NEWS.md

In epiworldR: Fast Agent-Based Epi Models

epiworldR 0.8.2.0

Changes

• In the ModelMeaslesQuarantine model, isolated individuals now have a different parameter for the number of days in isolation. Previously, the same parameter was used for both isolated and quarantined individuals. The new parameter is isolation_period.

• The ModelMeaslesQuarantine model changed a couple of parameter names to improve consistency. We also improved the documentation of the model.

• The mixing models were using the wrong sampling scheme for the contact event between agents. The new implementation allows using the regular basic reproductive number calculation for its calibration.

• The functions distribute_(virus|tool)_to_set now have an additional argument that allows restricting the set of agents.

Other Changes

• Added more tests to the ModelMeaslesQuarantine model, as well as to the set_distribution*, distribute_*, and get_agents_states functions.

• A large overhaul memory management was performed (C++ side), decreasing the memory footprint by one order of magnitude in some cases.

epiworldR 0.8.1.0

New Features

• Adds the ModelMeaslesQuarantine model, which implements a measles model with quarantine.

• Adds the capability of generating model diagrams using mermaid through the draw_mermaid() model function and the ModelDiagram set of functions.

Enhancements

• Adds an advanced usage vignette.

• Adds more extensive input parameter checks during model creation.

Bug Fixes

• Fixes an error in the index case calculation of the Rt function. Getting the Rt was not recovering the index cases with no transmissions.

epiworldR 0.6.1.0

• Updates to reflect changes in the epiworld C++ library (mostly bug fixes)

• Package now requires R version >=4.1.0, because it uses the pipe |>

epiworldR 0.6.0.0

• The package now includes the LFMCMC module that implements the likelihood-free Markov Chain Monte Carlo algorithm. This module is used to estimate the parameters of the models.

• The new function add_param() allows the user to add parameters to the model.

• The new function rm_globalevent() allows the user to remove global events from the model.

• The function today() returns the current day (step) of the simulation.

• We changed the versioning system. To allow the R package to increase version number while preserving epiworld (C++) versioning, we added a fourth number that indicates R-only patches (similar to RcppArmadillo).

epiworldR 0.3-2

• Starting version 0.3-0, epiworldR is versioned using the same version as the C++ library, epiworld.

• Adds the new mixing models ModelSIRMixing and ModelSEIRMixing.

• Ports the Entity class. Entities are used to group agents within a model.

• Refactors add_tool, add_virus, and add_entity simplifying syntax. Now, these functions only receive the model and object. Prevalence is specified in the object itself. add_tool_n and add_virus_n are now deprecated.

• globalaction_* are now defunct. Use globalevent_* instead.

• New functions to specify how viruses, tools, and entities are distributed among agents: distribute_viruses, distribute_tools, and distribute_entities.

epiworldR 0.1-0

• Force model to update agents' states when running a simulation. This was causing issues when calling run_multiple() after a single call of run(). Reported on 14.

epiworldR 0.0-4

• Added missing checks of tool class when adding a model with add_too_n.

• Various small improvements.

epiworldR 0.0-3

• Added the following models: ModelSEIRD, ModelSEIRDCONN, ModelSIRD, ModelSIRDCONN, and ModelSISD.

• Fixed a bug reported on issue 6.

epiworldR 0.0-2

• Added a NEWS.md file to track changes to the package.

• Fixed bug reported by CRAN about reference to nullptr.

• Renamed arguments across Models in favor of consistency.

• Figures now show virus/tool name instead of id.

• Fixed bug in run_multiple and added more tests (C++).

• Redid autoconf and Makevars using RcppArmadillo as a template for checking for OpenMP.

epiworldR documentation built on June 8, 2025, 1:48 p.m.