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sbtools: A package connecting R to cloud-based data for collaborative online research

The adoption of high-quality tools for collaboration and reproducible research such as R and Github is becoming more common in many research fields. While Github and other version management systems are excellent resources, they were originally designed to handle code and scale poorly to large text-based or binary datasets. A number of scientific data repositories are coming online and are often focused on dataset archival and publication. To handle collaborative workflows using large scientific datasets, there is increasing need to connect cloud-based online data storage to R. In this article, we describe how the new R package sbtools enables direct access to the advanced online data functionality provided by ScienceBase, the U.S. Geological Survey’s online scientific data storage platform.

The R Journal

Fall and winter foods of northern pintails in the Sacramento Valley, California

Food habits of northern pintails ( Anas acuta ) were investigated on 3 national wildlife refuges in the western portion of the Sacramento Valley, California, from August to March 1979-82. Pintails consumed >97% (aggregate % dry wt) plant food during diurnal foraging on national wildlife refuge rice, summer- irrigated, and summer-dry habitats from August through January. Invertebrate use increased to 28.9-65.6% of the diet in these habitats during February and March. Rice, swamp timothy ( Heleochloa schoenoides ), flatsedges ( Cyperus spp.), common barnyardgrass ( Echinochloa crusgalli ), southern naiad ( Najas guadalupensis ), and smartweed ( Polygonum spp.) seeds, miscellaneous vegetation, snails (Gastropoda), and midge (Diptera) and water beetle (Coleoptera) larvae were most important. These foods usually were taken proportional to or greater than availability. Rice was the most important food of pintails feeding nocturnally off the refuges in harvested rice fields from October through January (99.7%) and February and March (63%; barnyardgrass formed 31% of the diet). In August and October, some pintails consumed invertebrates or bulrush ( Scirpus spp.) seedlings in marshes soon after feeding in refuge rice (Aug) or harvested commercial rice fields (Oct), thereby increasing dietary protein. In late winter, females and males obtained similar (P > 0.05) percentages of invertebrates from refuge habitats. Important dietary seeds and invertebrates contained high protein or metabolizable energy content. Management should maintain adequate seed production in fall and mid-winter and invertebrate biomass in late winter.

California

Estimating carcass fat and protein in northern pintails during the nonbreeding season

I used northern pintails ( Anas acuta ) collected from August through March 1979-82 in the Sacramento Valley, California to derive equations to predict ether-extracted carcass fat, carcass protein, and skeletal lean dry weight. Ether-extracted carcass fat was best predicted by total fat depot weight (wet skin, abdominal fat, and intestinal fat) (r 2 = 0.94) and estimates based on carcass water content (r 2 = 0.93-0.98). Measured carcass protein was best predicted by a multiple regression including total protein depot weight (breast muscles, leg muscles, and gizzard) and tarsus length (R 2 = 0.79). I predicted skeletal lean dry weight by a multiple regression incorporating culmen, tarsus, and wing length (R 2 = 0.77). Predicted carcass fat agreed well with measured carcass fat in an independent data set of 30 pintails using total fat depot (r 2 = 0.92-0.96) and carcass water (r 2 = 0.97-0.99), but predicted carcass protein agreed less well with measured protein.

California

Effect of restrictive harvest regulations on survival and recovery rates of American black ducks

Population management of waterfowl requires an understanding of the effects of changes in hunting regulations on harvest and survival rates. Mean survival and recovery rates of American black ducks (Anas rubripes) were estimated during 3 periods of increasingly restrictive harvest regulations: 1950-66, 1967-82, and 1983-93. From the first to the second period, direct recovery rates declined for at least 1 age class in 4 of 6 reference areas, with a mean decline of 14% for adult and 7% for immature black ducks. From the second to the third period, direct recovery rates declined in all areas, declines averaging 37% for adults and 27% for immatures. Estimated mean survival rates increased from the first to the second period, consistent with a model of additivity of hunting mortality. Limited evidence existed for increases in survival rates from the second to the third period for immature males. For adults, however, survival increased less between these periods than would be expected if hunting mortality were additive and changes in recovery rates were proportional to changes in hunting mortality. Changes in survival and recovery rates of black ducks banded postseason were similar to those of adults banded preseason. Comparisons among estimates by degree blocks of latitude and longitude indicate that, at least between 1967 and 1983, estimated survival rates of immature and adult black ducks were lower in areas with high direct recovery rates. Smaller samples of banded birds and changes in banding locations in recent years may be limiting ability to evaluate consequences of recent changes in harvest rates. These correlation-based studies are limited in their ability to explain causes of observed changes in survival rates, suggesting the need for alternative approaches such as adaptive harvest management to increase understanding of the effects of hunting on black duck populations.

