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Reproducibility starts at the source: R, Python, and Julia Packages for retrieving USGS hydrologic data

Much of modern science takes place in a computational environment, and, increasingly, that environment is programmed using R, Python, or Julia. Furthermore, most scientific data now live on the cloud, so the first step in many workflows is to query a cloud database and load the response into a computational environment for further analysis. Thus, tools that facilitate programmatic data retrieval represent a critical component in reproducible scientific workflows. Earth science is no different in this regard. To fulfill that basic need, we developed R, Python, and Julia packages providing programmatic access to the U.S. Geological Survey’s National Water Information System database and the multi-agency Water Quality Portal. Together, these packages create a common interface for retrieving hydrologic data in the Jupyter ecosystem, which is widely used in water research, operations, and teaching. Source code, documentation, and tutorials for the packages are available on GitHub. Users can go there to learn, raise issues, or contribute improvements within a single platform, which helps foster better engagement and collaboration between data providers and their users.

Water↗

An update of USGS bear-real-time earthquake shaking and impact products

We report on advancements in both hazard and consequence modeling that form the core of the U.S. Geological Survey’s (USGS) strategy to improve rapid earthquake shaking and loss estimates. Whereas our primary goal is to improve our operational capabilities of the USGS National Earthquake Information Center, the science, software, and datasets behind these systems continue to advance uses and studies of earthquake shaking and impact by the seismological, engineering, financial, and risk modeling communities. Several important updates to our integrated shaking and impact products are outlined and we introduce new earthquake information products that have recently been brought online, including rapid ground failure estimates and more spatially refined loss estimates domestically (in the U.S). We continue to compile, develop, and refine key openly available models and datasets that contribute to calibrating these systems and report on the collection and storage of new inventories. We also describe some of the basic operational considerations in the current generation of these shaking and loss-estimation systems. A key aspect of the product integration and development is leveraging earthquake-hazard and loss-modeling science done internally (within the USGS) and by external researchers and collaborators. Lastly, we outline new opportunities for further research and development by emphasizing scientific, data, and application gaps and challenges that must be solved in order to improve our shaking and impact information tools.

Conference Paper↗

Science, conservation, and camera traps

Biologists commonly perceive camera traps as a new tool that enables them to enter the hitherto secret world of wild animals. Camera traps are being used in a wide range of studies dealing with animal ecology, behavior, and conservation. Our intention in this volume is not to simply present the various uses of camera traps, but to focus on their use in the conduct of science and conservation. In this chapter, we provide an overview of these two broad classes of endeavor and sketch the manner in which camera traps are likely to be able to contribute to them. Our main point here is that neither photographs of individual animals, nor detection history data, nor parameter estimates generated from detection histories are the ultimate objective of a camera trap study directed at either science or management. Instead, the ultimate objectives are best viewed as either gaining an understanding of how ecological systems work (science) or trying to make wise decisions that move systems from less desirable to more desirable states (conservation, management). Therefore, we briefly describe here basic approaches to science and management, emphasizing the role of field data and associated analyses in these processes. We provide examples of ways in which camera trap data can inform science and management.

Book chapter↗

2019 Joint Agency Commercial Imagery Evaluation—Land remote sensing satellite compendium

The Joint Agency Commercial Imagery Evaluation (JACIE) is a collaboration between five Federal agencies that are major users and producers of satellite land remote sensing data. In recent years, the JACIE group has observed ever-increasing numbers of remote sensing satellites being launched. This rapidly growing wave of new systems creates a need for a single reference for land remote sensing satellites that provides basic system specifications and linkage to any JACIE assessment that may have been completed on existing systems. This volume has been assembled by the Requirements, Capabilities, and Analysis for Earth Observation Project under the U.S. Geological Survey National Land Imaging Program as a contribution to the JACIE community. This is the first edition of the JACIE compendium, which is planned to be updated and released annually.

