Data from: Data-driven management — A dynamic occupancy approach to enhanced rabies surveillance prioritization

Metadata:
Identification_Information:
Citation:
Citation_Information:
Originator: Davis, Amy J.
Originator: Kirby, Jordona D.
Originator: Chipman, Richard B.
Originator: Nelson, Kathleen M.
Originator: Gilbert, Amy T.
Publication_Date: 2021
Title:
Data from: Data-driven management — A dynamic occupancy approach to enhanced rabies surveillance prioritization
Geospatial_Data_Presentation_Form: tabular digital data
Series_Information:
Series_Name: Research Dataset Series
Publication_Information:
Publication_Place: Fort Collins, CO
Publisher: USDA, APHIS, WS National Wildlife Research Center
Online_Linkage: https://doi.org/10.2737/NWRC-RDS-2021-002
Description:
Abstract:
Rabies lyssavirus (RABV) is enzootic in raccoons across the eastern United States. Intensive management of RABV by oral rabies vaccination (ORV) has prevented its spread westward and shown evidence of local elimination in raccoon populations of the northeastern United States. The USDA, Wildlife Services, National Rabies Management Program (NRMP) collaborates with other agencies to implement broad-scale ORV and conducts extensive monitoring to measure the effectiveness of the management. Enhanced Rabies Surveillance (ERS) was initiated during 2005 and updated in 2016 to direct surveillance efforts toward higher-value specimens by assigning points to different methods of encountering specimens for collection (strange-acting, roadkill, surveillance-trapped, etc.; specimen point values ranged from 1 to 15). The data provided are ERS data from 2016–2019 spanning from Alabama to Maine. The eastern U.S. was split into two regions: the northeastern U.S. (New York, Vermont, New Hampshire, and Maine) and the lower eastern U.S. (Alabama, Georgia, Kentucky, North Carolina, Ohio, Pennsylvania, Tennessee, Virginia, and West Virginia). Only the counties within the ERS area were included from each state. The two regions were overlayed with a 10 by 10 kilometer grid. The data include the region, grid ID, season, year, surveillance category, state, county, and the number of positive rabies samples as well as the number of total surveillance samples collected.
Purpose:
These data were collected as part of the Enhanced Rabies Surveillance program to monitor for the raccoon variant of the rabies virus along the eastern United States.
Supplemental_Information:
For more information about this study and these data, see Davis et al. (2021).