Journal of Wildlife Management

Modelling postfledging survival and age-specific breeding probabilities in species with delayed maturity: A case study of Roseate Terns at Falkner Island, Connecticut

We modeled postfledging survival and age-specific breeding probabilities in endangered Roseate Terns (Sterna dougallii) at Falkner Island, Connecticut, USA using capture-recapture data from 1988-1998 of birds ringed as chicks and as adults. While no individuals bred as 2-yr-olds during this period, about three-quarters of the young that survived and returned as 3-yr-olds nested, and virtually all surviving birds had begun breeding by the time they reached 5 years of age. We found no evidence of temporal variation in age of first breeding of birds from different cohorts. There was significant temporal variation in the annual survival of adults and the survival over the typical 3-yr maturation period of prebreeding birds, with extremely low values for both groups from the 1991 breeding season. The estimated overwinter survival rate (0.62) for adults from 1991-1992 was about three-quarters the usual rate of about 0.83, but the low survival of fledglings from 1991 resulted in less than 25% of the otherwise expected number of young from that cohort returning as breeding birds; this suggests that fledglings suffered a greater proportional decrease in survival than did adults. The survival estimates of young from 1989 and 1990 show that these cohorts were not negatively influenced by the events that decimated the young from 1991, and the young from 1992 and 1993 had above-average survival estimates. The apparent decrease since 1996 in development of fidelity of new recruits to this site is suspected due mainly to nocturnal disturbance and predation of chicks causing low productivity.

Connecticut

Spectral element modelling of fault-plane reflections arising from fluid pressure distributions

The presence of fault-plane reflections in seismic images, besides indicating the locations of faults, offers a possible source of information on the properties of these poorly understood zones. To better understand the physical mechanism giving rise to fault-plane reflections in compacting sedimentary basins, we numerically model the full elastic wavefield via the spectral element method (SEM) for several different fault models. Using well log data from the South Eugene Island field, offshore Louisiana, we derive empirical relationships between the elastic parameters (e.g. P-wave velocity and density) and the effective-stress along both normal compaction and unloading paths. These empirical relationships guide the numerical modelling and allow the investigation of how differences in fluid pressure modify the elastic wavefield. We choose to simulate the elastic wave equation via SEM since irregular model geometries can be accommodated and slip boundary conditions at an interface, such as a fault or fracture, are implemented naturally. The method we employ for including a slip interface retains the desirable qualities of SEM in that it is explicit in time and, therefore, does not require the inversion of a large matrix. We performa complete numerical study by forward modelling seismic shot gathers over a faulted earth model using SEM followed by seismic processing of the simulated data. With this procedure, we construct post-stack time-migrated images of the kind that are routinely interpreted in the seismic exploration industry. We dip filter the seismic images to highlight the fault-plane reflections prior to making amplitude maps along the fault plane. With these amplitude maps, we compare the reflectivity from the different fault models to diagnose which physical mechanism contributes most to observed fault reflectivity. To lend physical meaning to the properties of a locally weak fault zone characterized as a slip interface, we propose an equivalent-layer model under the assumption of weak scattering. This allows us to use the empirical relationships between density, velocity and effective stress from the South Eugene Island field to relate a slip interface to an amount of excess pore-pressure in a fault zone. ?? 2007 The Authors Journal compilation ?? 2007 RAS.