Circular↗

2020 Joint Agency Commercial Imagery Evaluation—Remote sensing satellite compendium

The Joint Agency Commercial Imagery Evaluation (JACIE) is a collaboration between five Federal agencies that are major users and producers of satellite land remote sensing data. In recent years, the JACIE group has observed ever-increasing numbers of remote sensing satellites being launched. This rapidly growing wave of new systems creates a need for a single reference for land remote sensing satellites that provides basic system specifications and linkage to any JACIE assessment that may have been completed on existing systems. This volume has been assembled by the Requirements, Capabilities, and Analysis for Earth Observation Project under the U.S. Geological Survey National Land Imaging Program as a contribution to the JACIE community. This is the second edition of the JACIE compendium, which is planned to be updated and released annually.

Circular↗

2022 Joint Agency Commercial Imagery Evaluation—Remote sensing satellite compendium

The Joint Agency Commercial Imagery Evaluation (JACIE) is a collaboration between six Federal agencies that are major users and producers of satellite land remote sensing data. In recent years, the JACIE group has observed ever-increasing numbers of remote sensing satellites being launched. This rapidly growing wave of new systems creates a need for a single reference for land remote sensing satellites that provides basic system specifications and linkage to any JACIE assessment that may have been completed on existing systems. This volume has been assembled by the Requirements, Capabilities, and Analysis for Earth Observation Project under the U.S. Geological Survey National Land Imaging Program as a contribution to the JACIE community. This is the third edition of the JACIE compendium, which is planned to be updated and released annually.

Circular↗

Differences in basin‐characteristics as reflected by precipitation‐runoff relations in San Bernardino and Eastern San Gabriel Mountain drainages

In interpretation and use of basic hydrological data as basis for planning any public works for conservation or control of water, there is great need for a careful and thorough analysis of the precipitation‐runoff relations. Moreover, when such relations may have been worked out for one particular basin, experience has shown that extreme caution must be used in any attempt to apply these relations to another basin even though superficially the latter may appear to be comparable with respect to physiography, meteorological conditions, and all of the other elements which contributed to the relations established for the first basin.

California↗

U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) Center-Fiscal Year 2009 Annual Report

The Earth Resources Observation and Science (EROS) Center is a U.S. Geological Survey (USGS) facility focused on providing science and imagery to better understand our Earth. As part of the USGS Geography Discipline, EROS contributes to the Land Remote Sensing (LRS) Program, the Geographic Analysis and Monitoring (GAM) Program, and the National Geospatial Program (NGP), as well as our Federal partners and cooperators. The work of the Center is shaped by the Earth sciences, the missions of our stakeholders, and implemented through strong program and project management and application of state-of-the-art information technologies. Fundamentally, EROS contributes to the understanding of a changing Earth through 'research to operations' activities that include developing, implementing, and operating remote sensing based terrestrial monitoring capabilities needed to address interdisciplinary science and applications objectives at all levels-both nationally and internationally. The Center's programs and projects continually strive to meet and/or exceed the changing needs of the USGS, the Department of the Interior, our Nation, and international constituents. The Center's multidisciplinary staff uses their unique expertise in remote sensing science and technologies to conduct basic and applied research, data acquisition, systems engineering, information access and management, and archive preservation to address the Nation's most critical needs. Of particular note is the role of EROS as the primary provider of Landsat data, the longest comprehensive global land Earth observation record ever collected. This report is intended to provide an overview of the scientific and engineering achievements and illustrate the range and scope of the activities and accomplishments at EROS throughout fiscal year (FY) 2009. Additional information concerning the scientific, engineering, and operational achievements can be obtained from the scientific papers and other documents published by EROS staff. We welcome comments and follow-up questions on any aspect of this Annual Report and invite any of our customers or partners to contact us at their convenience. To communicate with us, or for more information about EROS, contact: Communications and Outreach, USGS EROS Center, 47914 252nd Street, Sioux Falls, South Dakota 57198, jsnelson@usgs.gov, http://eros.usgs.gov/.

