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At least 163 records · Page 9Linked to original sources
USGS2019

Bringing Bayesian models to life

Bringing Bayesian Models to Life empowers the reader to extend, enhance, and implement statistical models for ecological and environmental data analysis. We open the black box and show the reader how to connect modern statistical models to computer algorithms. These algorithms allow the user to fit models that answer their scientific questions without needing to rely on automated Bayesian software. We show how to handcraft statistical models that are useful in ecological and environmental science including: linear and generalized linear models, spatial and time series models, occupancy and capture-recapture models, animal movement models, spatio-temporal models, and integrated population-models.

Book↗
USGS2007

Prediction of lethal/effective concentration/dose in the presence of multiple auxiliary covariates and components of variance

Predictors of the percentile lethal/effective concentration/dose are commonly used measures of efficacy and toxicity. Typically such quantal-response predictors (e.g., the exposure required to kill 50% of some population) are estimated from simple bioassays wherein organisms are exposed to a gradient of several concentrations of a single agent. The toxicity of an agent may be influenced by auxiliary covariates, however, and more complicated experimental designs may introduce multiple variance components. Prediction methods lag examples of those cases. A conventional two-stage approach consists of multiple bivariate predictions of, say, medial lethal concentration followed by regression of those predictions on the auxiliary covariates. We propose a more effective and parsimonious class of generalized nonlinear mixed-effects models for prediction of lethal/effective dose/concentration from auxiliary covariates. We demonstrate examples using data from a study regarding the effects of pH and additions of variable quantities 2???,5???-dichloro-4???- nitrosalicylanilide (niclosamide) on the toxicity of 3-trifluoromethyl-4- nitrophenol to larval sea lamprey (Petromyzon marinus). The new models yielded unbiased predictions and root-mean-squared errors (RMSEs) of prediction for the exposure required to kill 50 and 99.9% of some population that were 29 to 82% smaller, respectively, than those from the conventional two-stage procedure. The model class is flexible and easily implemented using commonly available software. ?? 2007 SETAC.

Environmental Toxicology and Chemistry↗
USGS2004

An economic analysis of alternative fertility control and associated management techniques for three BLM wild horse herds

Contemporary cost projections were computed for several alternative strategies that could be used by BLM to manage three wild horse populations. The alternatives included existing gather and selective removal methods, combined with potential contraceptive applications of varying duration and other potentially useful management techniques. Costs were projected for a 20-year economic life using the Jenkins wild horse population model and cost estimates from BLM that reflect state-by-state per horse removal, adoption, long-term holding, and contraceptive application expenses. Important findings include: Application of currently available 2-year contraceptives appears capable of reducing variable operating costs for wild horse populations by about 21% on average. Application of 3-year contraceptives, when fully tested and available, may be capable of reducing variable operating costs by about 27% on average. Combining contraceptives with modest changes to herd sex ratio (e.g., 55-60% males) can trim existing costs by about 31%. All savings are predicted to increase when contraception is applied in conjunction with the proposed removal policy that targets horses age zero to four, instead of zero to five. Reductions in herd size result in greater predicted variation in annual operating expenses for each herd, especially below about 200 animals, but are always at least ±20%. Because the horse program’s variable operating costs only make up about one half of the total program costs (which include fixed and sunk costs), even with aggressive contraceptive management, total program costs could only be reduced by about 17%. This would still save about $7.7 million per year. None of the contraceptive options examined eliminated the need for long-term holding facilities over the 20-year period simulated, but the number of horses held may be reduced by about 23% with aggressive contraceptive treatment. Cost estimates are most sensitive to adoption age and per day holding costs. There are opportunities to improve both the population modeling software and the modeling processes used in assembling Herd Management Area environmental assessments.

