Software

This software release contains the code necessary to run the chronic wasting disease (CWD) and elk habitat selection models used to support the U.S. Forest Service decision on whether to continue to permit supplemental feeding of elk on USFS land. The models allow for four different management alternatives: continued feeding, emergency feeding, phase-out after three years, or no feeding...

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...

Code will be submitted to the Dryad repository upon acceptance of the manuscript. These R code are used for simulations and case studies. Simulations include data for generating age-period survival data. We have provided code for each of the 10 models that were fit using NIMBLE, where each model has four R scripts including: 1) A script to execute and run all the additional R scripts for...

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 submitted to Journal of Environmental Management and ScienceBase for running Bayesian hierarchical models on a dataset that was collected using expert elicitation of a panel of 15 experts on the etiology of stony coral tissue loss disease and its impacts on coral reefs. The code is for a rapid prototyping method for quantifying belief weights for competing hypotheses about the...

This repository contains all of the scripts to reproduce the analyses, figures, and tables associated with the manuscript Lee et al. in prep. The scripts are organized in the order in which they should be run. Briefly, the files do the following: format the data, fit the model, create the figures, and create the tables.

This repository contains all of the scripts to reproduce the analyses, figures, and tables associated with the manuscript Glorioso et al. in review. The scripts are organized into folders, and the folders are numbered in the order in which they should be executed. Briefly, there are six folders that do the following: (1) format the data, (2) fit the model, (3) run the population...

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...

The purpose of this study was to estimate the survival of giant gartersnakes (Thamnophis gigas) prior to and following translocation, as well as to evaluate the use of captive rearing as a conservation tool for giant gartersnakes. We used Kaplan-Meier and Cox Proportional Hazards models to estimate survival rates and estimate the effects of group identity (marsh donor, rice donor, and...

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...

Code to reproduce analyses of turtle occupancy in the Sacramento Valley and Sacramento-San Joaquin River Delta

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...