Geophysical Journal International

Multimodel inference and adaptive management

Ecology is an inherently complex science coping with correlated variables, nonlinear interactions and multiple scales of pattern and process, making it difficult for experiments to result in clear, strong inference. Natural resource managers, policy makers, and stakeholders rely on science to provide timely and accurate management recommendations. However, the time necessary to untangle the complexities of interactions within ecosystems is often far greater than the time available to make management decisions. One method of coping with this problem is multimodel inference. Multimodel inference assesses uncertainty by calculating likelihoods among multiple competing hypotheses, but multimodel inference results are often equivocal. Despite this, there may be pressure for ecologists to provide management recommendations regardless of the strength of their study’s inference. We reviewed papers in the Journal of Wildlife Management (JWM) and the journal Conservation Biology (CB) to quantify the prevalence of multimodel inference approaches, the resulting inference (weak versus strong), and how authors dealt with the uncertainty. Thirty-eight percent and 14%, respectively, of articles in the JWM and CB used multimodel inference approaches. Strong inference was rarely observed, with only 7% of JWM and 20% of CB articles resulting in strong inference. We found the majority of weak inference papers in both journals (59%) gave specific management recommendations. Model selection uncertainty was ignored in most recommendations for management. We suggest that adaptive management is an ideal method to resolve uncertainty when research results in weak inference.

Journal of Environmental Management

Wetlands in agricultural landscapes—Significant findings and recent advances from CEAP-Wetlands

The Wetlands Component of the USDA's Conservation Effects Assessment Project (CEAP-Wetlands) is a multi-agency effort advancing science related to quantifying and interpreting effects and effectiveness of conservation practices and programs on ecosystem services provided by wetlands in agricultural landscapes. This special section originated from a symposium held at the 73rd Soil and Water Conservation Society's International Annual Conference in Albuquerque New Mexico, July 29 to August 1, 2018. The symposium was jointly organized by the USDA Natural Resources Conservation Service and the US Geological Survey. To facilitate CEAP-Wetlands efforts, several regional assessments were conducted across the United States. These regional assessments were designed to address science gaps hindering wetland conservation and to develop tools facilitating conservation assessments. Conservation decisions affect not just agricultural wetlands, but also the services that these complex ecosystems provide to society. Papers in this special section of the Journal of Soil and Water Conservation present key findings and recent advances from several CEAP-Wetlands regional assessments and discuss the significant contributions of each assessment to an ever-increasing understanding of wetland ecosystems and their provisioning of ecosystem services. Modeling efforts using the Agricultural Policy and Environmental eXtender (APEX) and other process-based models are an integral component of CEAP-Wetlands. Results of these modeling efforts are also presented, and conservation implications are discussed.

Journal of Soil and Water Conservation

Comment on “An unconfined groundwater model of the Death Valley Regional Flow System and a comparison to its confined predecessor” by R.W.H. Carroll, G.M. Pohll and R.L. Hershey [Journal of Hydrology 373/3–4, pp. 316–328]

Carroll et al. (2009) state that the United States Geological Survey (USGS) Death Valley Regional Flow System (DVRFS) model, which is based on MODFLOW, is “conceptually inaccurate in that it models an unconfined aquifer as a confined system and does not simulate unconfined drawdown in transient pumping simulations.” Carroll et al. (2009) claim that “more realistic estimates of water availability” can be produced by a SURFACT-based model of the DVRFS that simulates unconfined groundwater flow and limits withdrawals from wells to avoid excessive drawdown. Differences in results from the original MODFLOW-based model and the SURFACT-based model stem primarily from application by Carroll et al. (2009) of head limits that can also be applied using the existing MODLOW model and not from any substantial difference in the accuracy with which the unconfined aquifer is represented in the two models. In a hypothetical 50-year predictive simulation presented by Carroll et al. (2009), large differences between the models are shown when simulating pumping from the lower clastic confining unit, where the transmissivity is nearly two orders of magnitude less than in an alluvial aquifer. Yet even for this extreme example, drawdowns and pumping rates from the MODFLOW and SURFACT models are similar when the head-limit capabilities of the MODFLOW MNW Package are applied. These similarities persist despite possible discrepancies between assigned hydraulic properties. The resulting comparison between the MODFLOW and SURFACT models of the DVRFS suggests that approximating the unconfined system in the DVRFS as a constant-saturated-thickness system (called a “confined system” by Carroll et al., 2009) performs very well.

