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Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

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At least 217 records · Page 12Linked to original sources
USGS2000

Coupled atmosphere-biophysics-hydrology models for environmental modeling

The formulation and implementation of LEAF-2, the Land Ecosystem–Atmosphere Feedback model, which comprises the representation of land–surface processes in the Regional Atmospheric Modeling System (RAMS), is described. LEAF-2 is a prognostic model for the temperature and water content of soil, snow cover, vegetation, and canopy air, and includes turbulent and radiative exchanges between these components and with the atmosphere. Subdivision of a RAMS surface grid cell into multiple areas of distinct land-use types is allowed, with each subgrid area, or patch, containing its own LEAF-2 model, and each patch interacts with the overlying atmospheric column with a weight proportional to its fractional area in the grid cell. A description is also given of TOPMODEL, a land hydrology model that represents surface and subsurface downslope lateral transport of groundwater. Details of the incorporation of a modified form of TOPMODEL into LEAF-2 are presented. Sensitivity tests of the coupled system are presented that demonstrate the potential importance of the patch representation and of lateral water transport in idealized model simulations. Independent studies that have applied LEAF-2 and verified its performance against observational data are cited. Linkage of RAMS and TOPMODEL through LEAF-2 creates a modeling system that can be used to explore the coupled atmosphere–biophysical–hydrologic response to altered climate forcing at local watershed and regional basin scales.

Journal of Applied Meteorology↗
USGS2017

Isotopic niches support the resource breadth hypothesis

Because a broad spectrum of resource use allows species to persist in a wide range of habitat types, and thus permits them to occupy large geographical areas, and because broadly distributed species have access to more diverse resource bases, the resource breadth hypothesis posits that the diversity of resources used by organisms should be positively related with the extent of their geographic ranges. We investigated isotopic niche width in a small radiation of South American birds in the genus Cinclodes . We analysed feathers of 12 species of Cinclodes to test the isotopic version of the resource breadth hypothesis and to examine the correlation between isotopic niche breadth and morphology. We found a positive correlation between the widths of hydrogen and oxygen isotopic niches (which estimate breadth of elevational range) and widths of the carbon and nitrogen isotopic niches (which estimates the diversity of resources consumed, and hence of habitats used). We also found a positive correlation between broad isotopic niches and wing morphology. Our study not only supports the resource breadth hypothesis but it also highlights the usefulness of stable isotope analyses as tools in the exploration of ecological niches. It is an example of a macroecological application of stable isotopes. It also illustrates the importance of scientific collections in ecological studies.

Journal of Animal Ecology↗
USGS2021

Poecivirus is present in individuals with beak deformities in seven species of North American birds

Avian keratin disorder (AKD), a disease of unknown etiology characterized by debilitating beak overgrowth, has increasingly affected wild bird populations since the 1990s. A novel picornavirus, poecivirus, is closely correlated with disease status in Black-capped Chickadees ( Poecile atricapillus ) in Alaska. However, our knowledge of the relationship between poecivirus and beak deformities in other species and other geographic areas remains limited. The growing geographic scope and number of species affected by AKD-like beak deformities require a better understanding of the causative agent to evaluate the population-level impacts of this epizootic. Here, we tested eight individuals from six avian species with AKD-consistent deformities for the presence of poecivirus: Mew Gull ( Larus canus ), Hairy Woodpecker ( Picoides villosus ), Black-billed Magpie ( Pica hudsonia ), American Crow ( Corvus brachyrhynchos ), Red-breasted Nuthatch ( Sitta canadensis ), and Blackpoll Warbler ( Setophaga striata ). The birds were sampled in Alaska and Maine (1999−2016). We used targeted PCR followed by Sanger sequencing to test for the presence of poecivirus in each specimen and to obtain viral genome sequence from virus-positive host individuals. We detected poecivirus in all individuals tested, but not in negative controls (water and tissue samples). Furthermore, we used unbiased metagenomic sequencing to test for the presence of other pathogens in six of these specimens (Hairy Woodpecker, two American Crows, two Red-breasted Nuthatches, Blackpoll Warbler). This analysis yielded additional viral sequences from several specimens, including the complete coding region of poecivirus from one Red-breasted Nuthatch, which we confirmed via targeted PCR followed by Sanger sequencing. This study demonstrates that poecivirus is present in individuals with AKD-consistent deformities from six avian species other than Black-capped Chickadee. While further investigation will be required to explore whether there exists a causal link between this virus and AKD, this study demonstrates that poecivirus is not geographically restricted to Alaska, but rather occurs elsewhere in North America.

