Software
Filter Total Items: 31
Code to analyze fuel breaks and exotic annual grass associations within sagebrush ecosystems of the western USA Code to analyze fuel breaks and exotic annual grass associations within sagebrush ecosystems of the western USA
Methods Summary This repository supports the manuscript "Invasion resistance varies by fuel break type in sagebrush ecosystems." The analysis evaluated the relationship between fuel break treatments and exotic annual grass cover across the sagebrush biome using two complementary approaches: 1. Space-for-Time Substitution Analysis: We used 52,109 Bureau of Land Management AIM vegetation...
Code to evaluate occupancy and surface availability of Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in northern California, 2023-2024 Code to evaluate occupancy and surface availability of Siskiyou Mountains salamanders (Plethodon stormi) and Scott Bar salamanders (P. asupak) in northern California, 2023-2024
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...
Code to estimate effects of rice growing on growth and survival of giant gartersnakes, Thamnophis gigas Code to estimate effects of rice growing on growth and survival of giant gartersnakes, Thamnophis gigas
This repository specifically contains code to reproduce analyses in: Rose, J.P., Nguyen, A.M., Jordan, A.C., Macias, D.A., Schoenig, E.J., Napolitano G.R., Kim, R., Ersan, J.S.M., Fulton, A.M., and Halstead, B.J. 2025. Rice cultivation supports growth and survival of a threatened semi-aquatic reptile. In review.
Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park Code to evaluate the effect of weather on the demography of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite National Park
This repository contains code to fit open population models to capture-mark-recapture data for Sierra Nevada yellow-legged frogs (Rana sierrae). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., Rose, J.P., and Fellers, G.M. 2025. Climate-induced extirpation of a population of Sierra Nevada yellow-legged frogs (Rana sierrae) in Yosemite...
Grazing Management Tool Grazing Management Tool
Science-based grazing management is crucial to preserving and improving rangeland productivity and sagebrush ecosystem health. By adjusting the timing, duration, frequency, and intensity of grazing, managers can contribute to ecosystem services such as fuel reduction and invasive annual grass control. They can also utilize rotational grazing to minimize or mitigate impacts on sensitive...
Code to examine habitat selection and survival of greater sage-grouse in Nevada and northeastern California Code to examine habitat selection and survival of greater sage-grouse in Nevada and northeastern California
This repository centralizes R code used to examine habitat selection and survival of greater sage-grouse (Centrocercus urophasianus) during multiple seasons and life stages, utilizing data collected from a wide range of study sites in Nevada and California, USA. The R script "selection_model.R" provides code for a GLMM framework with regularization within a Bayesian modeling environment...
Code for Population and survival models of greater sage-grouse to investigate effects of precipitation and drought in the Great Basin, USA Code for Population and survival models of greater sage-grouse to investigate effects of precipitation and drought in the Great Basin, USA
This repository includes R code to run nest, brood, and adult hierarchical logistic exposure models, used for analyzing survival responses of Greater sage-grouse (Centrocercus urophasianus) to a suite of environmental covariates, with emphasis on precipitation and/or drought effects. An example population state-space model (the top model according to WAIC; see manuscript results and...
Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam Code to create periodic matrix models and simulate population reintroductions for four lizards on Guam
This repository contains code to construct periodic matrix models representing the demography of four lizard species native to or extant on Guam.
Custom Wildlife Report Example for Sacramento National Wildlife Refuge 1.0.0 Custom Wildlife Report Example for Sacramento National Wildlife Refuge 1.0.0
The Custom Wildlife Report Example for Sacramento National Wildlife Refuge provides an approach for summarizing wildlife GPS data and creates tables, maps, and visualizations. Specifically, the Custom Wildlife Report Example for Sacramento National Wildlife Refuge, creates an interactive HTML report document that lets users interact with maps of waterfowl locations and filter and sort...
Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022 Code to evaluate the effect of the 2021 Dixie Fire on the occurrence of foothill yellow-legged frogs (Rana boylii) in northeastern California in 2022
This repository contains code to fit a static occupancy model to time-to-detection data for foothill yellow-legged frogs (Rana boylii). This repository specifically contains code to reproduce analyses in: Halstead, B.J., Kleeman, P.M., and Rose, J.P., 2024, Using structural causal modeling to infer the effects of wildfire on foothill yellow-legged frog occurrence: Journal of Fish and...
Geofetch Geofetch
geofetch is an R package that provides an interface for interacting with online rasters. By making use of drivers from the Geospatial Data Abstraction Library (GDAL) for accessing online rasters, it facilitates efficient raster operations by only retrieving data that falls in the user-specified area of interest. The package is built so that adding interfaces to new datasets is simple...
Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae Code for multi-scale occupancy analysis of Temblor legless lizards, Anniella alexanderae
This repository contains code to fit Multi-scale Occupancy Models to survey data for Temblor legless lizards (Anniella alexanderae) This repository specifically contains code to reproduce analyses in: Rose, J.P., Camp, S.M., Sheikh, Z.N., Johnson, C.B., Lei, S.H., Napolitano, G.R., Schoenig, E.J., Macias, D.A., Jordan, A.C., and Halstead, B.J. 2024. Multi-scale occupancy surveys reveal