Death Valley

Ecology of Siberian Taimen Hucho taimen in the Lake Baikal Basin

Taimen Hucho taimen historically inhabited most tributaries and littoral areas of Lake Baikal, in south central Siberia, where they supported subsistence and commercial fisheries. Logging, pollution, and overfishing have caused dramatic population declines or local extinction of most stocks. Most of what is known about this species has been published in eastern journals and therefore is not readily available to western scientists. New data collected during the 1980s and 1990s have been combined with other reports to provide an overview of the biology and life history of this species. Taimen are long-lived fish and can reach ages of 29 years and sizes up to 60 kg. Populations can either be strictly riverine or anadromous. Adults from both life histories ascend rivers in spring to spawn and feed, and less extensive migrations occur in fall to prey on spawning omul ( Coregonus autumnalis migratorius ). Principal food items for age 1 and 2 taimen are macroinvertebrates, but young taimen quickly become piscivorous at age 2 when they consume mainly black Baikal grayling ( Thymallus arcticus baicalensis ), and sculpins ( Taracottus kneri, Cottus kesslerij ). Males reach sexual maturity at ages 7 to 8 and later for females at ages 8 to 9. Average egg production per female was about 22,000 eggs. Parasite burdens are heavy but composed of few species and mediated by prey items consumed. This fish is a highly-specialized predator and plays an indispensable role in the structure of fish communities in mountains and foothills. Taimen conservation in the Baikal region is impossible without adoption and implementation of a dedicated rehabilitation program that includes the protection of remaining populations and habitat, and possibly introduction of hatchery-reared fish in selected areas where habitat remains, but parental stocks are low.

Journal of Great Lakes Research

Inferring fault rheology from low-frequency earthquakes on the San Andreas

Families of recurring low-frequency earthquakes (LFEs) within nonvolcanic tremor (NVT) on the San Andreas fault in central California show strong sensitivity to shear stress induced by the daily tidal cycle. LFEs occur at all levels of the tidal shear stress and are in phase with the very small, ~400 Pa, stress amplitude. To quantitatively explain the correlation, we use a model from the existing literature that assumes the LFE sources are small, persistent regions that repeatedly fail during shear of a much larger scale, otherwise aseismically creeping fault zone. The LFE source patches see tectonic loading, creep of the surrounding fault which may be modulated by the tidal stress, and direct tidal loading. If the patches are small relative to the surrounding creeping fault then the stressing is dominated by fault creep, and if patch failure occurs at a threshold stress, then the resulting seismicity rate is proportional to the fault creep rate or fault zone strain rate. Using the seismicity rate as a proxy for strain rate and the tidal shear stress, we fit the data with possible fault rheologies that produce creep in laboratory experiments at temperatures of 400 to 600°C appropriate for the LFE source depth. The rheological properties of rock-forming minerals for dislocation creep and dislocation glide are not consistent with the observed fault creep because strong correlation between small stress perturbations and strain rate requires perturbation on the order of the ambient stress. The observed tidal modulation restricts ambient stress to be at most a few kilopascal, much lower than rock strength. A purely rate dependent friction is consistent with the observations only if the product of the friction rate dependence and effective normal stress is ~ 0.5 kPa. Extrapolating the friction rate strengthening dependence of phyllosilicates (talc) to depth would require the effective normal stress to be ~50 kPa, implying pore pressure is lithostatic. If the LFE source is on the order of tens of meters, as required by the model, rate-weakening friction rate dependence (e.g., olivine) at 400 to 600°C requires that the minimum effective pressure at the LFE source is ~ 2.5 MPa.

California

Interactions between waves, sediment, and turbulence on a shallow estuarine mudflat

Measurements were collected on a shallow estuarine mudflat in northern San Francisco Bay to examine the physical processes controlling waves, turbulence, sediment resuspension, and their interactions. Tides alone forced weak to moderate currents of 10–30 cm s -1 in depths of 0–3 m, and maintained a background suspension of 30–50 mg L21 of fine sediment. In the presence of wind waves, bottom orbital velocities spanned 20–30 cm s -1 , suspended-sediment concentrations (SSC) at 15 and 30 cm above the bed (cmab) increased by 1–2 orders of magnitude, and vertical gradients in SSC were strong enough to produce turbulence-limiting stratification, with gradient Richardson numbers exceeding 0.25. Simultaneously, turbulent stresses (decomposed from wave motions) increased by an order of magnitude. The apparent contradiction of energetic turbulence in the presence of strong stratification was reconciled by considering the turbulent kinetic energy (TKE) budget: in general, dissipation and buoyancy flux were balanced by local shear production, and each of these terms increased during wave events. The classic wave-current boundary layer model represented the observations qualitatively, but not quantitatively since the velocity profile could not be approximated as logarithmic. Rather, the mean shear was elevated by the Stokes drift return flow and wind-generated surface stress, which diffused sediment upward and limited stratification. Our findings highlight a pathway for waves to supply energy to both the production and destruction of turbulence, and demonstrate that in such shallow depths, TKE and SSC can be elevated over more of the water column than predicted by traditional models.

