NEWS


epinowcast 0.3.9000

Contributors

@athowes and @seabbs contributed code to this release.

@medewitt, and @seabbs reviewed pull requests for this release.

@pearsonca, @athowes, @medewitt, and @seabbs reported bugs, made suggestions, or contributed to discussions that led to improvements in this release.

Breaking changes

Bugs

Package

Documentation

Depreciations

epinowcast 0.3.0

This release brings a range of enhancements, new features, and bug fixes, reflecting the effort of a large number of contributors. It has a single breaking change, which adjusts the default max_delay parameter in enw_process_data() to be the maximum observed delay in the input data. This change aims to encourage users to tailor this setting to their specific datasets and to give them a more reasonable default if they do not.

The package infrastructure has also had significant updates, including improved search functionality on the pkgdown website, the adoption of an organization-level pkgdown theme, the ability to cache Stan models across R sessions, and additional continuous integration tests.

Model enhancements include updated internal handling of PMF discretization and support for non-parametric reference date models, alongside documentation improvements that provide clearer guidance and examples for users.

A range of bug fixes have been implemented, including a fix for a bug in the enw_expectation() module that was causing issues with models containing multiple time series.

Full details on the changes in this release can be found in the following sections or in the GitHub release notes. To see the development timeline of this release see the 0.3.0 project.

Contributors

@jamesmbaazam, @medewitt, @sbfnk, @adrian-lison, @kathsherratt, @natemcintosh, @Bisaloo and @seabbs contributed code to this release.

@jamesmbaazam, @adrian-lison, @sbfnk, @bisaloo, @pearsonca, @natemcintosh, and @seabbs reviewed pull requests for this release.

@jbracher, @medewitt, @kathsherratt, @jamesmbaazam, @zsusswein, @TimTaylor, @sbfnk, @natemcintosh, @pearsonca, @bisaloo, @parksw3, @adrian-lison, and @seabbs reported bugs, made suggestions, or contributed to discussions that led to improvements in this release.

Breaking changes

Bugs

Package

Model

Documentation

Depreciations

epinowcast 0.2.2

This is a minor release that fixes a bug in the handling of optional initial conditions that was introduced by a recent change in cmdstan 2.32.1. Upgrading is recommended for all users who wish to use versions of cmdstan beyond 2.32.0. In addition to fixing this issue, the release also includes some minor documentation and vignette improvements, along with enhancements in input checking.

Contributors

@sbfnk and @seabbs contributed code to this release.

@seabbs reviewed pull requests for this release.

@sbfnk and @seabbs reported bugs, made suggestions, or contributed to discussions that led to improvements in this release.

Bugs

Package

Documentation

epinowcast 0.2.1

In this release, we focused on improving the internal code structure, documentation, and development infrastructure of the package to make it easier to maintain and extend functionality in the future. We also fixed a number of bugs and made some minor improvements to the interface. These changes included extending test and documentation coverage across all package functions, improving internal data checking and internalization, and removing some deprecated functions.

While these changes are not expected to impact most users, we recommend that all users upgrade to this version. We also suggest that users who have fitted models with both random effects and random walks should refit these models and compare the output to previous fits in order to understand the impact of a bug in the specification of these models that was fixed in this release.

This release lays the groundwork for planned features in 0.3.0 and 0.4.0 including: support for non-parametric delays, non-daily data with a non-daily process model (i.e. weekly data with a weekly process model), additional flexibility specifying generation times and latent reporting delays, improved case studies, and adding support for forecasting.

Full details on the changes in this release can be found in the following sections or in the GitHub release notes. To see the development timeline of this release see the 0.2.1 project.

Contributors

@adrian-lison, @Bisaloo, @pearsonca, @FelixGuenther, @Lnrivas, @seabbs, @sbfnk, and @jhellewell14 made code contributions to this release.

@pearsonca, @Bisaloo, @adrian-lison, and @seabbs reviewed pull requests for this release.

@Gulfa, @WardBrian, @parkws3, @adrian-lison, @Bisaloo, @pearsonca, @FelixGuenther, @Lnrivas, @seabbs, @sbfnk and @jhellewell14 reported bugs, made suggestions, or contributed to discussions that led to improvements in this release.

Potentially breaking changes

Bugs

Depreciations

Package

Documentation

epinowcast 0.2.0

This release adds several extensions to our modelling framework, including modelling of missing data, flexible modelling of the generative process underlying case counts, an optional renewal equation-based generative process (enabling direct estimation of the effective reproduction number), and convolution-based latent reporting delays (enabling the modelling of both directly observed and unobserved delays as well as partial ascertainment). Much of the methodology used in these extensions is based on work done by Adrian Lison and is currently being evaluated.

On top of model extensions this release also adds a range of quality of life features, such as a helper functions for constructing convolution matrices and combining probability mass functions. It also comes with improved computational efficiency, thanks to a refactoring of the hazard model computations to the log scale and extended parallelisation of the likelihood that is optimised for the structure of the input data. We have also extended the package documentation and streamlined the contribution process.

As a large-scale project, the package remains in an experimental state, though it is sufficiently stable for both research and production usage. More core development is needed to improve post-processing, pre-processing, documentation coverage, and evaluate optimal configurations in different settings) please see our community site, contributing guide, and list of issues/proposed features if interested in being involved (any scale of contribution is warmly welcomed including user feedback, requests to extend our functionality to cover your setting, and evaluating the package for your context). This is a community project that needs support from its users in order to provide improved tools for real-time infectious disease surveillance.

We thank @adrian-lison, @choi-hannah, @sbfnk, @Bisaloo, @seabbs, @pearsonca, and @pratikunterwegs for code contributions to this release. We also thank all community members for their contributions including @jhellewell14, @FelixGuenther, @parksw3, and @jbracher.

Full details on the changes in this release can be found in the following sections.

Package

Model

Documentation

Bugs

epinowcast 0.1.0

This is a major release focusing on improving the user experience, and preparing for future package extensions, with an increase in modularity, development of a flexible and full-featured formula interface, and hopefully future-proofing as far as possible. This prepares the ground for future model extensions which will allow a broad range of real-time infectious disease questions to be better answered. These extensions include:

If interested in contributing to these features, or other aspects of package development (for example improving post-processing, the coverage of documentation, or contributing case studies) please see our contributing guide and/or just reach out. This is a community project that needs support from its users in order to provide improved tools for real-time infectious disease surveillance.

This release contains multiple breaking changes. If needing the old interface please install 0.0.7 from GitHub. For ease, we have stratified changes below into interface, package, documentation, and model changes. Note the package is still flagged as experimental but is in regular use by the authors.

@adrian-lison, @sbfnk, and @seabbs contributed to this release.

Interface

Package

Model

Documentation

Internals

epinowcast 0.0.7

epinowcast 0.0.6

epinowcast 0.0.5

epinowcast 0.0.4

epinowcast 0.0.3

epinowcast 0.0.2

epinowcast 0.0.1