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Changelog

Source: NEWS.md

epiworldR 0.17.1-0

Syncs the C++ core with epiworld 0.17.1.

New features

User-visible changes

  • The "auto" transmission mode picks the cheaper step more reliably around the peak of large outbreaks on heterogeneous networks, where it used to pull although pushing was cheaper. Its threshold kappa now defaults to 0.5 (was 0.25). Seeded results of network models can change, since a different day-by-day choice draws different random numbers; the distribution of outcomes is the same.

  • Pulling is slightly faster (about 5% on small-world networks).

epiworldR 0.17.0-1

User-visible changes

  • The GeoPops vignette (“Using external network data: GeoPops synthetic populations”) is now an article on the package website only, and its GeoPops extract is no longer installed with the package (system.file("extdata", "geopops", package = "epiworldR") is gone). The data now lives next to the article in the GitHub repository, under vignettes/articles/geopops. This keeps the package within CRAN’s size limit.

Internal changes

  • Vignette figures are rendered at standard (1x) instead of retina (2x) resolution, and unused README images were removed from man/figures. Both reduce the package size.

epiworldR 0.17.0-0

Syncs the C++ core with epiworld 0.17.0.

New features

  • bubbles() gains a ties argument that controls what being in a bubble together does to the contact network. "existing", the default, keeps the previous behaviour: the bubble is only a transmission rule. "complete" also ties every pair of agents sharing a bubble while the policy is in force, so households become complete and merged households meet in full. The ties are withdrawn when the bubbles are redrawn, when the policy lifts, and on the last day of the run, so a run always leaves the network as it found it. "complete" requires an undirected network. See the updated “Social bubbles” vignette for an example.

User-visible changes

  • Directed networks are now directed. Networks built with agents_from_edgelist(..., directed = TRUE) or agents_smallworld(..., d = TRUE) were silently made undirected. A tie source -> target is now kept by the source only: target is one of source’s neighbors, and since agents are exposed to their own neighbors, target can infect source but not the reverse. get_network() now returns the ties as given. Results change for directed networks; undirected networks give the same results as before.

  • Directed networks no longer use the queuing system, so large directed networks may run slower.

  • agents_from_edgelist() builds the network about 10 times faster (under 20 ms instead of about 150 ms for 100,000 agents with 10 ties each). agents_smallworld() and agents_sbm() are somewhat faster too. The networks, and so the results for a given seed, are unchanged.

Bug fixes

epiworldR 0.16.1-0

Syncs the C++ core with epiworld 0.16.1.

User-visible changes

  • Network models (ModelSIR(), ModelSIS(), ModelSISD(), ModelSIRD(), ModelSEIR(), ModelSEIRD(), and models built with update_fun_susceptible()) now simulate transmission faster. At each step, the model either has infected agents push infection to their neighbors or has susceptible agents pull it from theirs, whichever is cheaper. Both give the same distribution of outcomes.

  • Results for a given seed change in those models, and wherever the random distribution functions below are used. Only the random draws change; the model’s behaviour does not.

Bug fixes

  • distribute_tool_to_set() and distribute_virus_to_set() no longer take time quadratic in the number of agents: the set of IDs was copied every time an agent received the tool or virus. Protecting 24,000 of 100,000 agents went from about 0.75 seconds to a few milliseconds.

  • distribute_tool_randomly() with agents_ids now picks agents from that set. It used to pick among the first length(agents_ids) agents of the model instead.

  • distribute_tool_randomly(), distribute_virus_randomly(), distribute_tool_to_entities() and distribute_virus_to_entities() now pick every candidate with the same probability. The last candidate was never picked for the first recipient, and the one before it was picked twice as often.

  • A transition or contact with probability exactly 1 now always happens. Before, the last option was chosen instead, so a death probability of 1 could end in recovery.

