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Unmarked: An R package for fitting hierarchical models of wildlife occurrence and abundance

Ecological research uses data collection techniques that are prone to substantial and unique types of measurement error to address scientific questions about species abundance and distribution. These data collection schemes include a number of survey methods in which unmarked individuals are counted, or determined to be present, at spatially- referenced sites. Examples include site occupancy sampling, repeated counts, distance sampling, removal sampling, and double observer sampling. To appropriately analyze these data, hierarchical models have been developed to separately model explanatory variables of both a latent abundance or occurrence process and a conditional detection process. Because these models have a straightforward interpretation paralleling mechanisms under which the data arose, they have recently gained immense popularity. The common hierarchical structure of these models is well-suited for a unified modeling interface. The R package unmarked provides such a unified modeling framework, including tools for data exploration, model fitting, model criticism, post-hoc analysis, and model comparison.

Journal of Statistical Software

Summary and abstracts of the Planetary Data Workshop, June 2012

The recent boom in the volume of digital data returned by international planetary science missions continues to both delight and confound users of those data. In just the past decade, the Planetary Data System (PDS), NASA’s official archive of scientific results from U.S. planetary missions, has seen a nearly 50-fold increase in the amount of data and now serves nearly half a petabyte. In only a handful of years, this volume is expected to approach 1 petabyte (1,000 terabytes or 1 quadrillion bytes). Although data providers, archivists, users, and developers have done a creditable job of providing search functions, download capabilities, and analysis and visualization tools, the new wealth of data necessitates more frequent and extensive discussion among users and developers about their current capabilities and their needs for improved and new tools. A workshop to address these and other topics, “Planetary Data: A Workshop for Users and Planetary Software Developers,” was held June 25–29, 2012, at Northern Arizona University (NAU) in Flagstaff, Arizona. A goal of the workshop was to present a summary of currently available tools, along with hands-on training and how-to guides, for acquiring, processing and working with a variety of digital planetary data. The meeting emphasized presentations by data users and mission providers during days 1 and 2, and developers had the floor on days 4 and 5 using an “unconference” format for day 5. Day 3 featured keynote talks by Laurence Soderblom (U.S. Geological Survey, USGS) and Dan Crichton (Jet Propulsion Laboratory, JPL) followed by a panel discussion, and then research and technical discussions about tools and capabilities under recent or current development. Software and tool demonstrations were held in break-out sessions in parallel with the oral session. Nearly 150 data users and developers from across the globe attended, and 22 National Aeronautics and space Administration (NASA) and non-NASA data providers and missions were represented. Presentations (some in video format) and tutorials are posted on the meeting site ( http://astrogeology.usgs.gov/groups/Planetary-Data-Workshop ).

Open-File Report

Landsat geometric and radiometric calibration and characterization

The U.S. Geological Survey (USGS) Earth Resources Observation and Science Calibration and Validation (Cal/Val) Center of Excellence (ECCOE) focuses on improving the accuracy, precision, calibration, and product quality of remote-sensing data, leveraging years of multiscale optical system geometric and radiometric calibration and characterization experience. The ECCOE Landsat Cal/Val team continually monitors the geometric and radiometric performance of active Landsat missions and makes calibration adjustments, as needed, to maintain data quality at the highest level ( Haque and others, 2024 ). The accuracy of the ECCOE team calibration adjustments gives other civil and commercial satellite programs around the globe a trusted criterion and reference point. The ECCOE team works with U.S. and international government agencies and commercial vendors to help harmonize data sources as more frequent, consistent views of Earth benefits scientific research. Since the program started, more than 50 years ago, Landsat data have improved. When advances in calibration and validation today are applied to past satellite missions, researchers can consistently see how land changes over decades. To maintain this criterion, the ECCOE team continues to seek new and better ways to calibrate and validate data, which includes using the moon for calibration and drones for ground validation (fig. 1).