Original publication date was 09/08/2021. Metadata updated on 10/14/2021 to include citation information for related journal article.
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 2016
Ending_Date: 2019
Currentness_Reference:
Ground condition
Status:
Progress: Complete
Maintenance_and_Update_Frequency: As Needed
Spatial_Domain:
Description_of_Geographic_Extent:
Eastern United States
Bounding_Coordinates:
West_Bounding_Coordinate: -88.24
East_Bounding_Coordinate: -66.95
North_Bounding_Coordinate: 47.46
South_Bounding_Coordinate: 32.30
Bounding_Altitudes:
Altitude_Minimum: 0
Altitude_Maximum: 2037
Altitude_Distance_Units: meters
Keywords:
Theme:
Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: biota
Theme:
Theme_Keyword_Thesaurus: National Research & Development Taxonomy
Theme_Keyword: Wildlife (or Fauna)
Theme_Keyword: Mammals
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: detection probability
Theme_Keyword: dynamic occupancy
Theme_Keyword: rabies lyssavirus
Theme_Keyword: raccoon
Theme_Keyword: procyon lotor
Theme_Keyword: science-based management
Theme_Keyword: surveillance
Theme_Keyword: wildlife disease
Place:
Place_Keyword_Thesaurus: None
Place_Keyword: eastern United States
Place_Keyword: New York
Place_Keyword: Vermont
Place_Keyword: New Hampshire
Place_Keyword: Maine
Place_Keyword: Alabama
Place_Keyword: Georgia
Place_Keyword: Kentucky
Place_Keyword: North Carolina
Place_Keyword: Ohio
Place_Keyword: Pennsylvania
Place_Keyword: Tennessee
Place_Keyword: Virginia
Place_Keyword: West Virginia
Taxonomy:
Keywords/Taxon:
Taxonomic_Keyword_Thesaurus:
None
Taxonomic_Keywords: single species
Taxonomic_Keywords: mammals
Taxonomic_System:
Classification_System/Authority:
Classification_System_Citation:
Citation_Information:
Originator: ITIS
Publication_Date: 2021
Title:
Integrated Taxonomic Information System
Geospatial_Data_Presentation_Form: database
Other_Citation_Details:
Retrieved [September, 8, 2021]
Online_Linkage: https://www.itis.gov
Taxonomic_Procedures:
Taxonomic_Classification:
Taxon_Rank_Name: Kingdom
Taxon_Rank_Value: Animalia
Applicable_Common_Name: Animal
Applicable_Common_Name: animaux
Applicable_Common_Name: animals
Taxonomic_Classification:
Taxon_Rank_Name: Subkingdom
Taxon_Rank_Value: Bilateria
Taxonomic_Classification:
Taxon_Rank_Name: Infrakingdom
Taxon_Rank_Value: Deuterostomia
Taxonomic_Classification:
Taxon_Rank_Name: Phylum
Taxon_Rank_Value: Chordata
Applicable_Common_Name: cordés
Applicable_Common_Name: cordado
Applicable_Common_Name: chordates
Taxonomic_Classification:
Taxon_Rank_Name: Subphylum
Taxon_Rank_Value: Vertebrata
Applicable_Common_Name: vertebrado
Applicable_Common_Name: vertébrés
Applicable_Common_Name: vertebrates
Taxonomic_Classification:
Taxon_Rank_Name: Infraphylum
Taxon_Rank_Value: Gnathostomata
Taxonomic_Classification:
Taxon_Rank_Name: Superclass
Taxon_Rank_Value: Tetrapoda
Taxonomic_Classification:
Taxon_Rank_Name: Class
Taxon_Rank_Value: Mammalia
Applicable_Common_Name: mammifères
Applicable_Common_Name: mamífero
Applicable_Common_Name: mammals
Taxonomic_Classification:
Taxon_Rank_Name: Subclass
Taxon_Rank_Value: Theria
Taxonomic_Classification:
Taxon_Rank_Name: Infraclass
Taxon_Rank_Value: Eutheria
Taxonomic_Classification:
Taxon_Rank_Name: Order
Taxon_Rank_Value: Carnivora
Applicable_Common_Name: cachorro do mato
Applicable_Common_Name: carnívoro
Applicable_Common_Name: gato do mato
Applicable_Common_Name: lontra
Applicable_Common_Name: carnivores
Applicable_Common_Name: carnivores
Taxonomic_Classification:
Taxon_Rank_Name: Suborder
Taxon_Rank_Value: Caniformia
Applicable_Common_Name: dog-like carnivores
Taxonomic_Classification:
Taxon_Rank_Name: Family
Taxon_Rank_Value: Procyonidae
Applicable_Common_Name: procyonids
Taxonomic_Classification:
Taxon_Rank_Name: Genus
Taxon_Rank_Value: Procyon
Applicable_Common_Name: raccoons
Taxonomic_Classification:
Taxon_Rank_Name: Species
Taxon_Rank_Value: Procyon lotor
Applicable_Common_Name: Raccoon
Applicable_Common_Name: northern raccoon
Applicable_Common_Name: Mapache común
Applicable_Common_Name: common raccoon
Applicable_Common_Name: raton laveur
Access_Constraints: None
Use_Constraints:
These data were collected using funding from the U.S. Government and can be used without additional permissions or fees. If you use these data in a publication, presentation, or other research product please use the following citation:

Davis, Amy J.; Kirby, Jordona D.; Chipman, Richard B.; Nelson, Kathleen M.; Gilbert, Amy T. 2021. Data from: Data-driven management — A dynamic occupancy approach to enhanced rabies surveillance prioritization. Research Dataset Series. USDA, APHIS, WS National Wildlife Research Center. Ft. Collins, Colorado. https://doi.org/10.2737/NWRC-RDS-2021-002
Point_of_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Amy Douglas
Contact_Organization: USDA, APHIS, Wildlife Service, National Wildlife Research Center
Contact_Position: Computational Biologist
Contact_Address:
Address_Type: mailing and physical
Address: 4101 LaPorte Ave
City: Fort Collins
State_or_Province: CO
Postal_Code: 80521
Country: USA
Contact_Voice_Telephone: 970-266-6313
Contact_Electronic_Mail_Address: amy.j.davis@usda.gov
Data_Set_Credit:
This project was funded by United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center.

