No significant changes on the user side.
(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).
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.
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.
epiworld version 0.11.2 including minor
patches to avoid warnings and notes from clang.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.
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).
virus_hist and tools_hist,
respectively. This has been fixed (new in epiworld 0.11.0).ModelMeaslesSchool,
ModelMeaslesMixing,
ModelMeaslesMixingRiskQuarantine, and the deprecated
ModelMeaslesQuarantine) have been moved to a separate
package. Users who need measles models should install the measles
package.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.
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).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.
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.
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.
ModelMeaslesQuarantine has been deprecated in
favor of ModelMeaslesSchool (change of name).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).
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.
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.
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.
Adds an advanced usage vignette.
Adds more extensive input parameter checks during model creation.
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 |>
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).
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.
run_multiple() after a
single call of run(). Reported on 14.Added missing checks of tool class when adding a model with
add_too_n.
Various small improvements.
Added the following models: ModelSEIRD,
ModelSEIRDCONN, ModelSIRD,
ModelSIRDCONN, and ModelSISD.
Fixed a bug reported on issue 6.
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.
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