Open-File Report↗

Quantitative comparison of some aesthetic factors among rivers

It is difficult to evaluate the factors contributing to aesthetic or nonmonetary aspects of a landscape. In contrast, aspects which lend themselves to cost-benefit comparisons are now treated in a routine way. As a result, nonmonetary values are described either in emotion-loaded words or else are mentioned and thence forgotten. The present report is a preliminary attempt to quantify some elements of aesthetic appeal while eliminating, insofar as possible, value judgments or personal preferences. If methods of recording such factors can be developed, the results promise to be a useful, new kind of basic data needed in many planning and decision-making circumstances. Such data would be especially useful when choices must be made among alternative courses of action. Such data would tend to provide a more prominent consideration of the nonmonetary aspects of a landscape. Assignment of quantitative estimates to aesthetic factors leads not so much to ratios of value as to relative rank positions. In fact, value itself tends to carry a connotation of preference, whereas ranking can more easily be used for categorization without attribution of preference and thus it tends to a void the introduction at too early a stage of differences in preference. Because the Federal Power Commission has been studying an application for a permit to construct one or more additional hydropower dams in the vicinity of Hells Canyon of the Snake River, the localities studied for the present discussion are in that region of Idaho. Hopefully, the data collected will provide some useful information on factors related to nonmonetary values in the region. The present discussion has been kept free of the preference judgments of the writer, and throughout the discussions observations are treated as facts.

Idaho↗

An introduced and a native vertebrate hybridize to form a genetic bridge to a second native species

The genetic impacts of hybridization between native and introduced species are of considerable conservation concern, while the possibility of reticulate evolution affects our basic understanding of how species arise and shapes how we use genetic data to understand evolutionary diversification. By using mitochondrial NADH dehydrogenase subunit 2 (ND2) sequences and 467 amplified fragment-length polymorphism nuclear DNA markers, we show that the introduced white sucker (Catostomus commersoni) has hybridized with two species native to the Colorado River Basin - the flannelmouth sucker (Catostomus latipinnis) and the bluehead sucker (Catostomus discobolus). Hybrids between the flannelmouth sucker and white sucker have facilitated introgression between the two native species, previously isolated by reproductive barriers, such that individuals exist with contributions from all three genomes. Most hybrids had the mitochondrial haplotype of the introduced white sucker, emphasizing its pivotal role in this three-way hybridization. Our findings highlight how introduced species can threaten the genetic integrity of not only one species but also multiple previously reproductively isolated species. Furthermore, this complex three-way reticulate (as opposed to strictly bifurcating) evolution suggests that seeking examples in other vertebrate systems might be productive. Although the present study involved an introduced species, similar patterns of hybridization could result from natural processes, including stream capture or geological formations (e.g., the Bering land bridge). ?? 2008 by The National Academy of Sciences of the USA.

Proceedings of the National Academy of Sciences of↗

U.S. Geological Survey (USGS) Earth Resources Observation and Science (EROS) Center-fiscal year 2010 annual report

The Earth Resources Observation and Science (EROS) Center is a U.S. Geological Survey (USGS) facility focused on providing science and imagery to better understand our Earth. The work of the Center is shaped by the earth sciences, the missions of our stakeholders, and implemented through strong program and project management, and application of state-of-the-art information technologies. Fundamentally, EROS contributes to the understanding of a changing Earth through 'research to operations' activities that include developing, implementing, and operating remote-sensing-based terrestrial monitoring capabilities needed to address interdisciplinary science and applications objectives at all levels-both nationally and internationally. The Center's programs and projects continually strive to meet, and where possible exceed, the changing needs of the USGS, the Department of the Interior, our Nation, and international constituents. The Center's multidisciplinary staff uses their unique expertise in remote sensing science and technologies to conduct basic and applied research, data acquisition, systems engineering, information access and management, and archive preservation to address the Nation's most critical needs. Of particular note is the role of EROS as the primary provider of Landsat data, the longest comprehensive global land Earth observation record ever collected. This report is intended to provide an overview of the scientific and engineering achievements and illustrate the range and scope of the activities and accomplishments at EROS throughout fiscal year (FY) 2010. Additional information concerning the scientific, engineering, and operational achievements can be obtained from the scientific papers and other documents published by EROS staff or by visiting our web site at http://eros.usgs.gov. We welcome comments and follow-up questions on any aspect of this Annual Report and invite any of our customers or partners to contact us at their convenience. To communicate with us, or for more information about EROS, contact: Communications and Outreach, USGS EROS Center, 47914 252nd Street, Sioux Falls, South Dakota 57198, jsnelson@usgs.gov, http://eros.usgs.gov/.