Alaska, Maine↗
USGS2021

Evaluating fish rescue as a drought adaptation strategy using a life cycle modeling approach for imperiled coho salmon

Projected intensification of drought as a result of climate change may reduce the capacity of streams to rear fish, exacerbating the challenge of recovering salmonid populations listed under the Endangered Species Act. Without management intervention, some stocks will likely go extinct as stream drying and fragmentation reduce juvenile survival to unsustainable levels. To offset drought‐related mortality, fish rescue programs have proliferated, whereby juvenile salmonids are captured and transferred to off‐site rearing facilities. However, the efficacy of this potential conservation tool remains poorly understood. We developed a life cycle model to examine the implications of fish rescue on the abundance of Coho Salmon Oncorhynchus kisutch across serial life stages. The simulation model examines scenarios with varying quantities of rescued fish, time in captivity, drought severity, and reduced smolt‐to‐adult return rates. Our results indicate that fish rescue can increase the abundance of adults and lower extinction risk, particularly for fish held in captivity for a full year. However, fish rescue can also decrease the abundance of adults and increase extinction risk if fish are held only for summer and there is limited winter habitat. We found that when fish rescue did increase returns, it functioned more like a stock enhancement program than a drought mitigation tool and it would likely lead to consecutive generations of captive rearing, which has been shown to have negative effects on fitness. We translated our model into an R Shiny application ( https://shiny.wdfw‐fish.us/CohoPopulationDynamics/ ) that allows users to explore how fish rescue affects Coho Salmon population dynamics through customized parameterization of the model to represent different systems or different assumptions about the effects of fish rescue.

North American Journal of Fisheries Management↗
USGS2016

Extending ordinal regression with a latent zero-augmented beta distribution

Ecological abundance data are often recorded on an ordinal scale in which the lowest category represents species absence. One common example is when plant species cover is visually assessedwithin bounded quadrats and then assigned to pre-defined cover class categories.We present an ordinal beta hurdle model that directly models ordinal category probabilitieswith a biologically realistic beta-distributed latent variable.Ahurdle-at-zero model allows ecologists to explore distribution (absence) and abundance processes in an integrated framework. This provides an alternative to cumulative link models when data are inconsistent with the assumption that the odds ofmoving into a higher category are the same for all categories (proportional odds). Graphical tools and a deviance information criterion were developed to assess whether a hurdle-at-zero model should be used for inferences rather than standard ordinal methods. Hurdle-at-zero and non-hurdle ordinal models fit to vegetation cover class data produced substantially different conclusions.The ordinal beta hurdle model yielded more precise parameter estimates than cumulative logit models, although out-of-sample predictions were similar. The ordinal beta hurdle model provides inferences directly on the latent biological variable of interest, percent cover, and supports exploration of more realistic ecological patterns and processes through the hurdle-at-zero or two-part specification.We provide JAGS code as an on-line supplement. Supplementary materials accompanying this paper appear on-line.

Journal of Agricultural, Biological, and Environme↗
USGS1998

Developmental geology of coalbed methane from shallow to deep in Rocky Mountain basins and in Cook Inlet-Matanuska Basin, Alaska, USA and Canada

