Software

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...

This code contains multiple scripts that (1) analyze Wood Thrush movement data, (2) simulate Wood Thrush movements in an individual-based model, and (3) analyze the results from these simulations.

Invasive species are a major cause of biodiversity loss and are notoriously expensive and challenging to manage. We developed a decision-analytic framework for evaluating invasive species removal strategies, given objectives of maximizing eradication probability and minimizing costs. The framework uses an existing estimation model for spatially referenced removal data – one of the most...

The multistater package can fit several types of multi-state models, including discrete-state discrete-time Hidden Markov Models using both maximum-likelihood and Bayesian approaches (HMMs) and discrete-state continuous-time state-space models (SSMs). The package was created to specify HMM and SSM designs that can be fit in both the frequentist and Bayesian paradigms within a single...

Diffusion chronometry is a powerful tool for estimating the time scales of magmatic processes. This MATLAB software can be used to estimate diffusion time scales using the forsterite content of olivine crystals. Estimates are obtained probabilistically, using a Bayesian framework, and account for uncertainties in data as well as any independent (prior) information.

The North American Breeding Bird Survey (BBS) (https://www.pwrc.usgs.gov/bbs/) has counted birds annually for over fifty year. Survey 'routes' each consist of 50 'stops' (counts) placed along a line. Inter-stop distances can vary from route to route and from year to year, and precise locations of each stop are not typically recorded. This script quantifies uncertainty in BBS stop...

In this tutorial, we will use London, England, one of the brightest cities on Earth, to show users how to convert provided Level-1 Radiance products to TOA Radiance, Reflectance, and Brightness for the area. The tutorial will also show how to pull and parse the metadata file (MTL file) for a Landsat scene; the MTL file is used to obtain the necessary parameters for calculating Radiance...

This tutorial demonstrates how users can access Landsat data stored within the AWS Cloud environment using basic commands. Landsat data stored in the AWS Cloud is located within the U.S. West (Oregon) us-west-2 region in a Requester Pays Simple Storage Services (S3) bucket. Users interested in utilizing direct access to Landsat data stored in S3 are encouraged to visit the Requester Pays...

The North American Bat Monitoring Program: R Data Connection Package can be used to extract and upload data to the NABat Monitoring Program through the GQL API. This software is written as a wrapper around the NABat GQL API. Documentation for the database and API can be found at https://sciencebase.usgs.gov/. This code includes the ability to reformat NABat data, upload NABat data...

ModelMuse is a graphical user interface (GUI) for the U.S. Geological Survey (USGS) models MODFLOW 6, MODFLOW–2005, MODFLOW-LGR, MODFLOW-LGR2, MODFLOW-NWT, MODFLOW-CFP, MODFLOW-OWHM versions 1 and 2, MODPATH, ZONEBUDGET, PHAST, SUTRA 2.2, SUTRA 3.0, SUTRA 4.0, MT3D-USGS, and WellFootprint and the non-USGS programs MT3DMS and PEST.

The syntheticdv2lff repository contains R language source code that document the workflow to compute low-streamflow (low-flow) frequency (LFF) statistics from previously estimated streamflow at level-12 hydrologic unit code (HUC12) pour points (watershed outlet locations) in the south-central and southeastern United States for 1950 through 2010 and associated bias correction. LFF...

For some sites and constituents the three dimensions of the Weighted Regressions on Time, Discharge, and Season (WRTDS) model do not capture all the important aspects of water quality variability. For example, in some locations hysteresis or antecedent flow conditions are important influences on water quality concentration and loads. In other places, daily flow is less predictive than...