Open-File Report↗
USGS2014

Land-cover mapping of Red Rock Canyon National Conservation Area and Coyote Springs, Piute-Eldorado Valley, and Mormon Mesa Areas of Critical Environmental Concern, Clark County, Nevada

DigitalGlobe’s QuickBird satellite high-resolution multispectral imagery was classified by using Visual Learning Systems’ Feature Analyst feature extraction software to produce land-cover data sets for the Red Rock Canyon National Conservation Area and the Coyote Springs, Piute-Eldorado Valley, and Mormon Mesa Areas of Critical Environmental Concern in Clark County, Nevada. Over 1,000 vegetation field samples were collected at the stand level. The field samples were classified to the National Vegetation Classification Standard, Version 2 hierarchy at the alliance level and above. Feature extraction models were developed for vegetation on the basis of the spectral and spatial characteristics of selected field samples by using the Feature Analyst hierarchical learning process. Individual model results were merged to create one data set for the Red Rock Canyon National Conservation Area and one for each of the Areas of Critical Environmental Concern. Field sample points and photographs were used to validate and update the data set after model results were merged. Non-vegetation data layers, such as roads and disturbed areas, were delineated from the imagery and added to the final data sets. The resulting land-cover data sets are significantly more detailed than previously were available, both in resolution and in vegetation classes.

Nevada↗
USGS2002

U.S. Geological Survey spatial data access

The U.S. Geological Survey (USGS) has done a progress review on improving access to its spatial data holdings over the Web. The USGS EROS Data Center has created three major Web-based interfaces to deliver spatial data to the general public; they are Earth Explorer, the Seamless Data Distribution System (SDDS), and the USGS Web Mapping Portal. Lessons were learned in developing these systems, and various resources were needed for their implementation. The USGS serves as a fact-finding agency in the U.S. Government that collects, monitors, analyzes, and provides scientific information about natural resource conditions and issues. To carry out its mission, the USGS has created and managed spatial data since its inception. Originally relying on paper maps, the USGS now uses advanced technology to produce digital representations of the Earth’s features. The spatial products of the USGS include both source and derivative data. Derivative datasets include Digital Orthophoto Quadrangles (DOQ), Digital Elevation Models, Digital Line Graphs, land-cover Digital Raster Graphics, and the seamless National Elevation Dataset. These products, created with automated processes, use aerial photographs, satellite images, or other cartographic information such as scanned paper maps as source data. With Earth Explorer, users can search multiple inventories through metadata queries and can browse satellite and DOQ imagery. They can place orders and make payment through secure credit card transactions. Some USGS spatial data can be accessed with SDDS. The SDDS uses an ArcIMS map service interface to identify the user’s areas of interest and determine the output format; it allows the user to either download the actual spatial data directly for small areas or place orders for larger areas to be delivered on media. The USGS Web Mapping Portal provides views of national and international datasets through an ArcIMS map service interface. In addition, the map portal posts news about new map services available from the USGS, many simultaneously published on the Environmental Systems Research Institute Geography Network. These three information systems use new software tools and expanded hardware to meet the requirements of the users. The systems are designed to handle the required workload and are relatively easy to enhance and maintain. The software tools give users a high level of functionality and help the system conform to industry standards. The hardware and software architecture is designed to handle the large amounts of spatial data and Internet traffic required by the information systems. Last, customer support was needed to answer questions, monitor e-mail, and report customer problems.

Journal of Geospatial Engineering↗
USGS2020

OpenCLC: An open-source software tool for similarity assessment of linear hydrographic features

The National Hydrography Dataset (NHD) is a foundational geospatial data source in the United States that enables extensive and diverse environmental research and supports decision-making in numerous contexts. However, the NHD requires regular validation and update given possible inconsistent initial collection and hydrographic changes. Furthermore, systems or tools that use NHD data must manage regular updates that occur within the high-resolution version of the NHD (NHD HR). This research contributes to filling this gap by establishing an open-source software tool named OpenCLC, which automatically identifies matching and mismatching line features between two sets of hydrographic flowlines. Aside from identifying differences among two version of NHD lines, results can be applied to improve the quality of NHD HR content. OpenCLC significantly outperforms the best available commercial off-the-shelf software in computational scalability, and it is made widely available as part of the CyberGIS Toolkit to benefit broad environmental and geospatial science communities.

