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Changelog

Source: NEWS.md

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

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.