Changelog

Source: NEWS.md

epiworldR 0.11.0.1

CRAN release: 2026-01-14

• Minor release fixing errors in tests in some OSs (reported by CRAN).

epiworldR 0.11.0.0

CRAN release: 2025-12-22

New Features

• New distribution functions distribute_virus_to_entities() and distribute_tool_to_entities() that allow distributing viruses and tools to agents based on their entity membership (new in epiworld 0.11.0).

• New function add_entities_from_dataframe() that allows adding multiple entities to a model based on a data.frame (wrapper around add_entity()).

• New functions get_outbreak_size() and get_active_cases() allow extracting timeseries of the outbreak size and number of active cases (individuals with a virus) (new in epiworld 0.11.0).

• New function get_hospitalizations() that allows extracting timeseries of hospitalizations from the model results (new in epiworld 0.11.0).

Bug Fixes

• The saver was not correctly saving the history of tools and viruses when using virus_hist and tools_hist, respectively. This has been fixed (new in epiworld 0.11.0).

Breaking Changes

• Measles models have been removed from epiworldR. The measles-specific models (ModelMeaslesSchool, ModelMeaslesMixing, ModelMeaslesMixingRiskQuarantine, and the deprecated ModelMeaslesQuarantine) have been moved to a separate package. Users who need measles models should install the measles package.

epiworldR 0.10.0.0

CRAN release: 2025-11-14

New Features

• New model ModelMeaslesMixingRiskQuarantine that implements a measles model with mixing, risk-based contacts, and quarantine has been added. This is part of a joint effort with our partners at the Utah Department of Health and Human Services (DHHS).

• Added print and plot methods for epiworld_diagram objects. This allows easy visualization of model diagrams generated with DiagrammeR.

Improvements

• The function run_multiple_get_results() has two new arguments: freader and ..., which allows the user to specify a custom function to read the results of each simulation (e.g., data.table::fread).

Bug Fixes

• The rewiring algorithm was not changing the edges, but only the weights of the edges. This has been fixed in epiworld 0.9.4.

• The saver associated with tools_hist had a bug that caused it to not save the history of tools correctly. This has been fixed in epiworld 0.10.0. This was detected during work with @margowheatley and @AliseMendoza.

Misc

• The ModelMeaslesQuarantine model has been updated to warn the user if the deprecated parameter vax_improved_recovery is used. This parameter is no longer used and has been removed.

• Various legacy C++ files have been removed from the inst/include/epiworld folder.

• We now include model diagrams in the documentation of each model (new feature of epiworld 0.10.0).

• Various improvements to the documentation of the package and models.

epiworldR 0.9.1.0

Improvements

• The C++ library has been updated to version 0.9.1, which includes several speed improvements. Some preliminary tests show x10 speedups.

• New model ModelSEIRMixingQuarantine that implements a SEIR model with quarantine and mixing has been added.

Other changes

• The Model ModelMeaslesQuarantine has been deprecated in favor of ModelMeaslesSchool (change of name).

epiworldR 0.8.3.0 (CRAN)

CRAN release: 2025-06-12

Improvements

• epiworld was storing empty entries in the transition matrix. This was making reading the saved data significantly slower.

Bug Fixes

• The run_multiple() function was failing to correctly backup the agents’ edgelist in the case of network models. This was due to a bug in the C++ library that was not correctly copying the edgelist. This has been fixed.

• When multiple transitions happened in a single step, e.g., I->E->S, the model was only recording E->S, but not I->S (which is the correct).

epiworldR 0.8.2.0

CRAN release: 2025-05-13

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

CRAN release: 2025-04-22

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

CRAN release: 2025-01-28

• 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

CRAN release: 2025-01-16

• 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

CRAN release: 2024-10-08

• 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

CRAN release: 2024-04-08

• 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

CRAN release: 2024-02-09

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

• Various small improvements.

epiworldR 0.0-3

CRAN release: 2023-09-08

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

• Fixed a bug reported on issue 6.

epiworldR 0.0-2

CRAN release: 2023-06-21

• 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.