Fact Sheet

Patterns and sources of fecal coliform bacteria in three streams in Virginia, 1999-2000

Surface-water impairment by fecal coliform bacteria is a water-quality issue of national scope and importance. In Virginia, more than 175 stream segments are on the Commonwealth's 1998 303(d) list of impaired waters because of elevated concentrations of fecal coliform bacteria. These fecal coliform-impaired stream segments require the development of total maximum daily load (TMDL) and associated implementation plans, but accurate information on the sources contributing these bacteria usually is lacking. The development of defendable fecal coliform TMDLs and management plans can benefit from reliable information on the bacteria sources that are responsible for the impairment. Bacterial source tracking (BST) recently has emerged as a powerful tool for identifying the sources of fecal coliform bacteria that impair surface waters. In a demonstration of BST technology, three watersheds on Virginia's 1998 303(d) list with diverse land-use practices (and potentially diverse bacteria sources) were studied. Accotink Creek is dominated by urban land uses, Christians Creek by agricultural land uses, and Blacks Run is affected by both urban and agricultural land uses. During the 20-month field study (March 1999?October 2000), water samples were collected from each stream during a range of flow conditions and seasons. For each sample, specific conductance, dissolved oxygen concentration, pH, turbidity, flow, and water temperature were measured. Fecal coliform concentrations of each water sample were determined using the membrane filtration technique. Next, Escherichia coli (E. coli) were isolated from the fecal coliform bacteria and their sources were identified using ribotyping (a method of 'genetic fingerprinting'). Study results provide enhanced understanding of the concentrations and sources of fecal coliform bacteria in these three watersheds. Continuum sampling (sampling along the length of the streams) indicated that elevated concentrations of fecal coliform bacteria (maximum observed concentration of 290,000 colonies/100 milliliters (col/100mL) could occur along the entire length of each stream, and that the samples collected at the downstream monitoring station of each stream were generally representative of the entire upstream reach. Seasonal patterns were observed in the base-flow fecal coliform concentrations of all streams; concentrations were typically highest in the summer and lowest in the winter. Fecal coliform concentrations were lowest during periods of base flow (typically 200?2,000 col/100mL) and increased by 3?4 orders of magnitude during storm events (as high as 700,000 col/100mL). Multiple linear regression models were developed to predict fecal coliform concentrations as a function of streamflow and other water-quality parameters. The source tracking technique provided identification of bacteria contributions from diverse sources that included (but were not limited to) humans, cattle, poultry, horses, dogs, cats, geese, ducks, raccoons, and deer. Seasonal patterns were observed in the contributions of cattle and poultry sources. There were relations between the identified sources of fecal coliform bacteria and the land-use practices within each watershed. There were only minor differences in the distribution of bacteria sources between low-flow periods and high-flow periods. A coupled approach that utilized both a large available source library and a smaller, location-specific source library provided the most success in identifying the unknown E. coli isolates. BST data should provide valuable support and guidance for producing more defendable and scientifically rigorous watershed models. Incorporation of these bacteria-source data into watershed management strategies also should result in the selection of more efficient source-reduction scenarios for improving water quality.

Water-Resources Investigations Report

EERI earthquake reconnaissance report: 2019 Ridgecrest earthquake sequence

The Ridgecrest Earthquake Sequence began the morning of 4 July 2019 with an M6.4 earthquake at 10:33 a.m., closely following several small foreshocks. The epicenter of this event was roughly 11 miles (18 km) east-northeast of Ridgecrest (Figure 1) within the Naval Air Weapons Station China Lake (NAWS-CL). Seismic and geologic data established that the M6.4 earthquake occurred primarily along a steeply dipping northeast-trending strike-slip fault with left-lateral slip. This earthquake and preliminary reports of damage in Ridgecrest and Trona and associated ground cracking triggered a response by earthquake scientists and engineers throughout the region. A California Earthquake Clearinghouse was established in Ridgecrest to help coordinate the scientific response effort and to share data.

