Nowcasting right-truncated epidemiological data is critical for timely public health decision-making, as reporting delays can create misleading impressions of declining trends in recent data. This package provides simple nowcasting methods for practical use based on using empirical delay distributions and uncertainty from past performance. It is also designed to be used as a baseline method for developers of new nowcasting methods. It supports standard data frame inputs with reference date, report date, and count columns, is compatible with ‘epinowcast’ objects, and also supports direct use of reporting triangles. Alongside an opinionated default workflow, it has a low-level pipe-friendly modular interface, allowing context-specific workflows. It can accommodate a wide spectrum of reporting schedules, including mixed patterns of reference and reporting (daily-weekly, weekly-daily). It also supports sharing delay distributions and uncertainty estimates between strata, as well as custom uncertainty models and delay estimation methods.
Installing the package
To install the development version from GitHub (warning! this version
may contain breaking changes and/or bugs), use the pak
package:
pak::pak(file.path("epinowcast", "baselinenowcast"))We provide a range of other documentation, case studies, and community spaces to ask (and answer!) questions:
Organisation Website
Our organisation website includes links to other resources, guest posts, and seminar schedule for both upcoming and past recordings.
Community Forum
Our community forum has areas for
question and answer
and considering new methods and
tools, among others. If
you are generally interested in real-time analysis of infectious
disease, you may find this useful even if you do not use
baselinenowcast.
We welcome contributions and new contributors! We particularly appreciate help on identifying and identified issues. Please check and add to the issues, and/or add a pull request and see our contributing guide for more information.
Please briefly describe your problem and what output you expect in an issue. See our contributing guide for more information.
Please note that the baselinenowcast project is released with a
Contributor Code of
Conduct.
By contributing to this project, you agree to abide by its terms.
If you use baselinenowcast in your work, please consider citing it
with citation("baselinenowcast").
All contributions to this project are gratefully acknowledged using the
allcontributors package
following the allcontributors
specification. Contributions of any kind are welcome!