The Rocky Mountain basins of western North America contain vast deposits of coal of Cretaceous through early Tertiary age. Coalbed methane is produced in Rocky Mountain basins at depths ranging from 45 m (150 ft) to 1981 m (6500 ft) from coal of lignite to low-volatile bituminous rank. Although some production has been established in almost all Rocky Mountain basins, commercial production occurs in only a few. despite more than two decades of exploration for coalbed methane in the Rocky Mountain region, it is still difficult to predict production characteristics of coalbed methane wells prior to drilling. Commonly cited problems include low permeabilities, high water production, and coals that are significantly undersaturated with respect to methane. Sources of coalbed gases can be early biogenic, formed during the early stages of coalification, thermogenic, formed during the main stages of coalification, or late stage biogenic, formed as a result of the reintroduction of methane-gnerating bacteria by groundwater after uplift and erosion. Examples of all three types of coalbed gases, and combinations of more than one type, can be found in the Rocky Mountain region. Coals in the Rocky Mountain region achieved their present ranks largely as a result of burial beneath sediments that accumulated during the Laramide orogeny (Late Cretaceous through the end of the eocene) or shortly after. Thermal events since the end of the orogeny have also locally elevated coal ranks. Coal beds in the upper part of high-volatile A bituminous rank or greater commonly occur within much more extensive basin-centered gas deposits which cover large areas of the deeper parts of most Rocky Mountain basins. Within these basin-centered deposits all lithologies, including coals, sandstones, and shales, are gas saturated, and very little water is produced. The interbedded coals and carbonaceous shales are probably the source of much of this gas. Basin-centered gas deposits become overpressured from hydrocarbon generation as they form, and this overpressuring is probably responsible for driving out most of the water. Sandstone permeabilities are low, in part because of diagenesis caused by highly reactive water given off during the early stages of coalification. Coals within these basin-centered deposits commonly have high gas contents and produce little water, but they generally occur at depths greater than 5000 ft and have low permeabilities. Significant uplift and removal of overburden has occurred throughout the Rocky Mountain region since the end of the Eocene, and much of this erosion occurred after regional uplift began about 10 Ma. The removal of overburden generally causes methane saturation levels in coals to decrease, and thus a significant drop in pressure is required to initiate methane production. The most successful coalbed methane production in the Rocky Mountain region occurs in areas where gas contents were increased by post-Eocene thermal events and/or the generation of late-stage biogenic gas. Methane-generating bacteria were apparently reintroduced into the coals in some areas after uplift and erosion, and subsequent changes in pressure and temperature, allowed surface waters to rewater the coals. Groundwater may also help open up cleat systems making coals more permeable to methane. If water production is excessive, however, the economics of producing methane are impacted by the cost of water disposal.The Rocky Mountain basins of western North America contain vast deposits of coal of Cretaceous through early Tertiary age. Coalbed methane is produced in Rocky Mountain basins at depths ranging from 45 to 1981 m from coal of lignite to low volatile bituminous rank. Despite more than two decades of exploration for coalbed methane in Rocky Mountain region, it is still difficult to predict production characteristics of coalbed methane wells prior to drilling. Sources of coalbed gases can be early biogenic, formed during the main stages of coa

International Journal of Coal Geology↗
USGS2024

Evolutionary perspectives on thiamine supplementation of managed Pacific salmonid populations

Thiamine deficiency complex (TDC) has been identified in an ever-expanding list of species and populations. In many documented occurrences of TDC in fishes, juvenile mortality can be high—up to 90% at the population level. Such sweeping demographic losses and concomitant decreases in genetic diversity due to TDC can be prevented by treating pre-spawn females or fertilized eggs with supplemental thiamine. However, some fisheries managers are hesitant to widely apply thiamine treatments due to the potential for unforeseen evolutionary consequences. With these concerns in mind, we first review the existing data regarding genetic adaptation to low-thiamine conditions and provide perspectives on evolution-informed treatment strategies with specific population examples. We also provide practical treatment information, consider the potential logistical constraints of thiamine supplementation, and explore the consequences of deciding against supplementation. Until new evidence bolsters or refutes the genetic adaptation hypothesis, we suggest that TDC mitigation strategies should be designed to support maximum population genetic diversity through thiamine supplementation.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2020

A 450-year record of environmental change from Castle Lake, California (USA), inferred from diatoms and organic geochemistry

