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At least 19 recordsLinked to original sources
USGS2019

The MTPy software package for magnetotelluric data analysis and visualisation

The magnetotelluric (MT) method is increasingly being applied to a wide variety of geoscience problems. However, the software available for MT data analysis and interpretation is still very limited in comparison to many of the more mature geophysical methods such as the gravity, magnetic or seismic reflection methods. MTPy is an open source Python package to assist with MT data processing, analysis, modelling, visualization and interpretation. It was initiated at the University of Adelaide in 2013 as a means to store and share Python code amongst the MT community (Krieger & Peacock, 2014). Here we provide an overview of the software and describe recent developments to MTPy. These include new functionality and a clean up and standardization of the source code, as well as the addition of an integrated testing suite, documentation, and examples in order to facilitate the use of MT in the wider geophysics community.

Journal of Open Source Software↗
USGS2024

CoastSeg: An accessible and extendable hub for satellite-derived-shoreline (SDS) detection and mapping

CoastSeg is an interactive browser-based program that aims to broaden the adoption of satellite-derived shoreline (SDS) detection and coastal landcover mapping workflows among coastal scientists and coastal resource management practitioners. SDS is a sub-field of coastal sciences that aims to detect and post-process a time-series of shoreline locations from publicly available satellite imagery. CoastSeg is a python package installed via pip into a conda environment that serves as an API for building custom SDS workflows. CoastSeg also provides full SDS workflow implementations via jupyter notebooks and python scripts that call functions and classes in the core CoastSeg API for specific workflows. Two fully functioning SDS workflows are already provided, and more could be added by collaborators in the SDS software community. All API codes, notebooks, scripts, and documentation are hosted on the CoastSeg GitHub repository.

Journal of Open Source Software↗
USGS2024

Aurora: An open-source Python implementation of the EMTF package for magnetotelluric data processing using MTH5 and mt-metadata

The Aurora software package robustly estimates single station and remote reference electromagnetic transfer functions (TFs) from magnetotelluric (MT) time series. Aurora is part of an open-source processing workflow that leverages the self-describing data container MTH5, which in turn leverages the general mt-metadata framework to manage metadata. These pre-existing packages simplify the processing by providing managed data structures, allowing for transfer functions to be generated with only a few lines of code. The processing depends on two inputs -- a table defining the data to use for TF estimation, and a JSON file specifying the processing parameters, both of which are generated automatically, and can be modified if desired. Output TFs are returned as mt_metadata objects, and can be exported to a variety of common formats for plotting, modeling and inversion.

Journal of Open Source Software↗
USGS2019

BbsAssistant: An R package for downloading and handling data and information from the North American Breeding Bird Survey

This R package contains functions for downloading and munging data from the U.S. Geological Surveys North American Breeding Bird Survey (BBS) via file transfer protocol (FTP) (Pardieck, Ziolkowski Jr, Lutmerding, & Hudson, 2018; J. R. Sauer et al., 2017). This package was created to allow the user to bulk-download the BBS point count and related (e.g., route-level conditions) via FTP, and to quickly subset the data by taxonomic classifications and/or geographical locations. This package also maintains data containing the trend and annual indices from the most recent (1996-2017) hierarchical population analyses (J. Sauer et al., 2017).

Journal of Open Source Software↗
USGS2022

FishStan: Hierarchical Bayesian models for fisheries

Fisheries managers and ecologists use statistical models to estimate population-level relations and demographic rates (e.g., length-maturity curves, growth curves, and mortality rates). These relations and rates provide insight into populations and inputs for other models. For example, growth curves may vary across lakes showing fish populations differ due to management actions or underlying environmental conditions. A fisheries manager could use this information to set lake-specific harvest limits or an ecologist could use this information to test scientific hypotheses about fish populations. The above example also demonstrates how populations exist within hierarchical structures where sub-populations may be nested within a meta-population. More generally, these hierarchical structures may be both biological (e.g., different lakes or river pools) and statistical (e.g., correlated error structures). Currently, limited options exist for fitting these hierarchical models and people seeking to use them often must program their own implementations. Furthermore, many fisheries managers and researchers may not have Bayesian programming skills, but many can use interactive languages such as R. Additionally, programs such as JAGS often require long run times (e.g., hours if not days) to fit hierarchical models and programs such as Stan can be more difficult to program because it is a compiled language. We created fishStan to share hierarchical models for fisheries and ecology in an easy-to-use R package.

