Dataset DOI: 10.5061/dryad.zcrjdfnsc

Description of the data and file structure

Our objective was to identify behavioral risk factors for SARS-CoV-2 by linking serostatus of individual deer to their space use and movement traits using multilevel logistic regression. Our sample consisted of white-tailed (Odocoileus virginianus) and mule deer (O. hemionus) wearing GPS devices from across an urban-rural gradient in the United States (1151 individuals, 20 sites, eight states). 

Note that the raw movement data (GPS points) are not made available in this dataset since they are sensitive and our data-sharing agreements forbid publication. Instead, we share a data frame that summarizes deer movement at an individual level and was input for our models.  We may be able to make the raw movement data available to individuals upon reasonable request.

Files and variables

File: 1MovementDataPrep_Generalized.R

Description: Contains the code used to clean raw movement data. Was used by collaborators on their data, which was then sent to the first author for analysis

File: 2ConcatenatingMovementData.R

Description: Contains code used to bring together and make consistent the cleaned movement data from various sites. 

File: 3TestingDataPrep.R

Description: Contains code to clean the SARS-CoV-2 test result data from the lab.

File: 5DataExploration.R

Description: Contains code that standardizes variables and briefly explores the data for trends.

File: 6Modeling.R

Description: Contains the code used to build and compare models based on the 4-month dataset, as well as for creating Figure S3

File: 4Site_Environmental_Layer_and_Covariate_Prep.R

Description: Contains the code that extracted and summarized demographic, space use, and movement data for each deer.

File: 7Sensitivity_Analysis.R

Description: Contains code that was used to compare results between the 2-,4-4, and 6-month covariate extraction windows.

File: 8Figures.R

Description: Contains code that was used to make the figures in the paper.

File: Covariate_Summary.csv

Description: This file contains the summarized data at the 2-month interval for each deer in the analysis. The raw movement data could be made available by the authors upon reasonable request. NaN indicates the number is not available (usually refers to samples that were PCR negative for SARS-CoV-2)? NA indicates values that are not available due to either not being tested or a negative result.

Variables

• Barcode: the ID number used to keep track of a given SARS-CoV-2 sampling event
• id: the ID number of the animal
• sex: sex of the animal
• test_date: the date on which the sampling event took place
• year_biological: the year in which an animal was sampled
• species: deer species of the animal
• age_class: Was the animal a juvenile or adult
• ww_conc_county_av: average amount of SCV2 DNA in the human wastewater in the previous 13 months in the study site county
• pop_dens_av: average human population density of points for a given animal.
• hfpt_av: average human footprint index value of points for a given animal.
• GAP_prop: proportion of deer locations in suitable deer habitat as determined by USGS GAP analysis
• dev_prop: proportion of points in NLCD development
• forest_prop: proportion of points in NLCD forest habitat
• state: state sampling event took place 
• site: site where sampling event took place
• positive_serology: was the event positive for SARS-COV-2 based on sVNT
• median_sl: median step length for each individual
• median_speed: median speed for each individual
• pop_dens_standardized: standardized (z-score) average human population density of points for a given animal.
• max_dist_mean: average maximum distance between points over 6 days
• max_dist_standardized: standardized (z-score) average maximum distance between points over 6 days
• ww_conc_standardized: standardized (z-score) average amount of SCV2 DNA in the human wastewater in the previous 13 months in the study site county

File: TestData.csv

Description: Gives the raw SARS-CoV-2 testing data used in our study.

Variables

• Barcode: USDA barcode assigned to a particular sample - should be unique in each row
• Animal_ID: ID assigned to a live-captured animal that will be used to track the individual over time - can repeat across rows if the animal is caught multiple times
• Collection_Date: Date that the sample was collected
• Collection_Site_Name: Site where the sample was collected
• State: State where the sample was collected
• Species: Species the sample was collected from (White-tailed Deer or Mule Deer)
• Sex: Sex of the individual the sample was collected from
• Age_Class: Age class of the individual the sample was collected from - fawn (<1 year), yearling (1-2), adult (2+), undetermined (age unknown)
• Harvest: What kind of sampling event was this: Live, Hunter (harvest), Agency (harvest or culling), Mortality
• N1_CQ_nasal: N1 quantification cycle for nasal swab sample
• N2_CQ_nasal: N2 quantification cycle for nasal swab sample
• Result_PCR_nasal: Result of nasal PCR test
• N1_CQ_oral: N1 quantification cycle for oral swab sample
• N2_CQ_oral: N2 quantification cycle for oral swab sample
• Result_PCR_oral: Result of oral PCR test. 
• R1PercentInh_sVNT_wildtype: Percent inhibition from the first sVNT run of a serum sample - run without omicron patch kit
• R2PercentInh_sVNT_wildtype: Percent inhibition from the second sVNT run of a serum sample - run without omicron patch kit
• AvePercentInh_sVNT_wildtype: Average percent inhibition from runs 1 and 2
• Result_sVNT_wildtype: Interpretation of average percent inhibition results
• R1PercentInh_sVNT_omicron: Percent inhibition from the first sVNT run of a serum sample - run with omicron patch kit
• R2PercentInh_sVNT_omicron: Percent inhibition from the second sVNT run of a serum sample - run with omicron patch kit
• AvePercentInh_sVNT_omicron: Average percent inhibition from runs 1 and 2
• Result_sVNT_omicron: Interpretation of average percent inhibition results
• R1PercentInh_Nobuto_wildtype: Percent inhibition from the first sVNT run of a Nobuto strip sample - run without omicron patch kit
• R2PercentInh_Nobuto_wildtype: Percent inhibition from the second sVNT run of a Nobuto strip sample - run without omicron patch kit
• AvePercentInh_Nobuto_wildtype: Average percent inhibition from runs 1 and 2
• Result_Nobuto_wildtype: Interpretation of average percent inhibition results
• R1PercentInh_Nobuto_omicron: Percent inhibition from the first sVNT run of a Nobuto strip sample - run with omicron patch kit
• R2PercentInh_Nobuto_omicron: Percent inhibition from the second sVNT run of a Nobuto strip sample - run with omicron patch kit
• AvePercentInh_Nobuto_omicron: Average percent inhibition for runs 1 and 2
• Result_Nobuto_omicron:Result_Nobuto_omicron: Interpretation of average percent inhibition

Code/software

Code was run in R version 4.4.2 via the RStudio IDE (version 2025.05.0). Required packages are in the code files. The order in which the scripts should be run is given by the numbers in the .R file names.