California

Instrumentation Guidelines for the Advanced National Seismic System

This document provides guidelines for the seismic-monitoring instrumentation used by long-term earthquake-monitoring stations that will sense ground motion, digitize and store the resulting signals in a local data acquisition unit, and optionally transmit these digital data. These guidelines are derived from specifications and requirements for data needed to address the nation's emergency response, engineering, and scientific needs as identified in U.S. Geological Survey Circular 1188 (1999). Data needs are discussed in terms of national, regional, and urban scales of monitoring in section 3. Functional performance specifications for instrumentation are introduced in section 4.3 and discussed in detail in section 6 in terms of instrument classes and definitions described in section 5. System aspects and testing recommendations are discussed in sections 7 and 8, respectively. Although U.S. Geological Survey Circular 1188 (1999) recommends that the Advanced National Seismic System (ANSS) include portable instrumentation, performance specifications for this element are not specifically addressed in this document. Nevertheless, these guidelines are largely applicable to portable instrumentation. Volcano monitoring instrumentation is also beyond the scope of this document. Guidance for ANSS structural-response monitoring is discussed briefly herein but details are deferred to the ANSS document by the ANSS Structural Response Monitoring Committee (U.S. Geological Survey, 2005). Aspects of station planning, siting, and installation other than instrumentation are beyond the scope of this document.

Open-File Report

Geographic information system datasets of regolith-thickness data, regolith-thickness contours, raster-based regolith thickness, and aquifer-test and specific-capacity data for the Lost Creek Designated Ground Water Basin, Weld, Adams, and Arapahoe Counties, Colorado

These datasets were compiled in support of U.S. Geological Survey Scientific-Investigations Report 2010-5082-Hydrogeology and Steady-State Numerical Simulation of Groundwater Flow in the Lost Creek Designated Ground Water Basin, Weld, Adams, and Arapahoe Counties, Colorado. The datasets were developed by the U.S. Geological Survey in cooperation with the Lost Creek Ground Water Management District and the Colorado Geological Survey. The four datasets are described as follows and methods used to develop the datasets are further described in Scientific-Investigations Report 2010-5082: (1) ds507_regolith_data: This point dataset contains geologic information concerning regolith (unconsolidated sediment) thickness and top-of-bedrock altitude at selected well and test-hole locations in and near the Lost Creek Designated Ground Water Basin, Weld, Adams, and Arapahoe Counties, Colorado. Data were compiled from published reports, consultant reports, and from lithologic logs of wells and test holes on file with the U.S. Geological Survey Colorado Water Science Center and the Colorado Division of Water Resources. (2) ds507_regthick_contours: This dataset consists of contours showing generalized lines of equal regolith thickness overlying bedrock in the Lost Creek Designated Ground Water Basin, Weld, Adams, and Arapahoe Counties, Colorado. Regolith thickness was contoured manually on the basis of information provided in the dataset ds507_regolith_data. (3) ds507_regthick_grid: This dataset consists of raster-based generalized thickness of regolith overlying bedrock in the Lost Creek Designated Ground Water Basin, Weld, Adams, and Arapahoe Counties, Colorado. Regolith thickness in this dataset was derived from contours presented in the dataset ds507_regthick_contours. (4) ds507_welltest_data: This point dataset contains estimates of aquifer transmissivity and hydraulic conductivity at selected well locations in the Lost Creek Designated Ground Water Basin, Weld, Adams, and Arapahoe Counties, Colorado. This dataset also contains hydrologic information used to estimate transmissivity from specific capacity at selected well locations. Data were compiled from published reports, consultant reports, and from well-test records on file with the U.S. Geological Survey Colorado Water Science Center and the Colorado Division of Water Resources.

Data Series

A simulation of historic hydrology and salinity in Everglades National Park: Coupling paleoecologic assemblage data with regression models

Restoration of Florida’s Everglades requires scientifically supportable hydrologic targets. This study establishes a restoration baseline by developing a method to simulate hydrologic and salinity conditions prior to anthropogenic changes. The method couples paleoecologic data on long-term historic ecosystem conditions with statistical models derived from observed meteorologic and hydrologic data that provide seasonal and annual variation. Results indicate that pre-drainage freshwater levels and hydroperiods in major sloughs of the Everglades were about 0.15 m higher and two to four times greater, respectively, on average compared to today’s values. Pre-drainage freshwater delivered to the wetlands and estuaries is estimated to be 2.5 to four times greater than the modern-day flow, and the largest deficit is during the dry season. In Florida Bay, salinity has increased between 5.3 and 20.1 with the largest differences in the areas near freshwater outflow points. These results suggest that additional freshwater flows to the Everglades are needed for restoration of the freshwater marshes of the Everglades and estuarine environment of Florida Bay, particularly near the end of the dry season.