California

Volcanic glass signatures in spectroscopic survey of newly proposed lunar pyroclastic deposits

Moon Mineralogy Mapper spectroscopic observations are used to assess the mineralogy of five sites that have recently been proposed to include lunar dark mantle deposits (DMDs). Volcanic glasses have, for the first time, clearly been identified at the location of three of the proposed pyroclastic deposits. This is the first time that volcanic glasses have been identified at such a small scale on the lunar surface from remote sensing observations. Deposits at Birt E, Schluter, and Walther A appear to be glassy DMDs. Deposits at Birt E and Schluter show (1) morphological evidence suggesting a likely vent and (2) mineralogical evidence indicative of the presence of volcanic glasses. The Walther A deposits, although they show no morphological evidence of vents, have the spectroscopic characteristics diagnostic of volcanic glasses. The deposits of the Freundlich-Sharonov basin are separated in two areas: (1) the Buys-Ballot deposits lack mineralogical and morphological evidence and thus are found to be associated with mare volcanism not with DMDs and (2) the Anderson crater deposits, which do not exhibit glassy DMD signatures, but they appear to be associated with possible vent structures and so may be classifiable as DMDs. Finally, dark deposits near the crater Kopff are found to be associated with likely mare volcanism and not associated with DMDs. The spectral identification of volcanic glass seen in many of the potential DMDs is a strong indicator of their pyroclastic origin.

Journal of Geophysical Research E: Planets

Linking channel hydrology with riparian wetland accretion in tidal rivers

The hydrologic processes by which tide affects river channel and riparian morphology within the tidal freshwater zone are poorly understood, yet are fundamental to predicting the fate of coastal rivers and wetlands as sea level rises. We investigated patterns of sediment accretion in riparian wetlands along the non-tidal through oligohaline portion of two coastal plain rivers in Maryland, U.S.A., and how flow velocity, water level, and suspended sediment concentration (SSC) in the channel may have contributed to those patterns. Sediment accretion was measured over a one year period using artificial marker horizons, channel hydrology was measured over a one month period using acoustic Doppler current profilers, and SSC was predicted from acoustic backscatter. Riparian sediment accretion was lowest at the non-tidal sites (mean and standard deviation = 8 ± 8 mm yr -1 ), highest at the upstream tidal freshwater forested wetlands (TFFW) (33 ± 28 mm yr -1 ), low at the midstream TFFW (12 ± 9 mm yr -1 ), and high at the oligohaline (fresh-to-brackish) marshes (19 ± 8 mm yr -1 ). Channel maximum flood and ebb velocity was 2-fold faster at the oligohaline than tidal freshwater zone on both tidal rivers, corresponding with the differences in in-channel SSC: the oligohaline zone's SSC was more than double the tidal freshwater zone's, and was greater than historical SSC at the non-tidal gages. The tidal wave characteristics differed between rivers, leading to significantly greater in-channel SSC during floodplain inundation in the weakly convergent than the strongly convergent tidal river. Overall sediment accretion was higher in the embayed river likely due to a single storm discharge and associated sedimentation.

