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Software

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

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hydrolink - python package

The term hydrolink is being defined as the linkage of spatial data to a stream network. This is similar to the analogy of providing an address on a road network and provides locational context and position within a stream network. Hydrolinking data to a common stream network allows information to be centralized helping support landscape scale analyses and modeling efforts. Versions of the National

Joint Ecosystem Modeling (JEM) Restoration Runs R Library

restoration_runs is a library of R-language scripts used to summarize/post-process output of Joint Ecosystem Modeling (JEM; https://jem.gov/) models used in Everglades restoration planning for projects such as the Lake Okeechobee System Operating Manual (LOSOM) and the Western Everglades Restoration Project (WERP). The scripts summarize model output and create graphs and maps for each model.

webmap---Interactive web maps using The National Map (TNM) services

The R package webmap creates interactive web maps using the JavaScript Leaflet library with base layers of The National Map (TNM). Map service endpoints are offered with no use restrictions and provide access to base geospatial information that describes the landscape of the United States and its territories. Base layers outside these areas are unavailable at higher spatial scales. This package is

Monosex control within integrated pest management

This repository contains code to simulate the use of YY-males and direct mortality such as harvest or pesticide applicaion as a control tools for different aquatic invasive species.

Simulations for assessing the suitability of YY-males as a control method across life histories

This repository contains code to simulate the use of YY-males as a control tool for different aquatic invasive species. The code uses the Meta-IPM Python package (https://doi.org/10.5066/P9PW673G) 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.

Habitat Risk Software

The Habitat Risk Software leverages a previously published Bayesian hierarchical model framework (Clayton and Kaldor 1987; Banderjee et al. 2004; Gelman et al. 2004; Evans et al. 2016) with opportunistic (hunter-harvest) wildlife surveillance disease testing data and publicly available geospatial (raster) data to estimate the geographical risk that a hunter will harvest a white-tailed deer (Odocoi

RESTORE/covESTUSAL, Source code for construction of covariates bound to daily salinity and specific conductance data for purposes of statistical modeling in coastal regions of the Gulf of Mexico, United States

The RESTORE/covESTUSAL software repository contains R language source code useful for the construction of input tables of daily salinity and specific conductance (response variables) from multi-agency monitoring stations and potential predictor variables (covariates) intended for reuse in statistical model construction in coastal regions of the Gulf of Mexico, United States. The source code is exp

occupancyTuts: A package for learning occupancy modeling with RPresence

Understanding how species are distributed in both space and time is a central question in ecology. Seemingly simple questions such as “How many individuals live in a particular patch?”, “Is a patch occupied by a target species?”, “How many species are there?”, and “what factors shape these pattern?” are questions routinely asked by ecologists. The tutorials in occupancyTuts will illustrate methods

grsg_lekdb: Compiling and standardizing greater sage-grouse lek databases, version 1.2.0

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 Plains of

Surface Velocity Tools (SurfVelTools)

SurfVelTools is a Python application and user interface for computing parameters associated with the Probability Concept method (Fulton and others, in review) parameters using velocity profile data collected in the stationing where the maximum in-channel velocity occurs. SurfVelTools will also compute streamflow (discharge) for a given Probability Concept result given a known cross-sectional area,

Evaluation of DNA yield from various tissue and sampling sources for use in single nucleotide polymorphism panels

R code to test for differences in DNA yield from of eight sample categories to gain insights into which provided adequate DNA to be used in ddRADseq or already developed SNP panels. We calculated mean, median and standard deviation with package psych using the describe() function. Additionally, we generated boxplots using package ggplot2 where the quantity for each tissue sample is categorized by

Application of the SEICarP Model to the Illinois River

This repository contains code to run the Spatially Explicit Invasive Carp Population (SEICarP) model in the Illinois Rive. The code uses the `SEICarP` R package. The code for this project assumes the reader is familiar with R, population modeling, and quantitative fisheries methods.