Estuaries and Coasts

Coordinating standards and applications for optical water quality sensor networks

Joint USGS-CUAHSI Workshop: In Situ Optical Water Quality Sensor Networks; Shepherdstown, West Virginia, 8-10 June 2011; Advanced in situ optical water quality sensors and new techniques for data analysis hold enormous promise for advancing scientific understanding of aquatic systems through measurements of important biogeochemical parameters at the time scales over which they vary. High-frequency and real-time water quality data also provide the opportunity for early warning of water quality deterioration, trend detection, and science-based decision support. However, developing networks of optical sensors in freshwater systems that report reliable and comparable data across and between sites remains a challenge to the research and monitoring community. To address this, the U.S. Geological Survey (USGS) and the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI), convened a 3-day workshop to explore ways to coordinate development of standards and applications for optical sensors, as well as handling, storage, and analysis of the continuous data they produce.

Conference Paper

Estimation of contact time among animals from telemetry data

Continuous processes in most applications are measured discretely with error. This complicates the task of detecting intersections and the number of intersections between two continuous processes (i.e., when the processes have the same value). Intersections of continuous processes are scientifically important but challenging to estimate from data. For example, in the field of animal ecology, intersections of the paths of moving animals tracked with satellite technologies can be used to understand disease transmission. We illustrate how to quantify contact between animals using telemetry data (i.e., the recorded locations of an animal over time). We introduce our method to quantify contact time with accessible concepts from introductory stochastic process literature, such as Brownian motion. Then, we provide two data examples using white-tailed deer ( Odocoileus virginianus ) and mule deer ( Odocoileus hemionus) telemetry data in a region with high prevalence of chronic wasting disease. Our work provides a needed connection between existing model-based literature for animal movement and rule-based literature for animal interaction. Further, our work illustrates a unique statistical problem receiving minimal attention with broad applicability in human and livestock tracking.

The American Statistician

Seismic-hazard maps for the conterminous United States, 2014

The maps presented here provide an update to the 2008 data contained in U.S Geological Survey Scientific Investigations Map 3195 ( http://pubs.usgs.gov/sim/3195/ ).Probabilistic seismic-hazard maps were prepared for the conterminous United States for 2014 portraying peak horizontal acceleration and horizontal spectral response acceleration for 0.2- and 1.0-second periods with probabilities of exceedance of 10 percent in 50 years and 2 percent in 50 years. All of the maps were prepared by combining the hazard derived from spatially smoothed historical seismicity with the hazard from fault-specific sources. The acceleration values contoured are the random horizontal component. The reference site condition is firm rock, defined as having an average shear-wave velocity of 760 m/s in the top 30 meters corresponding to the boundary between NEHRP (National Earthquake Hazards Reduction program) site classes B and C. This data set represents the results of calculations of hazard curves for a grid of points with a spacing of 0.05 degrees in latitude and longitude. The grid of points was contoured to produce the final representation of the seismic hazard. These maps are intended to summarize the available quantitative information about seismic ground motion hazard for the conterminous United States from geologic and geophysical sources.