Open-File Report↗

Using demography and movement behavior to predict range expansion of the southern sea otter.

In addition to forecasting population growth, basic demographic data combined with movement data provide a means for predicting rates of range expansion. Quantitative models of range expansion have rarely been applied to large vertebrates, although such tools could be useful for restoration and management of many threatened but recovering populations. Using the southern sea otter ( Enhydra lutris nereis ) as a case study, we utilized integro-difference equations in combination with a stage-structured projection matrix that incorporated spatial variation in dispersal and demography to make forecasts of population recovery and range recolonization. In addition to these basic predictions, we emphasize how to make these modeling predictions useful in a management context through the inclusion of parameter uncertainty and sensitivity analysis. Our models resulted in hind-cast (1989–2003) predictions of net population growth and range expansion that closely matched observed patterns. We next made projections of future range expansion and population growth, incorporating uncertainty in all model parameters, and explored the sensitivity of model predictions to variation in spatially explicit survival and dispersal rates. The predicted rate of southward range expansion (median = 5.2 km/yr) was sensitive to both dispersal and survival rates; elasticity analysis indicated that changes in adult survival would have the greatest potential effect on the rate of range expansion, while perturbation analysis showed that variation in subadult dispersal contributed most to variance in model predictions. Variation in survival and dispersal of females at the south end of the range contributed most of the variance in predicted southward range expansion. Our approach provides guidance for the acquisition of further data and a means of forecasting the consequence of specific management actions. Similar methods could aid in the management of other recovering populations.

Ecological Applications↗

Final report and archive of the swath bathymetry and ancillary data collected in the Puerto Rico Trench region in 2002 and 2003

In 2002 and 2003, the U.S. Geological Survey (USGS), in cooperation with the National Oceanic and Atmospheric Administration (NOAA), conducted three exploration cruises that mapped for the first time the morphology of the entire tectonic plate boundary stretching from the Dominican Republic in the west to the Lesser Antilles in the east, a distance of approximately 700 kilometers (430 miles). Observations from these three exploration cruises, coupled with computer modeling and published Global Positioning System (GPS) results and earthquake focal mechanisms, have provided new information that is changing the evaluation of the seismic and tsunami hazard from this plate boundary. The observations collected during these cruises also contributed to the basic understanding of the mechanisms that govern plate tectonics, in this case, the creation of the island of Puerto Rico and the deep trench north of it. Results of the sea floor mapping have been an important component of the study of tsunami and earthquake hazards to the northeastern Caribbean and the U.S. Atlantic coast off the United States.