SoftwareX↗
USGS2012

Social.Water - A crowdsourcing tool for environmental data acquisition

Remote telemetry has a long history of use for collection of environmental measurements. With the rise of mobile phones and SMS text-messaging capacity, many members of the general pubic carry communications equipment in their pockets at all times. Enabling the general public to provide environmental data through text messages has the potential both to provide additional data to scientific projects and also to raise awareness of the projects through participation. Hydrologic measurements – some of which can be made without training, involve a single measurement, and are often made in rural areas – are well-suited to text-message conveyance. Many other environmental measurements are similarly well-suited for this technology. Social.Water is a software package, written in Python, that collects, parses, and categorizes text messages sent to a dedicated phone number, updates a simple database, and posts both graphical results and the database on the Web. Social.Water was designed as the backend to the Crowdhydrology project and is written in an object-oriented design that makes customization and modification straightforward.

Computers & Geosciences↗
USGS2008

An Overview of the GIS Weasel

This fact sheet provides a high-level description of the GIS Weasel, a software system designed to aid users in preparing spatial information as input to lumped and distributed parameter environmental simulation models (ESMs). The GIS Weasel provides geographic information system (GIS) tools to help create maps of geographic features relevant to the application of a user?s ESM and to generate parameters from those maps. The operation of the GIS Weasel does not require a user to be a GIS expert, only that a user has an understanding of the spatial information requirements of the model. The GIS Weasel software system provides a GIS-based graphical user interface (GUI), C programming language executables, and general utility scripts. The software will run on any computing platform where ArcInfo Workstation (version 8.1 or later) and the GRID extension are accessible. The user controls the GIS Weasel by interacting with menus, maps, and tables.

Fact Sheet↗
USGS1995

Watershed boundaries and digital elevation model of Oklahoma derived from 1:100,000-scale digital topographic maps

This document provides a general description of the procedures used to develop the data sets included on this compact disc. This compact disc contains watershed boundaries for Oklahoma, a digital elevation model, and other data sets derived from the digital elevation model. The digital elevation model was produced using the ANUDEM software package, written by Michael Hutchinson and licensed from the Centre for Resource and Environmental Studies at The Australian National University. Elevation data (hypsography) and streams (hydrography) from digital versions of the U.S. Geological Survey 1:100,000-scale topographic maps were used by the ANUDEM package to produce a hydrologically conditioned digital elevation model with a 60-meter cell size. This digital elevation model is well suited for drainage-basin delineation using automated techniques. Additional data sets include flow-direction, flow-accumulation, and shaded-relief grids, all derived from the digital elevation model, and the hydrography data set used in producing the digital elevation model. The watershed boundaries derived from the digital elevation model have been edited to be consistent with contours and streams from the U.S. Geological Survey 1:100,000-scale topographic maps. The watershed data set includes boundaries for 11-digit Hydrologic Unit Codes (watersheds) within Oklahoma, and 8-digit Hydrologic Unit Codes (cataloging units) outside Oklahoma. Cataloging-unit boundaries based on 1:250,000-scale maps outside Oklahoma for the Arkansas, Red, and White River basins are included. The other data sets cover Oklahoma, and where available, portions of 1:100,000-scale quadrangles adjoining Oklahoma.

Oklahoma↗
USGS2007

Development of the Hydroecological Integrity Assessment Process for Determining Environmental Flows for New Jersey Streams

