Geology topics

John M. Donovan

Publications and source records attributed to John M. Donovan.

6 recordsLinked to original sources

USGS2024

The influence of time, tide, and place on fine scale nekton distribution: Insights from the San Francisco Estuary

The location of estuarine organisms varies based on geophysical cycles and environmental conditions, which can strongly bias understanding of organism abundance and distribution. In the San Francisco Estuary, California, extensive monitoring surveys have provided insight into the life history and ecology of certain commercially important or legislatively protected fish species. However, there remains substantial uncertainty in factors influencing the vertical and lateral distributions of many other nekton species in the San Francisco Estuary, including longfin smelt Spirinchus thaleichthys , for whom such distributional information may highly influence interpretation of existing data. We carried out paired sampling using surface and demersal gears to address three questions: (1) Does diel phase influence the vertical position of nekton (e.g., surface versus demersal)? (2) Do environmental conditions, specifically turbidity, influence the vertical and lateral positions of nekton (e.g., center channel versus peripheral shoal)? (3) Does tidal variability influence vertical and lateral distributions of nekton? We documented variability in sampled nekton densities across diel phase (day/night), vertical position (surface/bottom), and lateral position (channel/shoal). Tidal phase and turbidity concentration influenced vertical and lateral distributions for some species at certain locations. Although infrequently encountered, we documented associations of longfin smelt with the lower water column and shoal habitats, with some evidence for upward vertical shifts in low light conditions brought about by nightfall or elevated turbidity. Observed habitat associations provide insight into how interacting geophysical and environmental factors may influence the distribution of nekton and thus the vulnerability of individual species to detection by sampling gears.

California↗

USGS2021

Precipitation-runoff processes in the Merced River Basin, Central California, with prospects for streamflow predictability, water years 1952–2013

The U.S. Geological Survey, in cooperation with the California Department of Water Resources (DWR), has constructed a new spatially detailed Precipitation-Runoff Modeling System (PRMS) model for the Merced River Basin, California, which is a tributary of the San Joaquin River in California. Operated through an Object User Interface (OUI) with Ensemble Streamflow Prediction (ESP) and daily climate distribution preprocessing functionality, the model is calibrated primarily to simulate (and eventually, forecast) year-to-year variations of inflows to Lake McClure during the critical April–July snowmelt season. The model is intended to become part of a suite of methods used by DWR for estimating daily streamflow from the Merced River Basin, especially during the snowmelt season. This study describes the results of the application of an analysis tool that simulates responses to climate and land-use variations at a higher spatial resolution than previously available to DWR. A geographic information system was used to delineate the model domain, that is, areas draining to a single outlet at U.S. Geological Survey streamflow-gaging station 11270900, Merced River below Merced Falls Dam, near Snell, CA (also known as California Data Exchange Center station MRC), and subdrainage areas, including four draining to internal gages used as calibration targets. Using this delineation, three contiguous subbasins were recognized and, along with the model domain and nested calibration targets, are the simulation units evaluated in this report. An auto-calibration tool, LUCA (Let Us CAlibrate), was used for each calibration node, from headwaters to basin outlet, and then parameters were manually adjusted to complete the calibration. The main objective was to match April–July snowmelt seasonal discharge values of simulated streamflow to observed (measured or reconstructed) discharge values. Calibration or validation periods used site-specific streamflows—mostly from October 1, 1988, through September 30, 2013—but differed according to the period-of-record available for the measurements collected at internal gages or reconstructed flows for the single outlet. The accuracy of the Merced PRMS streamflow simulations varied seasonally, as compared to observed values. Based on statistical results, the Merced PRMS model satisfactorily simulated snowmelt seasonal streamflows. April–July calibrations for all areas had small negative bias (not greater than 7 percent) and low relative error (less than 8 percent). Less satisfactory performance for other seasons was attributed to several factors: (1) high uncertainty in low or zero flows in summer and fall, (2) lack of accounting for basin withdrawals and anthropogenic water use, (3) unavailability and (or) inaccuracy of observed (measured) meteorological input data, and (4) uncertainty in reconstructed streamflow data. With some additional refinement, the Merced PRMS model may be used for forecasting seasonal and longer-term streamflow variations; evaluating forecasted and past climate and land cover changes; providing water-resource managers with a consistent and documented method for estimating streamflow at ungaged sites within the basin; and aiding environmental studies, hydraulic design, water management, and water-quality projects in the Merced River Basin.

California↗

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↗

USGS2009

User Manual for the Data-Series Interface of the Gr Application Software

This manual describes the data-series interface for the Gr Application software. Basic tasks such as plotting, editing, manipulating, and printing data series are presented. The properties of the various types of data objects and graphical objects used within the application, and the relationships between them also are presented. Descriptions of compatible data-series file formats are provided.

Open-File Report↗

USGS2004

VPV--The velocity profile viewer user manual

The Velocity Profile Viewer (VPV) is a tool for visualizing time series of velocity profiles developed by the U.S. Geological Survey (USGS). The USGS uses VPV to preview and present measured velocity data from acoustic Doppler current profilers and simulated velocity data from three-dimensional estuarine, river, and lake hydrodynamic models. The data can be viewed as an animated three-dimensional profile or as a stack of time-series graphs that each represents a location in the water column. The graphically displayed data are shown at each time step like frames of animation. The animation can play at several different speeds or can be suspended on one frame. The viewing angle and time can be manipulated using mouse interaction. A number of options control the appearance of the profile and the graphs. VPV cannot edit or save data, but it can create a Post-Script file showing the velocity profile in three dimensions. This user manual describes how to use each of these features. VPV is available and can be downloaded for free from the World Wide Web at http://ca.water.usgs.gov/program/sfbay/vpv.

Open-File Report↗

USGS2001

Hierarchical programming for data storage and visualization

Graphics software is an essential tool for interpreting, analyzing, and presenting data from multidimensional hydrodynamic models used in estuarine and coastal ocean studies. The post-processing of time-varying three-dimensional model output presents unique requirements for data visualization because of the large volume of data that can be generated and the multitude of time scales that must be examined. Such data can relate to estuarine or coastal ocean environments and come from numerical models or field instruments. One useful software tool for the display, editing, visualization, and printing of graphical data is the Gr application, written by the first author for use in U.S. Geological Survey San Francisco Bay Program. The Gr application has been made available to the public via the Internet since the year 2000. The Gr application is written in the Java (Sun Microsystems, Nov. 29, 2001) programming language and uses the Extensible Markup Language standard for hierarchical data storage. Gr presents a hierarchy of objects to the user that can be edited using a common interface. Java's object-oriented capabilities allow Gr to treat data, graphics, and tools equally and to save them all to a single XML file.

Conference Paper↗