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Data and reproducibility scripts from: A method for characterizing disease emergence curves from paired pathogen detection and serology data

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posted on 2024-06-04, 21:42 authored by JOSHUA HEWITTJOSHUA HEWITT, Grete Wilson-Henjum, Derek Collins, Jourdan M. Ringenberg, Christopher Quintanal, Robert Pleszewski, Jeffrey C. Chandler, Thomas J. DeLiberto, Kim M. Pepin

The zip file contains data and analysis scripts written in R to analyze SARS-CoV-2 disease surveillance data (PCR and serological test results) from white-tailed deer in 3 counties in the United States. The zip file's README file contains additional descriptions about the workflow and output.

The manuscript to which this repository is a supplement describes data collection, processing, and analysis steps.

Funding

USDA-APHIS: American Rescue Plan

History

Data contact name

Hewitt, Joshua M.

Data contact email

Joshua.hewitt2@usda.gov

Publisher

Ag Data Commons

Intended use

The data and analysis scripts can be used to reproduce results for the manuscript to which this repository is a supplement. The analysis scripts also provide access to full posterior distributions, which can be used to explore and visualize model output in greater detail.

Use limitations

Data are anonymized and provided for 3 counties. The manuscript to which this repository is a supplement describes additional assumptions and limitations about the model and analysis. The simulation script is intended to be run on a high performance compute cluster running SLURM workload management software.

Temporal Extent Start Date

2021-10-17

Temporal Extent End Date

2022-10-02

Frequency

  • daily

Theme

  • Non-geospatial

Geographic location - description

Three anonymous counties in the northeast United States

ISO Topic Category

  • environment

National Agricultural Library Thesaurus terms

microbial detection; serology; disease surveillance; polymerase chain reaction; immunologic techniques; Odocoileus virginianus; United States; data collection; models; computer software; data collection; models; serology; deer; reverse transcriptase polymerase chain reaction; enzymes; antibodies; neutralization tests

OMB Bureau Code

  • 005:32 - Animal and Plant Health Inspection Service

Pending citation

  • No

Public Access Level

  • Public

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    Categories

    Keywords

    data fusionepidemiological process modelhierarchical modelingpaired data

    Licence

    CC BY 4.0

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