  • get_hist_tool() now labels the tool column with the model’s tool names. It previously used the virus names instead, and could read past the end of the name list (undefined behaviour) when a model had more tools than viruses.

epiworldR 0.15.1-1

User-visible changes

  • Updated LFMCMC vignette example parameters for improved reliability. Users should be aware that LFMCMC results are sensitive to parameter choices, and incorporating informative priors is strongly recommended for real analyses.

epiworldR 0.15.1-0

User-visible changes

  • The new function bubbles() implements social-bubble contact restrictions on network models, with the household- and peer-based rules used during COVID-19 (see the “Social bubbles on a small-world network” vignette). How leaky the bubbles are is held in a model parameter ("Bubble transmission factor" by default), which scales transmission along out-of-bubble contacts and can be read with get_param() and changed with set_param() at any point. Each copy of a model keeps its own bubbles, so replicates run on any number of threads. sample_household_sizes() draws household sizes to go with it.

  • New vignette, “Using external network data: GeoPops synthetic populations”, showing how to bring an externally-generated population and its contact networks into a model with agents_from_edgelist(), and how to give transmission a weekday/weekend rhythm with the global events module. It comes with a small extract of a GeoPops synthetic population in system.file("extdata", "geopops", package = "epiworldR").

  • The new functions get_contact_matrix() and set_contact_matrix() allow users to access contact matrices in mixing models.

  • Saved run_multiple() results now have documented plotting support, including transition-matrix diagrams through plot_multiple_transition().

  • The new helper compute_ts_ci_area() computes polygon and median-line data for plotting uncertainty intervals in time series.

  • draw_mermaid() is now documented with the model-diagram helpers and consistently returns an epiworld_diagram object.

Bugs

  • The ModelSEIRMixingQuarantine model was not officially tracking hospitalizations. This means that using the saver to extract hospitalizations would return zero.

  • Using globalevent_fun() with run_multiple(..., nthreads > 1) was not compatible because R is not thread-safe. run_multiple() now warns the user and automatically switches to nthreads = 1.

epiworldR 0.15.0-0

  • Updates to epiworld C++ 0.15.0.

User-visible changes

  • The ModelSEIRMixingQuarantine now features a single hospitalization state instead of two. The model now assumes that hospitalized individuals are detected immediately and trigger the quarantine process.

  • The package now includes the function agents_sbm(), which implements the Stochastic-Block Model by Batahelj and Brandes (2005).

  • The mixing models–ModelSEIRMixing(), ModelSIRMixing(), and ModelSEIRMixingQuarantine()–lost the contact_rate parameter in favor of a more flexible model: instead of using mixing matrices (row-stochastic), the model now uses a contact matrix, which allows groups to have different contact rates.

  • New model builder functions Model(), add_state(),update_fun_susceptible(), and update_fun_rate() expose a new approach to build models in the package. Using these functions, users can create models from zero (to hero!). The package includes a new vignette demonstrating its usage.

  • The new function compute_reproduction_number() provides a way to estimate either the basic or the effective reproductive number. This is most useful for mixing models.

Internal changes

  • Fixes a bug in how GlobalEvents polymorphism is implemented in the core library.

  • Removed the measles-related headers (were unused by this package).

  • Introduced an optimization for accelerating binomial draws based on Le Cam’s inequality. The function defaults to poisson draws (faster) in case of rare events.

epiworldR 0.14.0.0

CRAN release: 2026-03-28

  • The way seed is passed to run() and run_multiple() has been modified to ensure comparability with the C++ version. Now, a random seed number is drawn only if seed is not specified.

Internal changes

  • (epiworld#189) Addressing memory access issues that arise when calling run_multiple using OpenMP. The latest version reduces usage of points (including smart) to make the code more reliable. No penalties on its performance are expected.

  • Switch vignette building engine to quarto.

epiworldR 0.13.0.0

CRAN release: 2026-03-12

No significant changes on the user side.

Internal changes

  • (epiworld#169) The Entities system was still causing issues. The system was refactored to use indices instead without any pointers.

  • (same issue) The system completely avoids binding via pointers (with the exception of DataBase). This provides a cleaner API reducing issues related to memory/address problems. Model::clone_ptr now returns smart pointers instead.

  • (epiworld#163) Changed the main engine for Pseudo Random Number Generation to xorshiro** (more in this website and this paper by Blackman and Vigna). This change makes random number generation significantly faster (twice as much, compared to Mersenne Twister).

epiworldR 0.12.0.0

CRAN release: 2026-02-21

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

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

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.