Scientific Investigations Map

2010 Petroleum resource assessment of the National Petroleum Reserve in Alaska (NPRA): GIS play maps

This report provides digital geographic information systems (GIS) files of maps for each of the 24 plays considered in the U.S. Geological Survey (USGS) 2010 updated petroleum resource assessment of the National Petroleum Reserve in Alaska (NPRA) (Houseknecht and others, 2010). These are the sample plays evaluated in a previous USGS assessment of the NPRA (Bird and Houseknecht, 2002a), maps of which were released in pdf format (Bird and Houseknecht, 2002b). The 2010 updated assessment of the NPRA evaluated each of the previously used 24 plays based on new geologic data available from exploration activities and scientific research. Quantitative assessments were revised for 11 plays, and no revisions were made for 9 plays. Estimates of the volume of technically recoverable, undiscovered oil, and nonassociated gas resources in these 20 plays are reported elsewhere (Houseknecht and others, 2010). Four plays quantitatively assessed in 2002 were eliminated from quantitative assessment for reasons explained by Houseknecht and others (2010). The NPRA assessment study area includes Federal and native onshore land and adjacent State offshore areas. A map showing the areal extent of each play was prepared by USGS geologists as a preliminary step in the assessment process. Boundaries were drawn on the basis of a variety of information, including seismic reflection data, results of exploration drilling, and regional patterns of rock properties. Play boundary polygons were captured by digitizing the play maps prepared by USGS geologists.

Alaska

Landsat Data Continuity Mission (LDCM) space to ground mission data architecture

The Landsat Data Continuity Mission (LDCM) is a scientific endeavor to extend the longest continuous multi-spectral imaging record of Earth's land surface. The observatory consists of a spacecraft bus integrated with two imaging instruments; the Operational Land Imager (OLI), built by Ball Aerospace & Technologies Corporation in Boulder, Colorado, and the Thermal Infrared Sensor (TIRS), an in-house instrument built at the Goddard Space Flight Center (GSFC). Both instruments are integrated aboard a fine-pointing, fully redundant, spacecraft bus built by Orbital Sciences Corporation, Gilbert, Arizona. The mission is scheduled for launch in January 2013. This paper will describe the innovative end-to-end approach for efficiently managing high volumes of simultaneous realtime and playback of image and ancillary data from the instruments to the reception at the United States Geological Survey's (USGS) Landsat Ground Network (LGN) and International Cooperator (IC) ground stations. The core enabling capability lies within the spacecraft Command and Data Handling (C&DH) system and Radio Frequency (RF) communications system implementation. Each of these systems uniquely contribute to the efficient processing of high speed image data (up to 265Mbps) from each instrument, and provide virtually error free data delivery to the ground. Onboard methods include a combination of lossless data compression, Consultative Committee for Space Data Systems (CCSDS) data formatting, a file-based/managed Solid State Recorder (SSR), and Low Density Parity Check (LDPC) forward error correction. The 440 Mbps wideband X-Band downlink uses Class 1 CCSDS File Delivery Protocol (CFDP), and an earth coverage antenna to deliver an average of 400 scenes per day to a combination of LGN and IC ground stations. This paper will also describe the integrated capabilities and processes at the LGN ground stations for data reception using adaptive filtering, and the mission operations approach fro- the LDCM Mission Operations Center (MOC) to perform the CFDP accounting, file retransmissions, and management of the autonomous features of the SSR.

Conference Paper

National Field Manual for the Collection of Water-Quality Data. U.S. Geological Survey Techniques of Water-Resources Investigations, Book 9

The mission of the Water Resources Discipline of the U.S. Geological Survey (USGS) is to provide the information and understanding needed for wise management of the Nation's water resources. Inherent in this mission is the responsibility to collect data that accurately describe the physical, chemical, and biological attributes of water systems. These data are used for environmental and resource assessments by the USGS, other government agenices and scientific organizations, and the general public. Reliable and quality-assured data are essential to the credibility and impartiality of the water-resources appraisals carried out by the USGS. The development and use of a National Field Manual is necessary to achieve consistency in the scientific methods and procedures used, to document those methods and procedures, and to maintain technical expertise. USGS field personnel use this manual to ensure that the data collected are of the quality required to fulfill our mission.