Journal of Open Source Software↗
USGS2025

anadrofish: Anadromous fish population responses to dams

Diadromous fishes world-wide experienced precipitous declines during the 19th and 20th centuries due to a combination of overfishing, pollution, and freshwater habitat loss through construction of dams (Limburg & Waldman, 2009). Following wide-spread fishing closures and large-scale remediation of many historical pollution sources, dams in coastal rivers remain as the largest tractable impediment to population recovery for many of these species (Waldman & Quinn, 2022). In some cases, dams reduce access to as much as 95% of freshwater and rearing habitat (Hall et al., 2011). These effects are especially pronounced for species that rely on long-distance migrations to spawning and rearing habitat upstream of barriers such as various alosines (herrings; e.g., American shad Alosa sapidissima , alewife A. pseudoharengus , and blueback herring A. aestivalis (Noonan et al., 2012)) and salmonines (trout and salmon; e.g., Salmo spp. (Parrish et al., 1998) and Oncorhynchus spp. (Quiñones et al., 2015). Traditional stock assessment tools such as per-recruit analyses often fail to capture management complexities related to diadromous life histories such as fish passage at dams, and integrated assessment models can be difficult to parameterize for data-poor species such as herrings (Atlantic States Marine Fisheries Commission, 2024). This has resulted in the development of species- and system-specific approaches to fisheries stock assessment and management strategy evaluation (Barber et al., 2018; Nieland et al., 2015; Roy et al., 2018; Stich et al., 2019). We created the anadrofish package (Stich, Hardesty, et al., 2025) for R (R Core Team, 2025) to provide a generalized approach that also allows broader application to novel species, systems, and scenarios.

Journal of Open Source Software↗
USGS2011

Adaptive finite volume methods with well-balanced Riemann solvers for modeling floods in rugged terrain: Application to the Malpasset dam-break flood (France, 1959)

The simulation of advancing flood waves over rugged topography, by solving the shallow-water equations with well-balanced high-resolution finite volume methods and block-structured dynamic adaptive mesh refinement (AMR), is described and validated in this paper. The efficiency of block-structured AMR makes large-scale problems tractable, and allows the use of accurate and stable methods developed for solving general hyperbolic problems on quadrilateral grids. Features indicative of flooding in rugged terrain, such as advancing wet-dry fronts and non-stationary steady states due to balanced source terms from variable topography, present unique challenges and require modifications such as special Riemann solvers. A well-balanced Riemann solver for inundation and general (non-stationary) flow over topography is tested in this context. The difficulties of modeling floods in rugged terrain, and the rationale for and efficacy of using AMR and well-balanced methods, are presented. The algorithms are validated by simulating the Malpasset dam-break flood (France, 1959), which has served as a benchmark problem previously. Historical field data, laboratory model data and other numerical simulation results (computed on static fitted meshes) are shown for comparison. The methods are implemented in GEOCLAW, a subset of the open-source CLAWPACK software. All the software is freely available at. Published in 2010 by John Wiley & Sons, Ltd.

International Journal for Numerical Methods in Flu↗
USGS2012

Description of the U.S. Geological Survey Geo Data Portal data integration framework

The U.S. Geological Survey has developed an open-standard data integration framework for working efficiently and effectively with large collections of climate and other geoscience data. A web interface accesses catalog datasets to find data services. Data resources can then be rendered for mapping and dataset metadata are derived directly from these web services. Algorithm configuration and information needed to retrieve data for processing are passed to a server where all large-volume data access and manipulation takes place. The data integration strategy described here was implemented by leveraging existing free and open source software. Details of the software used are omitted; rather, emphasis is placed on how open-standard web services and data encodings can be used in an architecture that integrates common geographic and atmospheric data.