Author Information:

Amy J. Davis
National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Fort Collins, CO

Jordona D. Kirby
National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Concord, NH

Richard B. Chipman
National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Concord, NH

Kathleen M. Nelson
National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Concord, NH

Amy T. Gilbert
National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection Service, U.S. Department of Agriculture, Fort Collins, CO
https://orcid.org/0000-0002-8256-0081
Cross_Reference:
Citation_Information:
Originator: Davis, Amy J.
Originator: Kirby, Jordona D.
Originator: Chipman, Richard B.
Originator: Nelson, Kathleen M.
Originator: Gilbert, Amy T.
Publication_Date: 2021
Title:
Data-driven management — A dynamic occupancy approach to enhanced rabies surveillance prioritization
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Viruses
Issue_Identification: 13(9): 1795
Online_Linkage: https://doi.org/10.3390/v13091795
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Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report:
The direct rapid immunohistochemical test (dRIT) for rabies has been evaluated to be 100% sensitive and specific at diagnosing rabies.
Logical_Consistency_Report:
Extensive data checking on sample locations and collection methods was conducted by field personnel and secondarily by Wildlife Services personnel.
Completeness_Report:
Only samples that were collected from specimens that were of sufficient quality to perform a dRIT rabies test were included in this data set. If a rabies test was not able to be conducted the data were not included.
Lineage:
Methodology:
Methodology_Type: Field
Methodolgy_Identifier:
Methodolgy_Keyword_Thesaurus:
None
Methodology_Keyword: cage trapping
Methodology_Keyword: road kill surveys
Methodology_Keyword: public reporting
Methodology_Description:
We used Enhanced Rabies Surveillance (ERS) data from raccoon specimens collected by USDA, APHIS, Wildlife Service (WS) during 2016–2019 across all counties within two regions of the eastern United States (northeastern and lower eastern U.S.). ERS uses a range of methods to collect surveillance samples and coordinate with a range of state and local agencies (USDA 2008, Kirby et al. 2017) in order to document changes in the incidence of RABV infection in target populations. The data include samples from raccoons or other species that tested positive for the racoon variant of the rabies virus, that were collected either by being reported by the public as being strange acting or found dead, by road kill surveys, being trapped for surveillance by WS personnel, or as nuisance animals reported by the public. The WS ERS surveillance data included: date of specimen collection, species, location (latitude and longitude), surveillance method, and RABV status (positive or negative). RABV status testing was conducted by testing brainstem tissue samples collected from each animal using a direct rapid immunohistochemical test.

Only the counties within the ERS area were included from each state. The two regions were overlayed with a 10 by 10 kilometer grid and then the number of positive rabies samples as well as the number of total surveillance samples collected were aggregated for each region, grid ID, season, state, county, and year. The grid IDs are specific to each region. The state and county information are provided as well. Some grids span more than one county or state and the county or state level information for each grid is provided.

For more information see Davis et al. (2021).
Methodology_Citation:
Citation_Information:
Originator: Davis, Amy J.
Originator: Kirby, Jordona D.
Originator: Chipman, Richard B.
Originator: Nelson, Kathleen M.
Originator: Gilbert, Amy T.
Publication_Date: 2021
Title:
Data-driven management — A dynamic occupancy approach to enhanced rabies surveillance prioritization
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Viruses
Issue_Identification: 13(9): 1795
Online_Linkage: https://doi.org/10.3390/v13091795
Methodology_Citation:
Citation_Information:
Originator: USDA
Publication_Date: 2008
Title:
North American rabies management plan
Geospatial_Data_Presentation_Form: document
Publication_Information:
Publication_Place: Concord, NH, USA
Publisher: U.S. Department of Agriculture
Methodology_Citation:
Citation_Information:
Originator: Kirby, Jordona D.
Originator: Chipman, Richard B.
Originator: Nelson, Kathleen M.
Originator: Rupprecht, Charles E.
Originator: Blanton, Jesse D.
Originator: Algeo, Timothy P.
Originator: Slate, Dennis
Publication_Date: 2008
Title:
Enhanced rabies surveillance to support effective oral rabies vaccination of raccoons in the eastern United States
Geospatial_Data_Presentation_Form: journal article
Series_Information:
Series_Name: Tropical Medicine and Infectious Disease
Issue_Identification: 2(3): 34
Online_Linkage: https://doi.org/10.3390/tropicalmed2030034
Process_Step:
Process_Description:
The data were aggregated to the grid cell level for analysis (Davis et al. 2021) and to make the data publicly available.
Process_Date: Unknown
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Entity_and_Attribute_Information:
Overview_Description:
Entity_and_Attribute_Overview:
Below you will find a list and description of the files included in this data publication.