Maryl

Transport of fine sediment over a coarse, immobile riverbed

Sediment transport in cobble-boulder rivers consists mostly of fine sediment moving over a coarse, immobile bed. Transport rate depends on several interrelated factors: boundary shear stress, the grain size and volume of fine sediment, and the configuration of fine sediment into interstitial deposits and bed forms. Existing models do not incorporate all of these factors. Approaches that partition stress face a daunting challenge because most of the boundary shear is exerted on immobile grains. We present an alternative approach that divides the bed into sand patches and interstitial deposits and is well constrained by two clear end-member cases: full sand cover and absence of sand. Entrainment from sand patches is a function of their aerial coverage. Entrainment from interstices among immobile grains is a function of sand elevation relative to the size of the immobile grains. The bed-sand coverage function is used to predict the ratio of the rate of entrainment from a partially covered bed to the rate of entrainment from a completely sand-covered bed, which is determined using a standard sand transport model. We implement the bed-sand coverage function in a morphodynamic routing model and test it against observations of sand bed elevation and suspended sand concentration for conditions of nonuniform fine sediment transport in a large flume with steady uniform flow over immobile hemispheres. The results suggest that this approach may provide a simple and robust method for predicting the transport and migration of fine sediment through rivers with coarse, immobile beds.

Journal of Geophysical Research F: Earth Surface

Relationships among seismic velocity, metamorphism, and seismic and aseismic fault slip in the Salton Sea Geothermal Field region

The Salton Sea Geothermal Field is one of the most geothermally and seismically active areas in California and presents an opportunity to study the effect of high-temperature metamorphism on the properties of seismogenic faults. The area includes numerous active tectonic faults that have recently been imaged with active source seismic reflection and refraction. We utilize the active source surveys, along with the abundant microseismicity data from a dense borehole seismic network, to image the 3-D variations in seismic velocity in the upper 5 km of the crust. There are strong velocity variations, up to ~30%, that correlate spatially with the distribution of shallow heat flow patterns. The combination of hydrothermal circulation and high-temperature contact metamorphism has significantly altered the shallow sandstone sedimentary layers within the geothermal field to denser, more feldspathic, rock with higher P wave velocity, as is seen in the numerous exploration wells within the field. This alteration appears to have a first-order effect on the frictional stability of shallow faults. In 2005, a large earthquake swarm and deformation event occurred. Analysis of interferometric synthetic aperture radar data and earthquake relocations indicates that the shallow aseismic fault creep that occurred in 2005 was localized on the Kalin fault system that lies just outside the region of high-temperature metamorphism. In contrast, the earthquake swarm, which includes all of the M > 4 earthquakes to have occurred within the Salton Sea Geothermal Field in the last 15 years, ruptured the Main Central Fault (MCF) system that is localized in the heart of the geothermal anomaly. The background microseismicity induced by the geothermal operations is also concentrated in the high-temperature regions in the vicinity of operational wells. However, while this microseismicity occurs over a few kilometer scale region, much of it is clustered in earthquake swarms that last from hours to a few days and are localized near the MCF system.

Salton Sea

Small crater modification on Meridiani Planum and implications for erosion rates and climate change on Mars

A morphometric and morphologic catalog of ~100 small craters imaged by the Opportunity rover over the 33.5&thinsp;km traverse between Eagle and Endeavour craters on Meridiani Planum shows craters in six stages of degradation that range from fresh and blocky to eroded and shallow depressions ringed by planed off rim blocks. The age of each morphologic class from <50&ndash;200&thinsp;ka to ~20&thinsp;Ma has been determined from the size-frequency distribution of craters in the catalog, the retention age of small craters on Meridiani Planum, and the age of the latest phase of ripple migration. The rate of degradation of the craters has been determined from crater depth, rim height, and ejecta removal over the class age. These rates show a rapid decrease from ~1&thinsp;m/Myr for craters < 1&thinsp;Ma to ~&thinsp;<0.1&thinsp;m/Myr for craters 10&ndash;20&thinsp;Ma, which can be explained by topographic diffusion with modeled diffusivities of ~10 &minus;6 &thinsp;m 2 /yr. In contrast to these relatively fast, short-term erosion rates, previously estimated average erosion rates on Mars over ~100 Myr and 3 Gyr timescales from the Amazonian and Hesperian are of order < 0.01&thinsp;m/Myr, which is 3&ndash;4 orders of magnitude slower than typical terrestrial rates. Erosion rates during the Middle-Late Noachian averaged over ~250 Myr, and ~700 Myr intervals are around 1&thinsp;m/Myr, comparable to slow terrestrial erosion rates calculated over similar timescales. This argues for a wet climate before ~3&thinsp;Ga in which liquid water was the erosional agent, followed by a dry environment dominated by slow eolian erosion.

Journal of Geophysical Research E: Planets