Code to evaluate occupancy and surface availability of Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in northern California, 2023-2024
September 9, 2025
The code in this repository generates and analyzes directed acyclic graphs (DAGs) representing hypotheses about variables affecting the occurrence and surface availability of Plethodon salamanders in northern California; formats data from field surveys and GIS for analysis; and analyzes multi-scale occupancy models, including model selection, to evaluate the model and variables with the best predictive performance for evaluating occurrence and surface availability of the salamanders.
Citation Information
| Publication Year | 2025 |
|---|---|
| Title | Code to evaluate occupancy and surface availability of Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in northern California, 2023-2024 |
| DOI | 10.5066/P13OD6HA |
| Authors | Brian J Halstead, Daniel A Macias, Casey D Moss, Patrick M Kleeman, Jonathan P Rose |
| Product Type | Software Release |
| Record Source | USGS Asset Identifier Service (AIS) |
| USGS Organization | Western Ecological Research Center - Headquarters |
| Rights | This work is marked with CC0 1.0 Universal |
Related
Occurrence and surface availability of Siskiyou Mountains Salamanders (Plethodon stormi) and Scott Bar Salamanders (P. asupak) in northern California Occurrence and surface availability of Siskiyou Mountains Salamanders (Plethodon stormi) and Scott Bar Salamanders (P. asupak) in northern California
Estimating the distributions of cryptic species is essential for conservation, yet our understanding is hampered by animal behavior and imperfect detection. We developed and implemented a multiscale occupancy survey protocol to estimate the probability of occurrence, probability of being active on the surface, and detection probability of two range-restricted terrestrial salamanders...
Authors
Brian J. Halstead, Daniel Antonio Macias, Casey D. Moss, Patrick M. Kleeman, Jonathan P. Rose
Brian Halstead
Research Wildlife Biologist
Research Wildlife Biologist
Email
Phone
Patrick M Kleeman
Supervisory Ecologist
Supervisory Ecologist
Email
Phone
Related
Occurrence and surface availability of Siskiyou Mountains Salamanders (Plethodon stormi) and Scott Bar Salamanders (P. asupak) in northern California Occurrence and surface availability of Siskiyou Mountains Salamanders (Plethodon stormi) and Scott Bar Salamanders (P. asupak) in northern California
Estimating the distributions of cryptic species is essential for conservation, yet our understanding is hampered by animal behavior and imperfect detection. We developed and implemented a multiscale occupancy survey protocol to estimate the probability of occurrence, probability of being active on the surface, and detection probability of two range-restricted terrestrial salamanders...
Authors
Brian J. Halstead, Daniel Antonio Macias, Casey D. Moss, Patrick M. Kleeman, Jonathan P. Rose
Brian Halstead
Research Wildlife Biologist
Research Wildlife Biologist
Email
Phone
Patrick M Kleeman
Supervisory Ecologist
Supervisory Ecologist
Email
Phone