Software

The aim of this software is to perform the simulations that evaluate the alternatives associated with the National Elk Refuge Bison and Elk Management Plan. In particular, it produces results associated with bison population dynamics, harvest, and conflict potential. For additional detail on the methodology and case study, please refer to: Cook, J.D., McEachran, M.C., Cotterill, G.G...

Package used to store and process data from the Multilevel Monitoring System (MLMS) used in wells within the U.S. Geological Survey (USGS) aquifer-monitoring network at the Idaho National Laboratory (INL) in Idaho. Supported by the U.S. Department of Energy (DOE), the USGS collected discrete measurements of hydraulic head at various depths from wells in the eastern Snake River Plain...

This is supporting code for the paper "Challenges and opportunities for data integration to improve estimation of migratory connectivity" by Jeffrey A. Hostetler, Emily B. Cohen, Christen M. Bossu, Amy L. Scarpignato, Kristen Ruegg, Andrea Contina, Clark S. Rushing, and Michael T. Hallworth in Methods in Ecology and Evolution. It allows the reader to run the simulations and case studies...

Catfishes are opportunistic feeders that are among the world's worst invasive species. Flathead catfish Pylodictus olivaris -- a large predatory catfish -- were first detected in the Susquehanna River, Pennsylvania, USA in 2002. Since then, they established a viable and rapidly growing population that is expanding its range throughout the river system. Although the predatory effects of...

This software was used to make derivatives of the features in the NHDPlusV2 geospatial dataset for use in hydrologic model applications. It is not intended for users to deploy/use and may produce unexpected results outside the workflow and environment in which it was implemented. For users seeking to deploy a version of this software, please see https://github.com/noaa-owp/hydrofab. The...

This repository is a code release to create and analyze simulated datasets to represent a tag-return study for the purposes of estimating annual removal rates of an invasive fish. The simulated scenarios cover ranges of parameters such as the number of fish tagged per year, magnitude of annual harvest rate, length of simulated study, probability of tag retention, probability of tag...

This package facilitates the analysis and evaluation of hydrologic model streamflow output during periods of drought. This package calculates the Cohen's Kappa, Spearman correlation coefficient, ratio of standard deviation, percent bias, normalized mean absolute error (NMAE) in the annual time series of drought duration, NMAE in the annual times series of the distance the minimum...

Code to estimate animal density from line transect surveys where auxiliary data are available to model the distribution of animals near the survey line and the distribution of animals across the study area.

This repository contains a R package with 2-level and 3-level occupancy models. The package also contains a set of tutorials designed to help users understand how to use and code occupancy models in Stan. The models include a statistical hierarchy that allows for multi-species modeling and estimating correlations among species. The models may also be used as a more general "random-effect...

Amid climate change and rapidly shifting land uses, effective methods for monitoring wildlife are critical to support scientifically-informed resource management decisions. As such, monitoring is motivated by ecological hypotheses or natural resource management objectives. The practice of using Autonomous Monitoring Units (AMUs) such as trail cameras or audio recorders to monitor...

Hyperpigmented melanistic lesions (HPMLs) are a visual anomaly documented on the skin of smallmouth bass Micropterus dolomieu in the Susquehanna River Basin, Pennsylvania and in numerous other geographical locations. Currently, there is a lack of information on environmental and fish characteristics that may influence the prevalence of HPMLs associated with a recently described...

This repository contains all of the scripts to reproduce the analyses, figures, and tables associated with the manuscript Gordon et al. in prep. There is 1 R script that does the following: (1) format the data, (2) explores the data, and (3) goes through the analyses for each objective.