[!CAUTION] This project is a work-in-progress. Any outputs may be misleading or even incorrect. Despite this project's early stage, all development is in public as part of the Center for Forecasting and Outbreak Analytics' goals around open development. Questions and suggestions are welcome through GitHub issues or a PR.
This project is an in-development R package for $R_t$ estimation using generalized additive models (GAMs).
Over the last few years, GAMs have been used with some success to estimate epidemic growth rates and nowcast cases (see Ward, 2021 and Mellor, 2023 for an overview of methods).
The R package {mgcv} provides a flexible, fast, and robust interface to fit penalized-spline based models.
However, the substantial research effort into spline-based approaches has not been unified into a shared R package.
This R package aims to become an opinionated re-implementation of the literature methods, with reasonable defaults for real-time epidemic modeling.
Development effort is optimized around real-time use-cases, with potential for right-truncation, noisy reporting, and uncertain data-generating processes.
It is meant to be a simple drop-in tool to be run alongside more computationally intensive implementations like {EpiNow2}.
This repository was created for use by CDC programs to collaborate on public health related projects in support of the CDC mission. GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.
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This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.
This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.
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