Techniques of Water-Resources Investigations

On the interpretation of satellite-derived gravity and magnetic data for studies of crustal geology and metallogenesis

Satellite-derived global gravity and magnetic maps have been shown to be useful in large-scale studies of the Earth's crust, despite the relative infancy of such studies. Numerous authors have made spatial associations of gravity or magnetic anomalies with geological provinces. Gravimetric interpretations are often made in terms of isostasy, regional variations of density, or of geodesy in general. Interpretations of satellite magnetic anomalies often base assumptions of overall crustal magnetism on concepts of the vertical and horizontal distribution of magnetic susceptibility, then make models of these assumed distributions. The opportunity of improving our satellite gravity and magnetic data through the proposed Geopotential Research Mission should considerably improve the scientific community's ability to analyze and interpret global magnetic and gravity data. As data processing techniques improve, we may expect to see even more useful results of the data.

Conference Paper

Update on the Center for Engineering Strong-Motion Data (CESMD)

he Center for Engineering Strong-Motion Data (CESMD), an internationally utilized joint center of the U.S. Geological Survey (USGS) and the California Geological Survey (CGS), provides a unified access point for earthquake strong-motion records and station metadata from the CGS California Strong-Motion Instrumentation Program (CSMIP), the USGS National Strong-Motion Project (NSMP), the USGS Advanced National Seismic System (ANSS), and other affiliates. The CESMD works closely with the ANSS and with the Consortium of Organizations for Strong-Motion Observation Systems (COSMOS) to engage with strong-motion networks in the U.S. and other countries to receive, process, and post records. The CESMD has recently developed new tools to facilitate access to strong-motion data and metadata for use in post-earthquake response and scientific research applications. The Center provides raw and processed strong-motion data via its Engineering Data Center (EDC) and the Virtual Data Center (VDC) web portals, currently hosting more than 60,000 records with peak ground accelerations greater than 0.1% g, from over 3,000 earthquakes. This short paper provides updates of the available strong-motion data, station metadata, recent enhancements and developments of the tools, and applications that are made available to users for accessing strong-motion data.

Conference Paper

Ultramafic float rocks at Jezero crater (Mars): Excavation of lower crustal rocks or mantle peridotites by impact cratering?

Based on observation and data from meteorites and in situ scientific missions, experiments as well as models, the Martian mantle is assumed to share some compositional and mineralogical affinity with the terrestrial mantle. However, there might be subtle differences like the Martian mantle being more ferroan. Yet, we do not have any direct analysis of a Martian mantle rock to confirm this assumption. NASA’s Perseverance rover found olivine-rich boulder-sized float rocks on the upper Jezero fan (Mars). These boulders have an ultramafic composition and their mineralogy is dominantly composed of Fo 73±3 olivine with high-Mg orthopyroxene, Cr-rich Ti-Fe oxides and minor plagioclase and high-Ca pyroxene. Microtextural and petrological analysis reveals that these minerals crystallized at equilibrium. In addition, these boulders are different from all the bedrocks analyzed by Perseverance along its traverse which are crustal igneous rocks and sediments. Comparing our data to Martian meteorites and available Mars bulk silicate models (BSM), we discuss that these boulders could represent primitive melts and/or lower crustal material, and we specifically hypothesize that they could be mantle peridotites. We propose that these putative mantle rocks could have been excavated by the succession of impacts from the shallow mantle or lower crust in the Isidis region where Jezero crater is located. These olivine-rich boulders could thereby constitute the first direct analysis of a Martian mantle rock.

Earth and Planetary Science Letters

Onshore industrial wind turbine locations for the United States up to March 2014

Wind energy is a rapidly growing form of renewable energy in the United States. While summary information on the total amounts of installed capacity are available by state, a free, centralized, national, turbine-level, geospatial dataset useful for scientific research, land and resource management, and other uses did not exist. Available in multiple formats and in a web application, these public domain data provide industrial-scale onshore wind turbine locations in the United States up to March 2014, corresponding facility information, and turbine technical specifications. Wind turbine records have been collected and compiled from various public sources, digitized or position verified from aerial imagery, and quality assured and quality controlled. Technical specifications for turbines were assigned based on the wind turbine make and model as described in public literature. In some cases, turbines were not seen in imagery or turbine information did not exist or was difficult to obtain. Uncertainty associated with these is recorded in a confidence rating.

Scientific Data