Puerto Rico↗

The Hawaiian Volcanoes Supersite: Open data for the benefit of science and society

The Hawaiian Volcanoes Supersite was established in 2008 with the goal of making large amounts of volcano monitoring data, especially satellite measurements, freely available at a site of international interest, scientific importance, and impactful natural hazards. The location was chosen because of the long history of volcanological research and innovation on the Island of Hawaiʻi, as well as the need for monitoring, assessing, and mitigating volcanic hazards for the local population. Ground-based data are provided by the U.S. Geological Survey Hawaiian Volcano Observatory, and several national space agencies have contributed thousands of satellite synthetic aperture radar and other data that would have otherwise required special grants or commercial purchase. Since the Hawaiian Volcanoes Supersite was initiated, the vast quantity of open space-based data has resulted in the development of new applications and methodologies, successful responses to volcanic crises, and research that has informed monitoring and hazards mitigation activities. While there remain opportunities for additional coordination among supersite users and for synergistic studies that make use of the full spectrum of available ground- and space-based data, the Hawaiian Volcanoes Supersite has achieved its goals of stimulating basic research to better understand Hawaiian volcanism and aiding in responses to hazardous geologic processes. The effort serves as a model for the benefits of open, low-latency, and comprehensive satellite data applied to disaster risk management and reduction, meeting a vision that has been laid out repeatedly in international agreements and accords.

Hawaii↗

Hydrology and glacier-lake-outburst floods (1987-2004) and water quality (1998-2003) of the Taku River near Juneau, Alaska

The Taku River Basin originates in British Columbia, Canada, and drains an area of 6,600 square miles at the U.S. Geological Survey's Taku River gaging station. Several mines operated within the basin prior to 1957, and mineral exploration has resumed signaling potential for future mining developments. The U.S. Geological Survey in cooperation with the Douglas Indian Association, Alaska Department of Environmental Conservation, and the U.S. Environmental Protection Agency conducted a water-quality and flood-hydrology study of the Taku River. Water-quality sampling of the Taku River from 1998 through 2003 established a baseline for assessing potential effects of future mining operations on water quality. The annual mean discharge of the Taku River is 13,700 cubic feet per second. The monthly mean discharge ranges from a minimum of 1,940 cubic feet per second in February to a maximum of 34,400 cubic feet per second in June. Nearly 90 percent of the annual discharge is from May through November. The highest spring discharges are sourced primarily from snowmelt and moderate discharges are sustained throughout the summer by glacial meltwaters. An ice cover usually forms over the Taku River in December persisting through the winter into March and occasionally into April. Glacier-lake-outburst floods originating from two glacier-dammed lakes along the margin of the Tulsequah Glacier in British Columbia, Canada, are the source of the greatest peak discharges on the Taku River. The largest flood during the period of record was 128,000 cubic feet per second on June 25, 2004, resulting from an outburst of Lake No Lake. Lake No Lake is the larger of the two lakes. The outburst-flood contribution to peak discharge was 80,000 cubic feet per second. The volume discharged from Lake No Lake is relatively consistent indicating drainage may be triggered when the lake reaches a critical stage. This suggests prediction of the timing of these outburst floods might be possible if lake-stage data were available. Further increases in the volume of Lake No Lake are unlikely as all tributary glaciers have retreated out of the lake basin. Decreasing outburst-flood volumes from Tulsequah Lake suggests a continued decline in the volume of this lake. Physical and chemical parameters and concentrations of basic water-quality constituents indicate good water quality. Samples collected at the Taku River gaging station contained low concentrations of trace elements in the dissolved phase. Trace elements sampled were within acceptable limits when compared with the Alaska Department of Environmental Conservation aquatic-life criteria for fresh waters. The highest concentrations of total trace elements sampled were collected during glacial-outburst floods and likely are associated with suspended sediments. Total trace-element concentrations generally increase with increasing water discharge, although a high correlation for all constituents sampled does not always exist.

Alaska↗

occupancyTuts: Occupancy modelling tutorials with RPresence

1. The occupancy modelling framework offers tremendous flexibility in estimating species abundance and distribution patterns while accounting for imperfect detection, and has seen rapid growth and adoption since its introduction at the beginning of the century. 2. At the same time, in an era of big data, there are increasing demands on developing quantitative skills and proficiency in young ecologists, many of whom lack the quantitative training needed to conduct research professionally. 3. We introduce occupancyTuts , an R package that features 28 learnr tutorials that teach the statistical underpinnings of several occupancy models. The tutorials include written content, instructional videos, R exercises, and quiz elements, covering a range of topics including statistical underpinnings, single- and dynamic-occupancy models, study design and several of the ‘spin-off’ models that extend the basic framework. 4. We plan for development of new tutorials that use RPresence as the analysis engine, and welcome new tutorial contributions that use other R packages as the analysis engine as well.

