The function InterventionMeaslesPEP() implements post-exposure prophylaxis featuring both MMR and IG. The process is highly configurable and can be attached to the ModelMeaslesSchool(). Not available yet for other models.
The models ModelMeaslesMixing() and ModelMeaslesMixingRiskQuarantine() no longer use contact_rate; instead, their contact_matrix stores the expected number of contacts between groups. Calibration can now be done with the new function calibrate_mixing_model().
Updated the documentation, examples, and contact-matrix helpers for the mixing models so they consistently treat contact_matrix as the full contact-rate matrix.
Aligned the package documentation and examples with the updated measles state names from {epiworldR}, replacing Exposed/Quarantined Exposed with Latent/Quarantined Latent where those names refer to model states.
Changed the default vaccine efficacy of Measles from 99% to 97%.
The contact tracing window parameter in ModelsMeaslesMixing() and ModelMeaslesMixingRiskQuarantine() was capturing agents that may have been in contact with infected cases way past the window. No important regressions observed from this change.
The Measles models were removed from {epiworldR}. This streamlines the development process. So, if we need to update Measles related models, we only need to update the {measles} R package, not {epiworldR} and {measles}.
The ModelMeaslesMixing includes parameter validation on the C++ side.
The latest version of epiworld optimizes the binomial sampler, switching to a Poisson sampler based on Le Cam's inequality.
The vaccination efficacy has been modified to reflect a probability (the original intent) instead of a rate. Previous versions were resulting in a higher than expected vaccinated individuals becoming infected (update from epiworldR 0.13.0.0).
Improved documentation regarding vaccination rates and probabilities across models.
epiworld (0.14.0), which introduced several important changes. You can read more about the changes here (the corresponding epiworldR PR is here.).Removed the configure script infrastructure (configure.ac, configure,
cleanup, src/Makevars.in) in favor of a static src/Makevars that uses
R's own $(SHLIB_OPENMP_CXXFLAGS) for OpenMP support. This addresses
CRAN policy compliance by removing unnecessary C++11 compiler testing and
custom OpenMP detection.
Added CXX_STD = CXX17 to src/Makevars and src/Makevars.win, and
SystemRequirements: C++17 to DESCRIPTION, as required by the epiworld
C++ headers (std::string_view, if constexpr).
This is the first release of the measles R package, a spin-off of the epiworldR package, focused on modeling measles transmission dynamics.
Added get_contact_matrix() and set_contact_matrix() functions to retrieve and modify the contact matrix for mixing models. These functions are available for:
ModelMeaslesMixingModelMeaslesMixingRiskQuarantineOther mixing models in epiworld will have these methods available in the near future.