A 39-cm sediment core from Castle Lake, California (USA) spans the last ~ 450 years and was analyzed for diatoms and organic geochemistry (δ 15 N, δ 13 C, and C:N), with the goal of determining sensitivity to natural climate variation and twentieth century anthropogenic effects. Castle Lake is a subalpine, nitrogen-limited lake with ~ 5 months of annual ice cover. Human impacts include light recreational use, past fish stocking, and experimental use by the Castle Lake Research Station. The base of the core (below 32 cm; pre mid-1700s) represents the period of maximum ice cover. In contrast, the end of the Little Ice Age (mid 1700s–early 1800s) is dominated by cyclotelloids (mostly Discostella stelligera ), indicating significant open-water periods, a condition that persisted into the early 1900s. Cyclotelloids began to decline in the 1960s and were replaced by the Fragilaria tenera grp. (peak in 1970s), succeeded by Asterionella formosa (peak ~ 2010), and accompanied by a reduction in δ 15 N values and a decrease in C:N that may represent increased atmospheric nitrogen deposition. Another anthropogenic signal was discerned in the core and was interpreted to be the result of an ammonium nitrate fertilization experiment of the epilimnion that was conducted in 1980 and 1981. This signal was manifested in the core largely by a negative excursion in δ 15 N, possibly caused by fractionation during denitrification in surface sediment. A phytoplankton monitoring dataset collected by the Castle Lake Research Station from 1967 to 1984 corroborates the timing of increased araphid euplanktonic species in the 1970s, and increases in two benthic diatoms ( Staurosirella pinnata and Tabellaria fenestrata) , entrained in the phytoplankton tows during the experimentation years. Both ice cover and nitrogen addition appear to be strong drivers that affected the lake diatoms, although additional drivers, such as fish stocking and associated cascade effects need further exploration. These data will be helpful for interpreting longer core records from Castle Lake, should the opportunity arise, as well as cores from similar systems in the region.

California↗
USGS2024

Physics-based forecasts of eruptive vent locations at calderas

Constraining stresses in the Earth's crust in volcanic regions is critical for understanding many mechanical processes related to eruptive activity. Dike pathways, in particular, are shaped by the orientation of principal stress axes. Therefore, accurate models of dike trajectories and future vent locations rely on accurate estimates of stresses in the subsurface. This work presents a framework for probabilistic constraint of the stress state of calderas by combining three-dimensional physics-based dike pathway models with observed past vent locations using a Monte Carlo approach. The retrieved stress state is then used to produce probability maps of future vent opening across a caldera. We test our stress inversion and vent forecast approach on synthetic scenarios, and find it successful depending on the distribution of the available vents and the complexity of the volcano's structural history. We explore the potential and limitations of the approach, show how its performance is sensitive to the assumptions in the models and available prior information, and discuss how it may be applied to real calderas.

Journal of Geophysical Research: Solid Earth↗
USGS2020

Coming of age: Morphometric variation in the hand skeletons of juvenile and adult Lesser Treeshrews (Scandentia: Tupaiidae: Tupaia minor Günther, 1876)

Morphometric analyses of the manus skeleton have proven useful in understanding species limits and morphological divergence among tupaiid treeshrews (Scandentia: Tupaiidae). Specimens in these studies are typically limited to mature individuals with fully erupted permanent dentition, which eliminates potentially confounding variation attributable to age, but can also exclude rare taxa and small island populations that are poorly represented in systematic collections. To determine the real limits associated with including immature animals in such studies, we used multivariate analyses to study sexual and age variation of the manus skeleton within two allopatric populations of the Lesser Treeshrew (Tupaia minor Günther, 1876) from the Malay Peninsula and from Borneo that we treated as separate samples. Individuals were aged using dental eruption of the permanent dentition. We also recorded the degree of epiphyseal fusion of the bones of the manus based on x-rays of study skins. We then tested our ability to distinguish the two populations using a series of discriminant function analyses of hand measurements from samples that included varying proportions of immature individuals and adults. We found no evidence of sexual dimorphism in hand proportions, permitting us to combine females and males in our samples. Epiphyseal fusion of the metacarpals and phalanges typically occurs by the time the third molars have completely erupted, and fusion of the distal epiphyses of the radius and ulna typically occurs by the time the permanent fourth premolars are in place. There is occasional asynchrony between dental age and epiphyseal fusion. In both populations, the hands of most infants and subadults provide morphometric values within the range of variation of adults, although they are typically distributed in the lower part of the adult range and have the potential to bias the sample toward lower mean size. The inclusion of infants and subadults when attempting to discriminate between two taxa generally results in lower rates of correct classifications, although the rates increase as the sample of immature individuals is limited to older subadults. As a general rule, we recommend that infants and subadults continue to be excluded from analyses when exploring taxonomic boundaries among treeshrews. In cases of extremely small sample sizes of adults, however, older subadults—in which the permanent third premolars are erupting or in place—can be used with appropriate caution.

