Software
An official USGS software project is code reviewed and approved at the bureau-level for distribution.
Filter Total Items: 962
Evaluating Elk Distribution and Conflict Under Proposed Management Alternatives at the National Elk Refuge in Jackson, Wyoming Evaluating Elk Distribution and Conflict Under Proposed Management Alternatives at the National Elk Refuge in Jackson, Wyoming
This software release contains the code necessary to produce the elk habitat selection models used to support the U.S. Fish and Wildlife Service feeding decisions for the National Elk Refuge. The models project elk space use under five management alternatives: continued feeding, no feeding, reduced ration, halt feeding after CWD threshold is met, and halt feeding after five years of...
Evaluating the effectiveness of joint species distribution modeling for riverine fish communities Evaluating the effectiveness of joint species distribution modeling for riverine fish communities
Species Distribution Models (JSDMs) allow for accounting for both environmental predictors and species dependencies within a single statistical modeling frameworks. However, it is unclear under what conditions incorporating residual species dependencies (conditional predictions) might outperform predictions made using only environmental information (marginal predictions). Here, we...
ever4cast ever4cast
The Everglades Forecasting application (EverForecast) is a hydrologic and multi-species management tool. Designed to support natural resource managers, the tool simulates near future water levels across the Florida Everglades and models the likely impacts on the habitats and populations of numerous species. EverForecast is part of the Joint Ecosystem Modeling (JEM) suite of tools. The...
Example application of MetaIPM to the Illinois River v2.0 Example application of MetaIPM to the Illinois River v2.0
This repository contains an example application of the Meta-IPM Python package (https://doi.org/10.5066/P9427H6M). The specific application focuses on the Illinois River using existing public data. The code for this project assumes the reader is familiar with Jupyter Notebooks, enough Conda and Python to install the Meta-IPM package, and population ecology. The example also assumes the...
Example code for implementing physics-informed neural networks and generating simulated data Example code for implementing physics-informed neural networks and generating simulated data
There are 2 Jupyter notebooks that are example code for implementing a physics informed neutral network, and the code is companion to the manuscript entitled: "Spatio-temporal ecological models via physics-informed neural net- works for studying chronic wasting disease" by Reyes et al. (2024). The first notebook simulates data, and the second notebook uses this simulated data when...
FishScale FishScale
FishScale estimates fish lengths, numeric abundance, and biomass density in underwater still images. This software package is further described in a journal article by Esselman et al. (in revision; Methods in Ecology and Evolution) entitled "A transferable approach for quantifying benthic fish sizes and densities in annotated underwater images". FishScale uses binary masks obtained from...
FlowAlert FlowAlert
A software designed to provide situational awareness on rainfall intensities relevant to potential runoff-generated debris flows in recently burned areas.
Formatting and rescaling water use data for the IWAAs National Report Formatting and rescaling water use data for the IWAAs National Report
This software release contains code to create the fractional intersectional weights used to crosswalk data from the National Water Use Program to the National Integrated Water Availability Assessment (IWAAs) projects. The Watershed Boundary Dataset (WBD) contains polygons that define the spatial boundaries of hydrologic units. These are periodically updated as these boundary definitions...
GARDEN - A flow vector tool for EDEN GARDEN - A flow vector tool for EDEN
The GrAdient-Related Discharge in an Everglades Network (GARDEN) software computes flow in the Greater Everglades with a command-line Python script (Python Software Foundation. The script validates command-line arguments, fetches necessary EDEN water-level and depth data by means of the Xarray Python package, and then converts the data to imperial units (centimeters to feet). The main...
Geofetch 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...
Global Animal Diel Activity Results Global Animal Diel Activity Results
This ShinyApp provides users the ability to subset animal diel activity results by species, country, or project.
grsg_lekdb: Compiling and standardizing greater sage-grouse lek databases (version 1.3.0) grsg_lekdb: Compiling and standardizing greater sage-grouse lek databases (version 1.3.0)
Greater sage-grouse (Centrocercus urophasianus; hereafter referred to as sage-grouse) are landscape-scale sagebrush obligate species and an important gamebird and iconic species of the West (Hanser & Knick, 2011; Rowland et al., 2006). They occupy the sagebrush biome in western North America, extending east of the Sierra Nevada/Cascade Mountain ranges to the western regions of the Great...