Multiple “spaces”: using wildlife surveillance, climatic variables, and spatial statistics to identify and map a climatic niche for endemic plague in California, U.S.A. 
Date repository last updated: November 22, 2022
- Ian D. Buller1 - Corresponding Author - ORCID
- Gregory M. Hacker2 - ORCID
- Mark G. Novak2
- James R. Tucker2
- A. Townsend Peterson3 - ORCID
- Lance A. Waller4 - Senior Author - ORCID
- Environmental Health Sciences, James T. Laney School of Graduate Studies, Emory University, Atlanta, GA, 30322, USA
- California Department of Public Health – Vector-Borne Disease Section, Sacramento, CA, 95814, USA
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
- Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA
We combine two analytic concepts (ecological niche modeling and spatial point processes) to identify plague-suitable climates and map their locations within California. Our approach uses serological samples from coyotes (Canis latrans), a sentinel species for plague, a zoonotic disease caused by the gram-negative bacterium, Yersinia pestis. The approach accounts for spatially heterogeneous sampling effort by considering locations of both seropositive (case) and seronegative (control) coyotes. Modification of Chapter 3 from Ian Buller's Doctoral Dissertation from Emory University (see Emory Theses and Dissertations Repository).
| Time | Event |
|---|---|
1981-2010 |
The Oregon State University Parameter-elevation Regression on Independent Slopes Model (PRISM) 30-year average climate normals at a 2.5 arcminute (~16 km2) resolution (see data availability section below). |
1983-2015 |
The California Department of Public Health – Vector-Borne Disease Section (CDPH-VBDS) digitized coyote blood samples tested for _Y. pestis_ antibodies (see data availability section below). |
October 2016 |
Project Initiation |
December 2020 |
The envi package in R published to the Comprehensive R Archive Network |
TBD |
Initial manuscript submission to _____ for peer-review |
TBD |
Manuscript accepted in _____ |
TBD |
Manuscript published in _____ |
This repository includes R scripts used to calculate a spatial relative risk function in "covariate space" and render the figures found in the following peer-reviewed manuscript:
Buller ID, Hacker GM, Novak MG, Tucker JR, Peterson AT, Waller LA. Multiple “spaces”: using wildlife surveillance, climatic variables, and spatial statistics to identify and map a climatic niche for endemic plague in California, U.S.A. _____ (Submitted)
| R Script | Description |
|---|---|
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Example paths for data. Must modify for your own system before beginning. |
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Load setting, prepare data, run the log RR model, and process the results to generate the figures. |
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Generate Figure 1 |
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Generate Figure 2 |
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Generate Figure 3 |
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Generate Supplemental Figure 1 |
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Generate Supplemental Figure 2 |
| Supplemental Figure 3 hand-generated, no code used | |
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Generate Supplemental Figure 4 |
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Generate Supplemental Figure 5 |
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Generate Supplemental Figure 6 |
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Generate Supplemental Figure 7 |
The repository also includes the code and resources to create the project hex sticker.
- Step 1: You must download the elevation BIL zipfile at 4km resolution from the PRISM data portal
- Step 2: Save the zipfile to the data directory in this repository
- Step 3: Set your own data paths to data in 'Paths.R' file
Wildlife plague surveillance data from the California Department of Public Health – Vector-Borne Disease Section (CDPH-VBDS) available upon request to CDPH-VBDS Infectious Diseases Branch - Surveillance and Statistics Section. The Oregon State University Parameter-elevation Regression on Independent Slopes Model (PRISM) 30-year average climate normals are available through the prism package in R or directly from the PRISM data portal.
For questions about the manuscript please e-mail the corresponding author Dr. Ian D. Buller.