The natural flow regime paradigm and parallel stream ecological concepts and theories have established the benefits of maintaining or restoring the full range of natural hydrologic variation for physiochemical processes, biodiversity, and the evolutionary potential of aquatic and riparian communities. A synthesis of recent advances in hydroecological research coupled with stream classification has resulted in a new process to determine environmental flows and assess hydrologic alteration. This process has national and international applicability. It allows classification of streams into hydrologic stream classes and identification of a set of non-redundant and ecologically relevant hydrologic indices for 10 critical sub-components of flow. Three computer programs have been developed for implementing the Hydroecological Integrity Assessment Process (HIP): (1) the Hydrologic Indices Tool (HIT), which calculates 171 ecologically relevant hydrologic indices on the basis of daily-flow and peak-flow stream-gage data; (2) the New Jersey Hydrologic Assessment Tool (NJHAT), which can be used to establish a hydrologic baseline period, provide options for setting baseline environmental-flow standards, and compare past and proposed streamflow alterations; and (3) the New Jersey Stream Classification Tool (NJSCT), designed for placing unclassified streams into pre-defined stream classes. Biological and multivariate response models including principal-component, cluster, and discriminant-function analyses aided in the development of software and implementation of the HIP for New Jersey. A pilot effort is currently underway by the New Jersey Department of Environmental Protection in which the HIP is being used to evaluate the effects of past and proposed surface-water use, ground-water extraction, and land-use changes on stream ecosystems while determining the most effective way to integrate the process into ongoing regulatory programs. Ultimately, this scientifically defensible process will help to quantify the effects of anthropogenic changes and development on hydrologic variability and help planners and resource managers balance current and future water requirements with ecological needs.

Scientific Investigations Report↗
USGS2013

The influence of coarse-scale environmental features on current and predicted future distributions of narrow-range endemic crayfish populations

1.A major limitation to effective management of narrow-range crayfish populations is the paucity of information on the spatial distribution of crayfish species and a general understanding of the interacting environmental variables that drive current and future potential distributional patterns. 2.Maximum Entropy Species Distribution Modeling Software (MaxEnt) was used to predict the current and future potential distributions of four endemic crayfish species in the Ouachita Mountains. Current distributions were modelled using climate, geology, soils, land use, landform and flow variables thought to be important to lotic crayfish. Potential changes in the distribution were forecast by using models trained on current conditions and projecting onto the landscape predicted under climate-change scenarios. 3.The modelled distribution of the four species closely resembled the perceived distribution of each species but also predicted populations in streams and catchments where they had not previously been collected. Soils, elevation and winter precipitation and temperature most strongly related to current distributions and represented 6587% of the predictive power of the models. Model accuracy was high for all models, and model predictions of new populations were verified through additional field sampling. 4.Current models created using two spatial resolutions (1 and 4.5km2) showed that fine-resolution data more accurately represented current distributions. For three of the four species, the 1-km2 resolution models resulted in more conservative predictions. However, the modelled distributional extent of Orconectes leptogonopodus was similar regardless of data resolution. Field validations indicated 1-km2 resolution models were more accurate than 4.5-km2 resolution models. 5.Future projected (4.5-km2 resolution models) model distributions indicated three of the four endemic species would have truncated ranges with low occurrence probabilities under the low-emission scenario, whereas two of four species would be severely restricted in range under moderatehigh emissions. Discrepancies in the two emission scenarios probably relate to the exclusion of behavioural adaptations from species-distribution models. 6.These model predictions illustrate possible impacts of climate change on narrow-range endemic crayfish populations. The predictions do not account for biotic interactions, migration, local habitat conditions or species adaptation. However, we identified the constraining landscape features acting on these populations that provide a framework for addressing habitat needs at a fine scale and developing targeted and systematic monitoring programmes.

Freshwater Biology↗
USGS2009

The National Map customer requirements: Findings from interviews and surveys

The purpose of this study was to receive customer feedback and to understand data and information requirements for The National Map. This report provides results and findings from interviews and surveys and will guide policy and operations decisions about data and information requirements leading to the development of a 5-year strategic plan for the National Geospatial Program. These findings are based on feedback from approximately 2,200 customers between February and August 2008. The U.S. Geological Survey (USGS) conducted more than 160 interviews with 200 individuals. The American Society for Photogrammetry and Remote Sensing (ASPRS) and the International Map Trade Association (IMTA) surveyed their memberships and received feedback from over 400 members. The Environmental Systems Research Institute (ESRI) received feedback from over 1,600 of its U.S.-based software users through an online survey sent to customers attending the ESRI International User Conference in the summer of 2008. The results of these surveys were shared with the USGS and have been included in this report.

