Software
Filter Total Items: 23
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
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 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
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...
Methylmercury Effects on Birds: Percent Injury Tool
Welcome to The Bird Mercury Tool website. Please follow the guidance below to download the tool and user guide. The Bird Mercury Tool: Estimating Methylmercury Injury to Birds can be used by practitioners to help interpret injury to birds caused by methylmercury concentrations in bird tissues or diet. The dataset, statistical models, and assumptions used within this tool have been...
Code to analyze static occupancy of northwestern pond turtles (Actinemys marmorata) in timberland streams in the interior foothills of northern California
The purpose of this study was to evaluate the distribution of northwestern pond turtles (Actinemys marmorata) and invasive American bullfrogs (Lithobates catesbeianus) in private timberland streams of interior northern California, USA. Fieldwork for the study occurred in 2021-2022 in Lassen, Plumas, Shasta, Tehama, and Trinity counties, California, and involved visual encounter surveys...
Code for a spatially interpolated integrated population model applied to simulations of spatially autocorrelated Greater Sage-Grouse (Centrocercus urophasianus) population data
This repository contains R code to: 1. Simulate spatially autocorrelated count and demographic data for 10 populations using mean and process variance estimates from a long-term (1938–2011), range-wide meta-analysis of Greater Sage-Grouse (Centrocercus urophasianus) population dynamics (Taylor et al., 2012). 2. Fit a spatially interpolated integrated population model (SIIPM) to the...
Code to fit spatially explicit capture-recapture models to trapping data for western deer mice (Peromyscus sonoriensis) at Point Reyes National Seashore
This repository contains code to fit Spatially-Explicit Capture Recapture (SECR) Models to trapping data for Peromyscus sonoriensis (deer mice) at Point Reyes National Seashore and reproduce analyses in the following manuscript: Rose, J.P., Parsons, L.S., Kleeman, P.M., and Halstead, B.J. 2024. Effect of invasive plant removal on the density of Peromyscus sonoriensis (western deer mice)...
Code to fit Integral Projection Models and simulate population reintroductions for San Francisco Gartersnakes, Thamnophis sirtalis tetrataenia
This repository contains code to fit Integral Projection Models and simulate population reintroductions for San Francisco gartersnakes (Thamnophis sirtalis tetrataenia) This repository specifically contains code to reproduce analyses in: Rose, J.P., Kim, R., Schoenig, E.J., Lien, P.C., and Halstead, B.J. in-review. Comparing reintroduction strategies for the endangered San Francisco...
Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California
Code to fit a Multiple Population Viability Analysis (MPVA) to time series of Foothill yellow-legged frog (Rana boylii) egg mass counts. Rose, J.P., and Halstead, B.J., 2023, Code for Multiple Population Viability Analysis of egg mass time series from the Foothill Yellow-legged Frogs (Rana boylii) in California: U.S. Geological Survey software release, https://doi.org/10.5066/P9QWX2GR...
Code for a hierarchical model of raven densities linked with sage-grouse nest survival to help guide management of subsidized avian predators, version 1.0
This repository includes R code to conduct hierarchical density surface modeling of common raven (Corvus corax) point count data and hierarchical shared frailty modeling of Greater sage-grouse (Centrocercus urophasianus) nest fates. The model components are quantitatively linked, such that estimates of raven density from the hierarchical distance sampling component are spatially...
Conservation Planning Tool for the Bi-State Distinct Population Segment of Greater Sage-grouse
The Bi-State conservation planning tool provides a science-based approach for prioritizing pinyon (Pinus spp.) and juniper (Juniperus osteosperma, J. occidentalis), hereafter, 'conifer', removal to improve habitat for greater sage-grouse (Centrocercus urophasianus) in the Bi-State Distinct Population Segment (DPS, U.S. Fish and Wildlife Service 2010). Conifer negatively affects sage...