\Data\SurveillanceData.csv: Comma-delimited ASCII text file containing the number of rabies positive samples and the number of total samples from rabies surveillance data by region (northeast or lower eastern United States), grid ID (site), season, year, and surveillance method.

Variables include:

Region = region (northeast or lowereast)

GridID = grid ID (site)

Season = season of year (Fall, Spring, Summer, Winter)

Year = year sample was taken

Category = type of sample (Found dead, Non-raccoon sample, Road kill, Strange acting, Surveillance trapped, Unknown, or NWCO-Other [which means Nuisance Wildlife Control Operators, these are animals that were reported as nuisance animals and collected by non-Wildlife Service personnel])

State = name of the state the samples were collected in within the grid

County = name of the county the samples were collected in within the grid

Rabies = number of rabies positive samples (0-8)

Samples = total number of samples taken
Entity_and_Attribute_Detail_Citation:
Davis, Amy J.; Kirby, Jordona D.; Chipman, Richard B.; Nelson, Kathleen M.; Gilbert, Amy T. 2021. Data from: Data-driven management — A dynamic occupancy approach to enhanced rabies surveillance prioritization. Viruses 13(9): 1795. https://doi.org/10.3390/v13091795
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Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: USDA Forest Service, Research and Development
Contact_Position: Research Data Archivist
Contact_Address:
Address_Type: mailing and physical
Address: 240 West Prospect Road
City: Fort Collins
State_or_Province: CO
Postal_Code: 80526
Country: USA
Contact_Voice_Telephone: see Contact Instructions
Contact Instructions: This contact information was current as of October 2021. For current information see Contact Us page on: https://doi.org/10.2737/RDS.
Resource_Description: NWRC-RDS-2021-002
Distribution_Liability:
Metadata documents have been reviewed for accuracy and completeness. Unless otherwise stated, all data and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. However, neither the author, the Archive, nor any part of the federal government can assure the reliability or suitability of these data for a particular purpose. The act of distribution shall not constitute any such warranty, and no responsibility is assumed for a user's application of these data or related materials.

The metadata, data, or related materials may be updated without notification. If a user believes errors are present in the metadata, data or related materials, please use the information in (1) Identification Information: Point of Contact, (2) Metadata Reference: Metadata Contact, or (3) Distribution Information: Distributor to notify the author or the Archive of the issues.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: ASCII
Format_Version_Number: see Format Specification
Format_Specification:
Comma-delimited ASCII text file (CSV)
File_Decompression_Technique: Files zipped with 7-Zip 19.0
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information:
Network_Address:
Network_Resource_Name: https://doi.org/10.2737/NWRC-RDS-2021-002
Fees: None
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Metadata_Reference_Information:
Metadata_Date: 20211014
Metadata_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Amy Douglas
Contact_Organization: USDA, APHIS, Wildlife Service, National Wildlife Research Center
Contact_Position: Computational Biologist
Contact_Address:
Address_Type: mailing and physical
Address: 4101 LaPorte Ave
City: Fort Collins
State_or_Province: CO
Postal_Code: 80521
Country: USA
Contact_Voice_Telephone: 970-266-6313
Contact_Electronic_Mail_Address: amy.j.davis@usda.gov
Metadata_Standard_Name: FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001.1-1999
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