Open-File Report↗
USGS2006

Quantitative evaluation of macrophage aggregates in brook trout Salvelinus fontinalis and rainbow trout Oncorhynchus mykiss

Macrophage aggregates (MAs) occur in various organs of fishes, especially the kidney, liver and spleen, and contain melanin, ceroid/lipofuscin and hemosiderin pigments. They have been used as indicators of a number of natural and anthropogenic stressors. Macrophage aggregates occur in salmonids but are poorly organized, irregularly shaped, and are generally smaller than those in derived teleosts. These features complicate quantification, and thus these fishes have seldom been used in studies correlating MAs with environmental stressors. To alleviate these complications, we developed color filtering algorithms for use with the software package ImagePro Plus ® (Media Cybernetics) that select and quantify pigmented area (i.e. colors ranging from gold to brown to black) in tissue sections. Image analysis results compared well with subjective scoring when tested on brook trout Salvelinus fontinalis and rainbow trout Oncorhynchus mykiss captured from high-elevation lakes or hatcheries. Macrophage aggregate pigments correlated positively with age and negatively with condition factor. Within individual fish, pigmentation correlated positively among organs, suggesting that the kidney, liver or spleen are suitable indicator organs. In age-matched fishes, MA pigments were not different between hatcheries and lakes in the organs examined. Between lakes, differences in pigments were observed in the kidney and spleen, but were not explained by age, condition factor, sex or maturation state. Our results indicate that quantification of the area occupied by MA pigments is an efficient and accurate means of evaluating MAs in salmonid organs and that organ pigmentation correlates with age and condition factor, as seen in studies with more derived fishes.

Diseases of Aquatic Organisms↗
USGS2019

User’s manual for the Draper climate-distribution software suite with data‑evaluation tools

Development of a time series of spatially distributed climate data is an important step in the process of developing physically based environmental models requiring distributed inputs of climate data beyond what is available from observations collected at climate stations. To prepare inputs required for model-mapping units across the study area, climate data (temperature and precipitation) are distributed by combining data from gridded surfaces of mean-monthly climate-data values with (often) widely spaced daily point observations. Examples of climate-data files used to develop PRMS-formatted input files for the Merced River Basin Precipitation-Runoff Modeling System (PRMS) are included in this manual. The Draper Climate-Distribution Software Suite (Draper Suite) consists of the Draper climate-distribution program (Draper) and several supporting pre- and post-processing applications. Draper combines spatially distributed input in the form of monthly averaged values for precipitation, maximum temperature, and minimum temperature with daily observed data from climate stations to estimate distributed climate-data values at predefined locations across a study area (typically a drainage basin) on a daily time step. Alternative methods are used when station data are limited or missing for a particular day. Draper uses a set of required and optional input and output files with defined formats and naming conventions. A shell application also is available to manage multiple runs of the Draper application. Other applications in the Draper Suite include (1) a tool to find and interactively remove outliers in the input data, (2) a tool to check and enforce a minimum daily temperature range, and (3) a tool to view output diagnostic information as time-series graphs. These tools can be used iteratively to evaluate and improve the results from Draper as part of a workflow involving physically based environmental models, such as the Precipitation-Runoff Modeling System (PRMS).

Techniques and Methods↗
USGS2024

Predicting the odds of chronic wasting disease with Habitat Risk software

Chronic wasting disease (CWD) is a transmissible spongiform encephalopathy that was first detected in captive cervids in Colorado, United States (US) in 1967, but has since spread into free-ranging white-tailed deer ( Odocoileus virginianus ) across the US and Canada as well as to Scandinavia and South Korea. In some areas, the disease is considered endemic in wild deer populations, and governmental wildlife agencies have employed epidemiological models to understand long-term environmental risk. However, continued rapid spread of CWD into new regions of the continent has underscored the need for extension of these models into broader tools applicable for wide use by wildlife agencies. Additionally, efforts to semi-automate models will facilitate access of technical scientific methods to broader users. We introduce software (Habitat Risk) designed to link a previously published epidemiological model with spatially referenced environmental and disease testing data to enable agency personnel to make up-to-date, localized, data-driven predictions regarding the odds of CWD detection in surrounding areas after an outbreak is discovered. Habitat Risk requires pre-processing publicly available environmental datasets and standardization of disease testing (surveillance) data, after which an autonomous computational workflow terminates in a user interface that displays an interactive map of disease risk. We demonstrated the use of the Habitat Risk software with surveillance data of white-tailed deer from Tennessee, USA.

