Program Repository for "Tools for Analyzing Infectious Disease Sequence Data and Forecasting Public Health Outcomes"
This repository contains all open source code developed for the studies, experiments, and publications for the Directed Research project entitled, "Merging Sequence Data with Epidemiological Forecasting to Predict Future Pandemics." This project began in Fiscal Year 2024 at Los Alamos National Lab under the Laboratory Directed Research and Development (LDRD) program. The project leads are:
- Sara Del Valle (PI) [email protected];
- Dave Osthus (co-PI) [email protected];
- Will Fischer (co-PI) [email protected].
For questions, issues, or clarifications on individual projects, contact information is available in the appropriate project directory.
This repository is organized according to several directories. Each directory contains the code for an individual study within this wider project. Additional directories will be added as projects complete. The current completed code bases are:
- incidence_for_sir: code to perform the studies and data application for publication 1 (see below);
- A.C. Murph, G.C. Gibson, L.B. VanDervort, N. Panda, L.A. Castro, S. Del Valle, D. Osthus. (202x). Incorporating Incidence Peak and Time Data for SIR Forecasting Applications. Undergoing Revisions.
These software have been approved for open source release and has been assigned O4726.
© 2024. Triad National Security, LLC. All rights reserved. This program was produced under U.S. Government contract 89233218CNA000001 for Los Alamos National Laboratory (LANL), which is operated by Triad National Security, LLC for the U.S. Department of Energy/National Nuclear Security Administration. All rights in the program are reserved by Triad National Security, LLC, and the U.S. Department of Energy/National Nuclear Security Administration. The Government is granted for itself and others acting on its behalf a nonexclusive, paid-up, irrevocable worldwide license in this material to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so.
This code repository is distributed under the BSD-3 License:
Copyright 2024. Triad National Security, LLC.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
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Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS” AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.