Model parameterization for all model classes has been substantially revised to improve organization and ability for expansion. Whereas previous models required input of parameters directly into the main functions (now: dcm, icm, and netsim), now the parameters are input into three parameter-processing functions: param, init, and control. The param function sets the core epidemic parameters, the init function sets the initial conditions, and the control function specifies other model settings. These functions are class-specific, so each function has a .dcm, .icm, or .net suffix.

Modeling functions have been renamed for clarity and consistency:

dcm is now used for deterministic compartmental models (replaces epiDCM)

icm is now used for stochastic individual contact models (replaces epiICM)

netest is now used for network model estimation (replaces epiNet.est)

netsim is now used for network model simulation (replaces epiNet.simTrans)

Network models with independence between epidemic/demographic processes and network structures (independent models) were previously first simulated with epiNet.simNet, and then those pre-simulated networks were input to epiNet.simTrans. Now the network model simulation is all handled within the simulation function, netsim.

Network model diagnostics have been moved from within the network estimation process (netest) to their own function: netdx. The parameter names for running, printing, and plotting the results of these diagnostics have been updated for consistency. See ?netdx and related functions.

Internal model functions have been significantly revised to improve efficiency.

The dcm function can handle model functions, parameter sets, and initial conditions of arbitrary complexity. See the HTML vignette on this topic at: https://www.epimodel.org/

Moved the package vignettes external to the package to reduce package size and build time.