Tennessee↗
USGS2012

Hybrid analysis of multiaxis electromagnetic data for discrimination of munitions and explosives of concern

The remediation of land containing munitions and explosives of concern, otherwise known as unexploded ordnance, is an ongoing problem facing the U.S. Department of Defense and similar agencies worldwide that have used or are transferring training ranges or munitions disposal areas to civilian control. The expense associated with cleanup of land previously used for military training and war provides impetus for research towards enhanced discrimination of buried unexploded ordnance. Towards reducing that expense, a multiaxis electromagnetic induction data collection and software system, called ALLTEM, was designed and tested with support from the U.S. Department of Defense Environmental Security Technology Certification Program. ALLTEM is an on-time time-domain system that uses a continuous triangle-wave excitation to measure the target-step response rather than traditional impulse response. The system cycles through three orthogonal transmitting loops and records a total of 19 different transmitting and receiving loop combinations with a nominal spatial data sampling interval of 20 cm. Recorded data are pre-processed and then used in a hybrid discrimination scheme involving both data-driven and numerical classification techniques. The data-driven classification scheme is accomplished in three steps. First, field observations are used to train a type of unsupervised artificial neural network, a self-organizing map (SOM). Second, the SOM is used to simultaneously estimate target parameters (depth, azimuth, inclination, item type and weight) by iterative minimization of the topographic error vectors. Third, the target classification is accomplished by evaluating histograms of the estimated parameters. The numerical classification scheme is also accomplished in three steps. First, the Biot–Savart law is used to model the primary magnetic fields from the transmitter coils and the secondary magnetic fields generated by currents induced in the target materials in the ground. Second, the target response is modelled by three orthogonal dipoles from prolate, oblate and triaxial ellipsoids with one long axis and two shorter axes. Each target consists of all three dipoles. Third, unknown target parameters are determined by comparing modelled to measured target responses. By comparing the rms error among the self-organizing map and numerical classification results, we achieved greater than 95 per cent detection and correct classification of the munitions and explosives of concern at the direct fire and indirect fire test areas at the UXO Standardized Test Site at the Aberdeen Proving Ground, Maryland in 2010.

Geophysical Journal International↗
USGS2009

Downsizer - A Graphical User Interface-Based Application for Browsing, Acquiring, and Formatting Time-Series Data for Hydrologic Modeling

The U.S. Geological Survey Downsizer is a computer application that selects, downloads, verifies, and formats station-based time-series data for environmental-resource models, particularly the Precipitation-Runoff Modeling System. Downsizer implements the client-server software architecture. The client presents a map-based, graphical user interface that is intuitive to modelers; the server provides streamflow and climate time-series data from over 40,000 measurement stations across the United States. This report is the Downsizer user's manual and provides (1) an overview of the software design, (2) installation instructions, (3) a description of the graphical user interface, (4) a description of selected output files, and (5) troubleshooting information.

Open-File Report↗
USGS1995

Geographic information system data sets of hydrogeologic conditions in Pequea and Mill Creek watersheds, Pennsylvania: Part I — Basic data

This report describes basic data used to develop Geographic Information System data sets of bedrock geology, sinkholes and closed depressions, and spring and well locations attributed with hydro- geologic and water-quality data in the Pequea and Mill Creek watersheds, a 210-square-mile area in Lancaster and Chester Counties, Pa. The data sets, which do not contain hydrogeologic interpretations, were developed by the use of ARC/INFO software during 1990-93 by the U.S. Geological Survey, in cooperation with the Pennsylvania Department of Environmental Resources. The U.S. Environmental Protection Agency proposes to use these noninter- pretive and interpretive data sets, and those from other sources, to aid in the assessment of ground- water vulnerability to pesticides in the Pequea and Mill Creek watersheds.

Pennsylvania↗