IEEE Journal of Selected Topics in Applied Earth O↗
USGS2024

Self-guided decision support groundwater modelling with Python

The GMDSI tutorial notebooks repository provides learners with a comprehensive set of tutorials for self-guided training on decision-support groundwater modelling using Python-based tools. Although targeted at groundwater modelling, they are based around model-agnostic tools and readily transferable to other environmental modelling workflows. The tutorials are divided into three parts. The first covers fundamental theoretical concepts. These are intended as background reading for reference on an as-needed basis. Tutorials in the second part introduce learners to some of the core concepts parameter estimation in a groundwater modelling context, as well as providing a gentle introduction to the PEST, PEST++ and pyEMU software. Lastly, the third part demonstrates how to implement highly-parameterized applied decision-support modelling workflows. The tutorials aim to provide examples of both “how to use” the software as well as “how to think” about using the software. A key advantage to using notebooks in this context is that the workflows described run the same code as practitioners would run on a large-scale real- world application. Using a small synthetic model facilitates rapid progression through the workflow.

Journal of Open Source Education↗
USGS2025

An approach to modeling abundance of marine wildlife over space and time using unstructured aerial surveys

Estimating spatial and temporal patterns in abundance is often a goal of ecological studies and can be useful for informing management decisions, such as determining the optimal placement of wildlife protection zones. However, estimating abundance can be difficult in practice, especially over large areas, because of imperfect detection, where individuals are present but not detected because of either availability or observer error. Several methods for estimating abundance that account for imperfect detection exist but can be logistically challenging to implement. We present a simpler approach to some of the more commonly used techniques for estimating the abundance of marine wildlife over space and time from unstructured aerial surveys. This approach combines a spatial model for count data with auxiliary information on detection probability obtained from small-scale or previous studies. We employ generalized linear models and generalized additive models with spatial habitat covariates to illustrate this approach using maximum-likelihood with free, open-source statistical software. This framework is intended to be accessible and flexible, requiring lower survey costs and less computation time than other alternatives for estimating abundance. Indeed, our simulation results show that this approach can reduce computation times, while appropriately characterizing uncertainty, compared to a Bayesian approach. We also present R code for our approach using an example of estimating Florida manatee ( Trichechus manatus latirostris ) abundance in Indian River County in Florida, USA. This approach could be applied to other study systems and marine wildlife species using unstructured aerial surveys.

Florida↗
USGS2019

Semiautomated process for enumeration of fishes from recreational-grade side-scan sonar imagery

The use of hydroacoustic techniques is increasing as scientists search for less invasive ways to monitor fish populations, and using recreational side‐scan sonar (SSS) imagery for monitoring has become more common in aquatic resource management over the last 15 years due in part to its low cost and user‐friendly interface. The time‐consuming nature of manually counting fish targets has limited the use of the data that is collected by these systems in research or management contexts. To reduce the time and effort that is required to enumerate acoustic targets that are presumed to be fish, we developed a semiautomated process that rapidly quantifies targets from recreational SSS imagery by using an open‐source image processing software. Perceived fish targets were enumerated using a set of macroinstructions that performed similarly to manual enumeration by three experienced assessors. This method reduced variation that arises from individual assessors and eliminated the prohibitive time constraints that are associated with manual processing. Herein, we describe how our semiautomated process could be used in fisheries management contexts after further research and development of sampling methods. Future research will focus on field validation, quantifying relative abundance, testing across a broader range of environmental conditions, and exploring other applications for fisheries management.N

North American Journal of Fisheries Management↗
USGS2015

New insight into California’s drought through open data

Historically unprecedented drought in California has brought water issues to the forefront of the nation’s attention. Crucial investigations that concern water policy, management, and research, in turn, require extensive information about the quality and quantity of California’s water. Unfortunately, key sources of pertinent data are unevenly distributed and frequently hard to find. Thankfully, the vital importance of integrating water data across federal, state, and tribal, academic, and private entities, has recently been recognized and addressed through federal initiatives such as the Climate Data Initiative of President Obama’s Climate Action Plan and the Advisory Committee on Water Information’s Open Water Data Initiative . Here, we demonstrate an application of integrated open water data, visualized and made available online using open source software, for the purpose of exploring the impact of the current California drought. Our collaborative approach and technical tools enabled a rapid, distributed development process. Many positive outcomes have resulted: the application received recognition within and outside of the Federal Government, inspired others to visualize open water data, spurred new collaborations for our group, and strengthened the collaborative relationships within the team of developers. In this article, we describe the technical tools and collaborative process that enabled the success of the application.

