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

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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

Joint Ecosystem Modeling (JEM) NetCDF R Package

R-language code library to support netCDF I/O. This package was written to ease the process of reading and writing netcdfs in R for the Joint Ecosystem Modeling (JEM; community. NetCDF files created using this package follow the Comprehensive Everglades Restoration Plan (CERP) data standards to facilitate data sharing among scientists in the Everglades area.

Inferring pathogen presence when sample misclassification and partial observation occur

This software contains four separate R scripts and one Matlab script that comprise an analysis to estimate the posterior probability of pathogen presence when sample misclassification and partial observations occur. We develop a Bayesian hierarchal framework that accommodates false negative, false positive, and uncertain detections and apply this framework to a case study of the fungal pathogen Ps

Code for Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses

Code will be submitted to the Dryad repository upon acceptance of the manuscript. These R code are used for simulations and case studies. Simulations include data for generating age-period survival data. We have provided code for each of the 10 models that were fit using NIMBLE, where each model has four R scripts including: 1) A script to execute and run all the additional R scripts for each simu

Code for Rapid prototyping for quantifying belief weights of competing hypotheses about emergent diseases

Code submitted to Journal of Environmental Management and ScienceBase for running Bayesian hierarchical models on a dataset that was collected using expert elicitation of a panel of 15 experts on the etiology of stony coral tissue loss disease and its impacts on coral reefs. The code is for a rapid prototyping method for quantifying belief weights for competing hypotheses about the etiology of dis

Toolbox for River Velocimetry using Images from Aircraft (TRiVIA)

# TRiVIA Toolbox for River Velocimetry using Images from Aircraft: TRiVIA ## Description The Toolbox for River Velocimetry using Images from Aircraft, or TRiVIA for short, is an application to facilitate estimation of surface flow velocities in river channels from various types of remotely sensed data acquired with a nadir-viewing geometry (i.e., looking straight down). Spatially distributed info

gravmagsubs: Gravitational and magnetic attraction of 3-D vertical rectangular prisms

gravmagsubs is a software package for the R language that provides tools for forward modeling gravity and magnetic anomalies from 3-D right rectangular prisms. The gravity anomaly is defined as the vertical component of gravitational acceleration, while the magnetic anomaly includes the effects of both induced and remanent magnetization. The package can model the total anomaly from a collection

Agisoft Metashape/Photoscan Automated Image Alignment and Error Reduction version 2.0

This repository contains python scripts which automate image alignment and sparse point cloud error reduction in the Agisoft Metashape/Photoscan structure from motion photogrammetry software package using the Agisoft Metashape Python API. The current version of the script (version 2.0) approximates the workflow described in U.S. Geological Survey Open-File Report 2021-1039 (Over et al., 2021). The

GageStats Services

The Gage Statistic (GageStats) Services were developed to provide gage characteristics and streamflow statistics to support the StreamStats application via RESTful principles. The StreamStats application uses GageStats Services to display the gages and related gage pages. These services provide U.S. Geological Survey developed and published gage characteristics such as drainage area or mean basin

USGS Model Catalog Tools and Metadata

Tools and metadata for the USGS Model Catalog.