@smjenness smjenness released this May 24, 2016 · 239 commits to master since this release

Assets 2

NEW FEATURES

  • Updates to as.phylo.transmat to 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 multiPhylo following the convention of
    ape::read.tree.

BUG FIXES

  • Corrected an error governing the birth rate of 2-group, open-population
    deterministic compartmental models (DCMs).

OTHER

  • Updated license to GPL-3.

@smjenness smjenness released this Mar 9, 2016 · 254 commits to master since this release

Assets 2

NEW FEATURES

  • Added multicore functionality to simulating stochastic network models with netsim. This
    only supports single-node frameworks currently, using the doParallel package. Run models
    in parallel by using the ncores parameter in control.net.
  • Modifications to the as.phylo.transmat function to construct the phylo tree with all
    network vertices as phylo-tips and all transmissions as phylo nodes.

OTHER

  • General code cleanup and improvement of package tests to increase coverage about 90%.

@smjenness smjenness released this Feb 1, 2016 · 284 commits to master since this release

Assets 2

This release updates the vignette building methods as required during CRAN submission of v1.2.3