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

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Analysis of Grass Carp eDNA Data

This product contains code to analyze a dataset that was collected to compare a LAMP assay and a qPCR assay for Grass Carp in a pond study. This repository contains the RMarkdown and R files used to analyze the data. It was created to allow for reproducible results. The code assumes the user is experience with R, especially the Tidyverse, and Stan.

inlcolor---Color palettes for the U.S. Geological Survey Idaho National Laboratory Project Office

The R package inlcolor provides access to a variety color schemes. Used to support packages and scripts written by researchers at the United States Geological Survey (USGS) Idaho National Laboratory Project Office (INLPO). Key features of this package are (1) a simple and consistent API, (2) support for qualitative, diverging, and sequential color schemes, (3) support for combining color pallets u

PopEquus: A Predictive Modeling Tool to Support Management Decisions for Free-roaming Horse Populations, Version 1.0.1

PopEquus is a website application that can be used to understand trade-offs and inform decisions in free-roaming horse (Equus caballus) population management. The application ( contains a predictive population modeling tool that can be used to simulate how different management actions drive changes in horse population size, while measuring management costs and o

rsgis v1.0

rsgis: A package to facilitate greater sage-grouse management in the western US The rsgis package centralizes several publicly available geospatial datasets that are essential to mapping and modeling for Greater sage-grouse (Centrocercus urophasianus) management applications, including important habitat and breeding areas for sage-grouse and political/regional boundaries. To cite the package, plea

raventools v1.0

raventools: A package to facilitate raven management in the western U.S. The raventools package centralizes several publicly available geospatial datasets that are essential to mapping and modeling for common raven (Corvus corax) management applications, including raven occurrence and density data, sensitive species distribution data, raven subsidy data, and Greater sage-grouse (Centrocercus uroph

Code to analyze multi-state, multi-scale dynamic occupancy models for amphibians in Yosemite National Park

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., weather) variab

Code to analyze survival data for Giant gatersnakes, Thamnophis gigas in Sacramento County, California from 2018 to 2021

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 translocatio


An R-package for the analysis of long-term changes in water quality and streamflow, including the water-quality method Weighted Regressions on Time, Discharge, and Season (WRTDS).

aqtsra, Utilities for preprocessing raw and approved unit-value time-series hydrometeorological data before statistical endeavors

The aqtsra package in the R language provides a light-weight utility for merging U.S. Geological Survey National Water Information System (NWIS) flat-file tables of raw and approved unit-value time-series data from the AQUARIUS Time-Series software. Provision is made for parsing time stamps, insertion of the day fraction into the year, and days since last site visit among other limited data-inspec

sciencebasepy: A Python library for programmatic interaction with the USGS ScienceBase platform

This Python module provides functionality for interacting with the USGS ScienceBase platform: ScienceBase is a Trusted Digital Repository (TDR) in the U.S. Geological Survey (USGS). The platform is developed and maintained by the USGS to provide shared, permission-controlled access to scientific data products and bureau resources. Rather than serving merely as

Special Contributing Area Loading Program

Special Contributing Area Loading Program (SCALP) is a hydrologic routing program that uses a linear-reservoir-in-series routing method. Inputs to SCALP include a user input file and runoff depth time series. The outputs of SCALP are outflow time series and a user log file. The user input file is a text file, and the runoff depth time series are contained in a Hydrologic Engineering Center Data St