BayGEO Journal↗
USGS2026

Computational electromagnetic geophysics for groundwater system studies: A review on established practices and recent advances

Identifying effective solutions for locating groundwater resources and ensuring the quality of drinking water is increasingly urgent, given the challenges posed by climate change and population growth. This review investigates electromagnetic geophysical imaging techniques, in both time- and frequency-domain, that can provide valuable insights for groundwater assessment. We explore computational electromagnetic methods used to evaluate electromagnetic data and several recent hydrogeophysical case studies. As open-source frameworks for modeling electromagnetic geophysical problems become available, a broader range of researchers can interpret their data with computationally advanced software. We provide an overview of documented open-source codes for evaluating electromagnetic data and analyze various hydrological targets in relation to their electromagnetic surveying technique and the computational method applied. Furthermore, we evaluate the potential of advanced computational techniques, including three-dimensional modeling, non-deterministic inversion and machine learning, to couple geophysical with numerical groundwater modeling and apply it in groundwater system studies. Despite obstacles such as complexity and resource demands, our findings indicate that the quantification and integration of predictive uncertainties from both electromagnetic and hydrological data and simulations would significantly improve the reliability of hydrogeophysical models. This can lead to a deeper understanding of groundwater systems and improved management practices.

Journal of Hydrology↗
USGS2019

Characterizing groundwater/surface-water interaction using hydrograph-separation techniques and groundwater-level data throughout the Mississippi Delta, USA

The Mississippi Delta, located in northwest Mississippi, is an area dense with industrial-level agriculture sustained by groundwater-dependent irrigation supplied by the Mississippi River Valley Alluvial aquifer (alluvial aquifer). The Delta provides agricultural commodities across the United States and around the world. Observed declines in groundwater altitudes and streamflow contemporaneous with increases in irrigation have raised concerns about future groundwater availability and the effects of groundwater withdrawals on streamflow. To quantify the impacts of groundwater withdrawals on streamflow and increase understanding of groundwater and surface-water interaction, hydrograph-separation techniques were used to estimate baseflow and identify statistical streamflow trends. The analysis was conducted using the U.S. Geological Survey Groundwater Toolbox open-source software and daily hydrologic data provided by a spatially-distributed network of paired groundwater wells and streamgaging sites. This study found that effects of groundwater withdrawals on streamflow were observed as statistically significant reductions in baseflow in areas with substantial groundwater-altitude declines. Hydrograph-separation and trend analyses may be applicable to assess the impacts of groundwater withdrawals in altered environments and streamflow may be used as a proxy for changes in groundwater availability. Characterizing and defining hydrologic relations between groundwater and surface water will help scientists and water-resource managers refine a regional groundwater-flow model that includes the Mississippi Delta that will be used to aid water-resource managers in future decisions concerning the alluvial aquifer.

Arkansas, Illinois, Kentucky, Louisiana, Mississip↗
USGS2022

NABat ML: Utilizing deep learning to enable crowdsourced development of automated, scalable solutions for documenting North American bat populations

