Changelog

Source: NEWS.md

epiworldR 0.12.0.0

Bug fixes

• Updates to epiworld version 0.12.0, including a patch to the ModelSEIRMixingQuarantine model. It was underestimating the outbreak size. This is a similar issue detected in the collection of the measles models.

• The ModelSEIRMixingQuarantine gained a couple of extra checks for validating the inputs.

Internal changes

• Simplified build configuration to comply with CRAN policies: removed custom configure script, using R’s built-in OpenMP settings ($(SHLIB_OPENMP_CXXFLAGS)) and specifying C++17 via CXX_STD in Makevars and SystemRequirements in DESCRIPTION.

• Changing how Entities are managed in the system, moved away from using pointers and instead use reference_wrapper.

epiworldR 0.11.2.0

CRAN release: 2026-02-03

• Updates to epiworld version 0.11.2 including minor patches to avoid warnings and notes from clang.

Bug Fixes

These changes will be reflected in the measles R package (so no changes for the epiworldR package):

• The measles school model was not including the number of recovered agents in the population that it could sample from, which resulted in a minor overestimation of the outbreak size (about 5 to 10 percent).

• The measles mixing models were assuming the number of available agents did not change when sampling contacts. This has been corrected. Outbreak sizes are now expected to be larger on average.

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.