Changes in version 0.8.3.0 (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).

                Changes in version 0.8.2.0 (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.

                Changes in version 0.8.1.0 (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.

                Changes in version 0.6.1.0 (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 |>

                Changes in version 0.6.0.0 (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).

                 Changes in version 0.3-2 (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.

                 Changes in version 0.1-0 (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.

                 Changes in version 0.0-4 (2024-02-09)                  

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

  - Various small improvements.

                 Changes in version 0.0-3 (2023-09-08)                  

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

  - Fixed a bug reported on issue 6.

                 Changes in version 0.0-2 (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.