Software

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 published separa

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 and samplin

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 simulated da

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) in Point

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 gartersnake (

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. This code

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 registered to sage

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-grouse surviva

This repository centralizes R code used to examine how the influence of fine-scale habitat characteristics on Greater sage-grouse (Centrocercus urophasianus) nest site selection and nest survival varies by mesic and xeric site conditions, utilizing data collected from a wide range of study sites in Nevada and California, USA. The R script "nest_selection_model.R" provides code for a GLMM framewor

rsgis: A package to facilitate greater sage-grouse management in the western US The rsgis package centralizes several publicly available geospatial datasets that are essential to mapping and modeling for Greater sage-grouse (Centrocercus urophasianus) management applications, including important habitat and breeding areas for sage-grouse and political/regional boundaries. To cite the package, plea

raventools: A package to facilitate raven management in the western U.S. The raventools package centralizes several publicly available geospatial datasets that are essential to mapping and modeling for common raven (Corvus corax) management applications, including raven occurrence and density data, sensitive species distribution data, raven subsidy data, and Greater sage-grouse (Centrocercus uroph

The purpose of this study was to evaluate how extreme variation in precipitation in the Sierra Nevada of California, USA, in the early 21st Century affected adult occupancy and the probability of reproduction of amphibians. The study used a 15-year data set to relate site characteristics to initial probability of occurrence of adults, and additional site-specific and dynamic (e.g., weather) variab