Bats play crucial ecological roles and provide valuable ecosystem services, yet many populations face serious threats from various ecological disturbances. The North American Bat Monitoring Program (NABat) aims to use its technology infrastructure to assess status and trends of bat populations, while developing innovative and community-driven conservation solutions. Here, we present NABat ML , an automated machine-learning algorithm that improves the scalability and scientific transparency of NABat acoustic monitoring. This model combines signal processing techniques and convolutional neural networks (CNNs) to detect and classify recorded bat echolocation calls. We developed our CNN model with internet-based computing resources (‘cloud environment’), and trained it on >600,000 spectrogram images. We also incorporated species range maps to improve the robustness and accuracy of the model for future ‘unseen’ data. We evaluated model performance using a comprehensive, independent, holdout dataset. NABat ML successfully distinguished 31 classes (30 species and a noise class) with overall weighted-average accuracy and precision rates of 92%, and ≥90% classification accuracy for 19 of the bat species. Using a single cloud-environment computing instance, the entire model training process took <16 h. Synthesis and applications . Our convolutional neural network (CNN)-based model, NABat ML , classifies 30 North American bat species using their recorded echolocation calls with an overall accuracy of 92%. In addition to providing highly accurate species-level classification, NABat ML and its outputs are compatible with Bayesian and other statistical techniques for measuring uncertainty in classification. Our model is open-source and reproducible, enabling future implementations as software on end-user devices and cloud-based web applications. These qualities make NABat ML highly suitable for applications ranging from grassroots community science initiatives to big-data methods developed and implemented by researchers and professional practitioners. We believe the transparency and accessibility of NABat ML will encourage broad-scale participation in bat monitoring, and enable development of innovative solutions needed to conserve North American bat species.

Journal of Applied Ecology↗
USGS2017

Using multi-date satellite imagery to monitor invasive grass species distribution in post-wildfire landscapes: An iterative, adaptable approach that employs open-source data and software

Among the most pressing concerns of land managers in post-wildfire landscapes are the establishment and spread of invasive species. Land managers need accurate maps of invasive species cover for targeted management post-disturbance that are easily transferable across space and time. In this study, we sought to develop an iterative, replicable methodology based on limited invasive species occurrence data, freely available remotely sensed data, and open source software to predict the distribution of Bromus tectorum (cheatgrass) in a post-wildfire landscape. We developed four species distribution models using eight spectral indices derived from five months of Landsat 8 Operational Land Imager (OLI) data in 2014. These months corresponded to both cheatgrass growing period and time of field data collection in the study area. The four models were improved using an iterative approach in which a threshold for cover was established, and all models had high sensitivity values when tested on an independent dataset. We also quantified the area at highest risk for invasion in future seasons given 2014 distribution, topographic covariates, and seed dispersal limitations. These models demonstrate the effectiveness of using derived multi-date spectral indices as proxies for species occurrence on the landscape, the importance of selecting thresholds for invasive species cover to evaluate ecological risk in species distribution models, and the applicability of Landsat 8 OLI and the Software for Assisted Habitat Modeling for targeted invasive species management.

International Journal of Applied Earth Observation↗
USGS1992

Map showing sediment isopachs in the deep-sea basins of the Pacific continental margin, Point Conception to Point Loma