Journal of Mammalogy↗
USGS2023

The Volcanic Hazard Maps Database: An initiative of the IAVCEI Commission on Volcanic Hazards and Risk

In this work we present the International Association of Volcanology and Chemistry of the Earth’s Interior (IAVCEI) Commission on Volcanic Hazards and Risk (CVHR) Volcanic Hazard Maps Database and the accompanying volcanichazardmaps.org website. Using input from a series of IAVCEI CVHR Working Group on Hazard Mapping workshops, we developed a classification scheme and terminology framework for categorizing, discussing, naming, and searching for hazard maps. ≥ The database and website aim to serve as a resource for the volcanology community to explore how different aspects of hazard map development and design have been addressed in different countries, for different hazard processes, and for different intended purposes and audiences. Additionally, they act as a tool for presenting hazard map options to stakeholder groups and serve as a learning resource that can be incorporated into educational materials and training courses. In this work, we present the database and website, discuss the classification scheme, explore the enormous diversity of hazard maps, and suggest ways that the database and website can be used by the volcanic hazard mapping community.

Journal of Applied Volcanology↗
USGS1999

Mining geology of the Pond Creek seam, Pikeville Formation, Middle Pennsylvanian, in part of the Eastern Kentucky Coal Field, USA

The Pond Creek seam is one of the leading producers of coal in the Eastern Kentucky Coal Field. The geologic factors that affect mining were investigated in several underground mines and categorized in terms of coal thickness, coal quality, and roof control. The limits of mining and thick coal are defined by splitting along the margin of the coal body. Within the coal body, local thickness variation occurs because of (1) leader coal benches filling narrow, elongated depressions, (2) rider coal benches coming near to or merging with the main bench, (3) overthrust coal benches being included along paleochannel margins, (4) cutouts occuring beneath paleochannels, and (5) very hard and unusual rock partings occuring along narrow, elongated trends. In the study area, the coal is mostly mined as a compliance product: sulfur contents are less than 1% and ash yields are less than 10%. Local increases in sulfur occur beneath sandstones, and are inferred to represent post-depositional migration of fluids through porous sands into the coal. Run-of-mine quality is also affected by several mine-roof conditions and trends of densely concentrated rock partings, which lead to increased in- and out-of-seam dilution and overall ash content of the mined coal. Roof control is largely a function of a heterolithic facies mosaic of coastal-estuarine origin, regional fracture trends, and unloading stress related to varying mine depth beneath the surface. Lateral variability of roof facies is the rule in most mines. The largest falls occur beneath modern valleys and parallel fractures, along paleochannel margins, within tidally affected 'stackrock,' and beneath rider coals. Shale spalling, kettlebottoms, and falls within other more isolated facies also occur. Many of the lithofacies, and falls related to bedding weaknesses within or between lithofacies, occur along northeast-southwest trends, which can be projected in advance of mining. Fracture-related falls occur independently of lithofacies trends along northwest-southeast trends, especially beneath modern valleys where overburden thickness decreases sharply. Differentiating roof falls related to these trends can aid in predicting roof quality in advance of mining.The Pond Creek-Lower Elkhorn seam has been an important exploration target because it typically has very low sulfur contents and ash yields. Geologic research in several large Pond Creek mines suggested variability in roof quality and coal thickness. Due to mine access, geologic problems encountered during mining are documented and described.

International Journal of Coal Geology↗
USGS2024

The potential for species distribution models to distinguish source populations from sinks

1. While species distribution models (SDM) are frequently used to predict species occurrences to help inform conservation management, there is limited evidence evaluating whether habitat suitability can reliably predict intrinsic growth rates or distinguish source from sink populations. Filling this knowledge gap is critical for conservation science, as applications of SDMs for management purposes ultimately depend on these typically unobserved population or metapopulation dynamics. 2. Using regression, we associate previously published population level estimates of intrinsic growth and abundance derived from a Bayesian analysis of mark-recapture data for 17 bird species found in the contiguous United States with SDM habitat suitability estimates fitted here to opportunistic data for these same species. We then use AUC to measure how well SDMs can distinguish populations categorized as sources and sinks, depending on their intrinsic growth rates estimated from the mark-recapture data. We built SDMs using two different approaches, boosted regression trees (BRT) and Generalized Linear Models (GLM), and compared their predictive performance. Each SDM was built with presence points obtained from eBird and 10 environmental variables previously selected to model intrinsic growth rates and abundance for these species. 3. We show that SDMs built with opportunistic data are poor predictors of species demography in general; both BRT and GLM explained very little spatial variation of intrinsic growth rate and population abundance (median R2 across 17 species was close to 0.1 for both SDM methods). SDMs do, however, estimate higher suitability for source populations as compared to sinks. Out of 13 species which had both source and sink populations, both BRT and GLM had AUC values greater than 0.7 for 7 species when discriminating between sources and sinks. 4. Habitat suitability have the potential to be a useful measure to indicate a population’s ability to sustain itself as a source population, however more research on a diverse set of taxa is essential to fully explore this potential. This interpretation of habitat suitability can be particularly useful for conservation practice, and identification of explicit cases of when and how SDMs fail to match population demography can be informative for advancing ecological theory.