Methods in Ecology and Evolution↗

History of natural flows--Kansas River

Through its Water Resources Division, the United States Geological Survey has become the major water-resources historian for the nation. The Geological Survey's collection of streamflow records in Kansas began on a very small scale in 1895 in response to some early irrigation interest, Since that time the program has grown, and we now have about 21 350 station-years of record accumulated. A station-year of record is defined as a continuous record of flow collected at a fixed point for a period of one year. Volume of data at hand, however, is not in itself an, adequate measure of its usefullness. An important element in historical streamflow data which enhances its value as a tool for the prediction of the future is the length of continuous records available in the area being studied. The records should be of sufficient length that they may be regarded as a reasonable sample of what has gone before and may be expected in the future. Table 1 gives a graphical inventory of the available streamflow records in Kansas. It shows that, in general, there is a fair coverage of stations with records of about thirty-seven years in length, This is not a long period as history goes but it does include considerable experience with floods and droughts. Although a large quantity of data on Kansas streamflow has been accumulated, hydrologists and planning engineers find that stream flow information for many areas of the State is considerably less than adequate. The problem of obtaining adequate coverage has been given careful study by the Kansas Water Resources Board in cooperation with the U. S. Geological Survey and a report entitled "Development of A Balanced Stream-Gaging Program For Kansas", has been published by the Board as Bulletin No. 4, That report presents an analysis of the existing stream-gaging program and recommendations for a program to meet the rapidly expanding needs for more comprehensive basic data. The Kansas River is formed near Junction City, Kansas, by the confluence of the Smoky Hill and Republican Rivers, From that point the river flows eastward about 175 miles to Kansas City where it empties into the Missouri River. The basic history of its natural flow can be depicted in general by the records from three gaging stations. The one at Bonner Springs, about 21 miles upstream from the mouth, may be considered as representing the total outflow from the basin; the one at Ogden, about 8 miles downstream from the confluence of the Smoky Hill and Republican Rivers, may be considered as representing the combined contribution of those streams to the Kansas River flow; and the one at Topeka, being only about 16 river miles nearer to Ogden than to Bonner Springs, may be considered as representing flows at the mid-point along the river.

Kansas↗

USA National Phenology Network’s volunteer-contributed observations yield predictive models of phenological transitions

In support of science and society, the USA National Phenology Network (USA-NPN) maintains a rapidly growing, continental-scale, species-rich dataset of plant and animal phenology observations that with over 10 million records is the largest such database in the United States. Contributed voluntarily by professional and citizen scientists, these opportunistically collected observations are characterized by spatial clustering, inconsistent spatial and temporal sampling, and short temporal depth. We explore the potential for developing models of phenophase transitions suitable for use at the continental scale, which could be applied to a wide range of resource management contexts. We constructed predictive models of the onset of breaking leaf buds, leaves, open flowers, and ripe fruits – phenophases that are the most abundant in the database and also relevant to management applications – for all species with available data, regardless of plant growth habit, location, geographic extent, or temporal depth of the observations. We implemented a very basic model formulation - thermal time models with a fixed start date. Sufficient data were available to construct 107 individual species × phenophase models. Of these, fifteen models (14%) met our criteria for model fit and error and were suitable for use across the majority of the species’ geographic ranges. These findings indicate that the USA-NPN dataset holds promise for further and more refined modeling efforts. Further, the candidate models that emerged could be used to produce real-time and short-term forecast maps of the timing of such transitions to directly support natural resource management.

PLoS ONE↗