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Software

An official USGS software project is code reviewed and approved at the bureau-level for distribution.

Filter Total Items: 597

Scenario Analysis of Management Alternatives for Free-roaming Horse Populations (Version 1.0.0)

PopEquus is a predictive modeling tool to support decisions related to the management of free-roaming horse populations. It permits the simulation and comparison of how management alternatives influence horse population size and metrics associated with management. This repository uses R scripts with predictive functions from the PopEquus model to simulate how management alternatives (e.g., removin

ADOM: A Data Orchestration Manager

A Data Orchestration Manager (ADOM) is a user interface designed to enforce data management goals by entwining and extending the open-source file management tool rclone. The rclone tool provides data movement and management functionality in and between supported end-user-defined endpoints, also known as remotes. ADOM takes rclone a step further by wrapping rclone functionality into USGS-specific f

Modeling widespread declines in walleye recruitment following zebra mussel invasion in Minnesota lakes

Invasive zebra mussels (Dreissena polymorpha) alter lake ecosystems and can negatively affect first-year growth of walleye (Sander vitreus), potentially lowering walleye recruitment success. We quantified walleye recruitment responses to zebra mussel invasion in Minnesota lakes using data from 1,438 electrofishing surveys across 348 lakes collected between 1993 and 2019 to measure walleye recruit

Accounting for spatio-temporal variation in catchability in joint species distribution models

1: Estimating relative abundance is critical for informing conservation and management efforts and for making inferences about the effects of environmental change on populations. Freshwater fisheries span large geographic regions, occupy diverse habitats, and consist of varying species assemblages. Monitoring schemes used to sample these diverse populations often result in populations being sample

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 registered to sage

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-grouse surviva

Version 2.3.0 of Coupled Ground-Water and Surface-Water Flow Model Based on the Integration of the Precipitation-Runoff Modeling System (PRMS) and the Modular Ground-Water Flow Model

GSFLOW is a coupled Groundwater and Surface-Water Flow model based on the integration of the U.S. Geological Survey Precipitation-Runoff Modeling System (PRMS; Markstrom and others, 2015) and the U.S. Geological Survey Modular Groundwater Flow Model (MODFLOW-2005, Harbaugh, 2005; MODFLOW-NWT, Niswonger and others, 2011). In addition to the basic PRMS and MODFLOW simulation methods, several additio

Code for: Leveraging local efforts to solve regional-scale ecological questions: using multiple sources of data and a multi-species occupancy model to explore bee-plant interactions

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.

DataRetrieval.jl

DataRetrieval.jl is a Julia alternative to the R dataRetrieval package for obtaining USGS water data directly from web services.

Coregonid

This repository contains code for the analysis from a study that examined mortality and qPCR detection in 4 groups of fish: an uninfected control group, an infected control group, and two treatment groups. The main goals were to determine if their were differences in mortality and qPCR detection of the parasite among the differing groups. Mortality was addressed using a Generalized Linear Mixed M

Software for SIR 'Effect of Data Pooling on Predictions From the Three-Part Method for Quantitative Mineral Resource Assessment-An Investigation of a Previous U.S. Geological Survey Assessment'

The Three-Part Method for Quantitative Mineral Resource Assessment has been used by the USGS to predict mineral resources since at least 1975. These predictions use pooled data, and the effects of the pooling on the predictions is investigated and reported in the forthcoming USGS publication. The calculations and figures for this report are performed with software that will be permanently stored i

RDAVT

RDAVT.r is an R Shiny-based app used to estimate immobile porosity, mobile porosity, and the mass transfer rate coefficient in dual-domain porosity media. The app allows for interactive fitting of the fluid versus bulk conductivity hysteresis curve from electrical tracer experiments using a semi-analytic graphical approach.