Journal of Animal Ecology↗
USGS2023

Climate change and the global redistribution of biodiversity: Substantial variation in empirical support for expected range shifts

Background Among the most widely predicted climate change-related impacts to biodiversity are geographic range shifts, whereby species shift their spatial distribution to track their climate niches. A series of commonly articulated hypotheses have emerged in the scientific literature suggesting species are expected to shift their distributions to higher latitudes, greater elevations, and deeper depths in response to rising temperatures associated with climate change. Yet, many species are not demonstrating range shifts consistent with these expectations. Here, we evaluate the impact of anthropogenic climate change (specifically, changes in temperature and precipitation) on species’ ranges, and assess whether expected range shifts are supported by the body of empirical evidence. Methods We conducted a Systematic Review, searching online databases and search engines in English. Studies were screened in a two-stage process (title/abstract review, followed by full-text review) to evaluate whether they met a list of eligibility criteria. Data coding, extraction, and study validity assessment was completed by a team of trained reviewers and each entry was validated by at least one secondary reviewer. We used logistic regression models to assess whether the direction of shift supported common range-shift expectations (i.e., shifts to higher latitudes and elevations, and deeper depths). We also estimated the magnitude of shifts for the subset of available range-shift data expressed in distance per time (i.e., km/decade). We accounted for methodological attributes at the study level as potential sources of variation. This allowed us to answer two questions: (1) are most species shifting in the direction we expect (i.e., each observation is assessed as support/fail to support our expectation); and (2) what is the average speed of range shifts? Review findings We found that less than half of all range-shift observations (46.60%) documented shifts towards higher latitudes, higher elevations, and greater marine depths, demonstrating significant variation in the empirical evidence for general range shift expectations. For the subset of studies looking at range shift rates, we found that species demonstrated significant average shifts towards higher latitudes (average = 11.8 km/dec) and higher elevations (average = 9 m/dec), although we failed to find significant evidence for shifts to greater marine depths. We found that methodological factors in individual range-shift studies had a significant impact on the reported direction and magnitude of shifts. Finally, we identified important variation across dimensions of range shifts (e.g., greater support for latitude and elevation shifts than depth), parameters (e.g., leading edge shifts faster than trailing edge for latitude), and taxonomic groups (e.g., faster latitudinal shifts for insects than plants). Conclusions Despite growing evidence that species are shifting their ranges in response to climate change, substantial variation exists in the extent to which definitively empirical observations confirm these expectations. Even though on average, rates of shift show significant movement to higher elevations and latitudes for many taxa, most species are not shifting in expected directions. Variation across dimensions and parameters of range shifts, as well as differences across taxonomic groups and variation driven by methodological factors, should be considered when assessing overall confidence in range-shift hypotheses. In order for managers to effectively plan for species redistribution, we need to better account for and predict which species will shift and by how much. The dataset produced for this analysis can be used for future research to explore additional hypotheses to better understand species range shifts.

Journal of Environmental Evidence↗
USGS2011

Estimating the hatchery fraction of a natural population: a Bayesian approach

There is strong and growing interest in estimating the proportion of hatchery fish that are in a natural population (the hatchery fraction). In a sample of fish from the relevant population, some are observed to be marked, indicating their origin as hatchery fish. The observed proportion of marked fish is usually less than the actual hatchery fraction, since the observed proportion is determined by the proportion originally marked, differential survival (usually lower) of marked fish relative to unmarked hatchery fish, and rates of mark retention and detection. Bayesian methods can work well in a setting such as this, in which empirical data are limited but for which there may be considerable expert judgment regarding these values. We explored a Bayesian estimation of the hatchery fraction using Monte Carlo–Markov chain methods. Based on our findings, we created an interactive Excel tool to implement the algorithm, which we have made available for free.