The U.S. Geological Survey conducted a series of cruises, EEZSCAN 84 (EEZ-SCAN 84 Scientific Staff, 1986), to collect reconnaissance data on the newly proclaimed Exclusive Economic Zone (EEZ), the area out to 200 nautical miles from the coastline of the United States. The cruises systematically surveyed the entire conterminous United States west coast EEZ using the Geological Long-Range Inclined Asdic (GLORIA) side-scan sonar, a 160-in 3 airgun seismic-reflection profiler, a 3.5-kHz high-resolution seismic-reflection profiler, a 10-kHz echo sounder, and a proton-precession magnetometer. The nominal trackline spacing throughout the survey was 30 km. Derivative maps of sediment thickness (I-2089-A, I-2090-A, I-2091-A) and depth to basement (I-2089-B, I-2090-B, I-2091-B) in the basins of the west coast EEZ were compiled from both the sonar-image dala and the deep-penetration seismic data obtained on these cruises. Only EEZ-SCAN 84 data were used for the map compilations because available data from other cruises in this region are sparsely located, have poor navigational control, or were obtained with seismic systems that were not powerful enough to resolve oceanic basement. For this map series, sediment thickness and depth to basement were determined only in the deep-ocean basin regions because the seismic system used on the EEZ-SCAN 84 cruises could not resolve oceanic basement beneath the thick sediments of the continental slope. All the data used to compile the maps are presented in the "Atlas of the Exclusive Economic Zone, Western Conterminous United States" (EEZ-SCAN 84 Scientific Staff, 1986). Basement Outcrops GLORIA imagery was used to locate areas of basement outcrop throughout the region. Where possible, sediment thickness on and immediately adjacent to basement outcrops was measured from seismic data. Where there was no bathymetric or seismic control, a seamount peak was assumed to have no sediment cover. A pattern is used on the map to indicate all basement outcrops. Data Reduction Acoustic basement in the basins, invariably oceanic Layer 2, was observed on all of the seismic records. One-way traveltime was measured from the sea floor to acoustic basement. Because the trackline spacing of about 30 km is relatively large compared to the data density along track, we chose to measure the sediment thickness every 0.5 hour or at an interval of approximately 7.5 km. Water depth was measured with a 10-kHz profiler. Depth to basement was calculated using the sea surface as the zero datum and adding the corrected water depth (Carter, 1980) to the sediment thickness. Acoustic travel times were converted to depths by first calculating a regression equation from the interval velocity versus depth data of Connard and others (1984). Their data base comprises a compilation of all available Deep Sea Drilling Project data plus wide-angle refraction data, which were collected in Cascadia Basin west of Oregon and represents the best data set available for the United States west coast EEZ. The regression equation was integrated to determine sediment thickness as a function of one-way traveltime . The resulting equation is z = 1400t + 0 .5t 2 where z is sediment thickness in meters, and t is one-way traveltime in seconds. Sediment thicknesses calculated using this equation were compared to values calculated from the general equation of Carlson and others (1986). Values for sediment thickness calculated by the two equations differed by no greater than 10 percent throughout the range of travel times. Bathymetry The bathymetry is from Chase and others (1981). The bathymetric data were compiled from a variety of sources, and data quality is inconsistent. Because of differences in navigational precision and density of coverage, the bathymetric contours of a feature may be at a different location than the corresponding isopleths derived from the EEZ-SCAN 84 data, or a feature may not be indicated on the bathymetry at all. These situations occur because either the feature is poorly located in the bathymetric data set or, especially in the outer EEZ, the bathymetric data are too sparse to have defined the existence of a feature. Acknowledgments Topographic digital data bases were corrected and verified by Christina Lief. Gerald Evenden developed the computer software system MAPGEN, used to compose this map. Reviews, suggestions, and technical contributions from Edward C. Escowitz and Florence Wong and advice about cartographic design from Will Stettner substantially improved the quality of this map. References Cited Carlson, R.L., Gangi, A.F., and Snow, K.R., 1986, Empirical reflection-traveltime/ depth and velocity/depth functions for the deep-sea sediment column: Journal of Geophysical Research, v. 91, no. B8, p. 8249-8266. Carter, D.J.T., 1980, Echo-sounding correction tables: Taunton, United Kingdom, Hydrographic Department, Ministry of Defence, 150 p. Chase, T.E., Wilde, Pat, Normark, W.R, Miller, C.P., Seekins, B.A., and Young, J.D., 1981, Offshore topography of the Western United States between 32&deg; and 49&deg; North latitudes: U.S. Geological Survey Open-File Report 81-443, scale 1:864,518 at 38&deg; latitude, 2 sheets. Connard, G., Couch, R., Keeling , K., Roy, J., and Troseth, S., 1984, Abyssal plain and continental net-objective sedimentary thicknesses, in Kulm, L.D., and others, eds., Western North America continental margin and adjacent ocean floor off Oregon and Washington, Atlas 1 of Regional Atlas Series, Ocean Margin Drilling Program: Woods Hole, Mass., Marine Science International, sheet 7. EEZ-SCAN 84 Scientific Staff, 1986, Atlas of the Exclusive Economic Zone, Western Conterminous United States: U.S. Geological Survey Miscellaneous Investigations Series I-1792, scale 1:500,000, 152 p. index map for I-2089-A See Also "U.S. Pacific West Coast Field Activities" (Paskevich and others, 2011; http://pubs.usgs.gov/of/2010/1332/htmldocs/pc/pc_overview.html). Paskevich, V.F., Wong, F.L., O?Malley, J.J., Stevenson, A.J., and Gutmacher, C.E., 2011, GLORIA sidescan-sonar imagery for parts of the U.S. Exclusive Economic Zone and adjacent areas: U.S. Geological Survey Open-File Report 2010?1332, available at http://pubs.usgs.gov/of/2010/1332/.

IMAP↗