North American Journal of Fisheries Management↗
USGS2020

colorspace: A toolbox for manipulating and assessing colors and palettes

The R package colorspace provides a flexible toolbox for selecting individual colors or color palettes, manipulating these colors, and employing them in statistical graphics and data visualizations. In particular, the package provides a broad range of color palettes based on the HCL (hue-chroma-luminance) color space. The three HCL dimensions have been shown to match those of the human visual system very well, thus facilitating intuitive selection of color palettes through trajectories in this space. Using the HCL color model, general strategies for three types of palettes are implemented: (1) Qualitative for coding categorical information, i.e., where no particular ordering of categories is available. (2) Sequential for coding ordered/numeric information, i.e., going from high to low (or vice versa). (3) Diverging for coding ordered/numeric information around a central neutral value, i.e., where colors diverge from neutral to two extremes. To aid selection and application of these palettes, the package also contains scales for use with ggplot2, shiny and tcltk apps for interactive exploration, visualizations of palette properties, accompanying manipulation utilities (like desaturation and lighten/darken), and emulation of color vision deficiencies. The shiny apps are also hosted online at http://hclwizard.org/.

Journal of Statistical Software↗
USGS2009

Geographic relatedness and predictability of Escherichia coli along a peninsular beach complex of Lake Michigan

To determine more accurately the real-time concentration of fecal indicator bacteria (FIB) in beach water, predictive modeling has been applied in several locations around the Great Lakes to individual or small groups of similar beaches. Using 24 beaches in Door County, Wisconsin, we attempted to expand predictive models to multiple beaches of complex geography. We examined the importance of geographic location and independent variables and the consequential limitations for potential beach or beach group models. An analysis of Escherichia coli populations over 4 yr revealed a geographic gradient to the beaches, with mean E. coli concentrations decreasing with increasing distance from the city of Sturgeon Bay. Beaches grouped strongly by water type (lake, bay, Sturgeon Bay) and proximity to one another, followed by presence of a storm or creek outfall or amount of shoreline enclosure. Predictive models developed for beach groups commonly included wave height and cumulative 48-h rainfall but generally explained little E. coli variation (adj. R 2 = 0.19-0.36). Generally low concentrations of E. coli at the beaches influenced the effectiveness of model results presumably because of low signal-to-noise ratios and the rarity of elevated concentrations. Our results highlight the importance of the sensitivity of regressors and the need for careful methods evaluation. Despite the attractiveness of predictive models as an alternative beach monitoring approach, it is likely that FIB fluctuations at some beaches defy simple prediction approaches. Regional, multi-beach, and individual beach predictive models should be explored alongside other techniques for improving monitoring reliability at Great Lakes beaches. Copyright ?? 2009 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Journal of Environmental Quality↗
USGS2020

Developing post-alert messaging for ShakeAlert, the earthquake early warning system for the West Coast of the United States of America

As ShakeAlert, the earthquake early warning system for the West Coast of the U.S., begins its transition to operational public alerting, we explore how post-alert messaging might represent system performance. Planned post-alert messaging can provide timely, crucial information to both emergency managers and ShakeAlert operators as well as calibrate expectations among various publics or public user groups and inform their responses to future alerts. There is a concern among the scientists and emergency managers that false alerts may negatively impact trust in the system, so quickly disseminated post-alert messages are necessary. For a new early warning system, such as ShakeAlert, this is particularly relevant given that the potentially affected population is likely to be unfamiliar with this system. We address this concern in six steps: (1) assessment of ShakeAlert performance to date, (2) characterization of human behavior and response to earthquake alerts, (3) presentation of a decision tree for issuing post-alert messages, (4) design of a critical set of post-alert messaging scenarios, (5) elaboration of these scenarios with message templates for a variety of communication channels, and (6) development of a typology of earthquake alerts. We further explore methods for monitoring and evaluating ShakeAlert post-alert messaging, for continuous improvement to the system.

California, Oregon, Washington, Idaho, Nevada, Uta↗