Marlys A. Updike | USGS Science

USGS1990

Reference manual for generation and analysis of Habitat Time Series: version II

The selection of an instream flow requirement for water resource management often requires the review of how the physical habitat changes through time. This review is referred to as 'Time Series Analysis." The Tune Series Library (fSLIB) is a group of programs to enter, transform, analyze, and display time series data for use in stream habitat assessment. A time series may be defined as a sequence of data recorded or calculated over time. Examples might be historical monthly flow, predicted monthly weighted usable area, daily electrical power generation, annual irrigation diversion, and so forth. The time series can be analyzed, both descriptively and analytically, to understand the importance of the variation in the events over time. This is especially useful in the development of instream flow needs based on habitat availability. The TSLIB group of programs assumes that you have an adequate study plan to guide you in your analysis. You need to already have knowledge about such things as time period and time step, species and life stages to consider, and appropriate comparisons or statistics to be produced and displayed or tabulated. Knowing your destination, you must first evaluate whether TSLIB can get you there. Remember, data are not answers . This publication is a reference manual to TSLIB and is intended to be a guide to the process of using the various programs in TSLIB. This manual is essentially limited to the hands-on use of the various programs. a TSLIB use interface program (called RTSM) has been developed to provide an integrated working environment where the use has a brief on-line description of each TSLIB program with the capability to run the TSLIB program while in the user interface. For information on the RTSM program, refer to Appendix F. Before applying the computer models described herein, it is recommended that the user enroll in the short course "Problem Solving with the Instream Flow Incremental Methodology (IFIM)." This course is offered by the Aquatic Systems Branch of the National Ecology Research Center. For more information about the TSLIB software, refer to the Memorandum of Understanding. Chapter 1 provides a brief introduction to the Instream Flow Incremental Methodology and TSLIB. Other chapters in this manual provide information on the different aspects of using the models. The information contained in the other chapters includes (2) acquisition, entry, manipulation, and listing of streamflow data; (3) entry, manipulation, and listing of the habitat-versus-streamflow function; (4) transferring streamflow data; (5) water resources systems analysis; (6) generation and analysis of daily streamflow and habitat values; (7) generation of the time series of monthly habitats; (8) manipulation, analysis, and display of month time series data; and (9) generation, analysis, and display of annual time series data. Each section includes documentation for the programs therein with at least one page of information for each program, including a program description, instructions for running the program, and sample output. The Appendixes contain the following: (A) sample file formats; (B) descriptions of default filenames; (C) alphabetical summary of batch-procedure files; (D) installing and running TSLIB on a microcomputer; (E) running TSLIB on a CDC Cyber computer; (F) using the TSLIB user interface program (RTSM); and (G) running WATSTORE on the USGS Amdahl mainframe computer. The number for this version of TSLIB--Version II-- is somewhat arbitrary, as the TSLIB programs were collected into a library some time ago; but operators tended to use and manage them as individual programs. Therefore, we will consider the group of programs from the past that were only on the CDC Cyber computer as Version 0; the programs from the past that were on both the Cyber and the IBM-compatible microcomputer as Version I; and the programs contained in this reference manual as Version II.

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USGS1989

Physical habitat simulation system reference manual: version II

There are four major components of a stream system that determine the productivity of the fishery (Karr and Dudley 1978). These are: (1) flow regime, (2) physical habitat structure (channel form, substrate distribution, and riparian vegetation), (3) water quality (including temperature), and (4) energy inputs from the watershed (sediments, nutrients, and organic matter). The complex interaction of these components determines the primary production, secondary production, and fish population of the stream reach. The basic components and interactions needed to simulate fish populations as a function of management alternatives are illustrated in Figure I.1. The assessment process utilizes a hierarchical and modular approach combined with computer simulation techniques. The modular components represent the "building blocks" for the simulation. The quality of the physical habitat is a function of flow and, therefore, varies in quality and quantity over the range of the flow regime. The conceptual framework of the Incremental Methodology and guidelines for its application are described in "A Guide to Stream Habitat Analysis Using the Instream Flow Incremental Methodology" (Bovee 1982). Simulation of physical habitat is accomplished using the physical structure of the stream and streamflow. The modification of physical habitat by temperature and water quality is analyzed separately from physical habitat simulation. Temperature in a stream varies with the seasons, local meteorological conditions, stream network configuration, and the flow regime; thus, the temperature influences on habitat must be analysed on a stream system basis. Water quality under natural conditions is strongly influenced by climate and the geological materials, with the result that there is considerable natural variation in water quality. When we add the activities of man, the possible range of water quality possibilities becomes rather large. Consequently, water quality must also be analysed on a stream system basis. Such analysis is outside the scope of this manual, which concentrates on simulation of physical habitat based on depth, velocity, and a channel index. The results form PHABSIM can be used alone or by using a series of habitat time series programs that have been developed to generate monthly or daily habitat time series from the Weighted Usable Area versus streamflow table resulting from the habitat simulation programs and streamflow time series data. Monthly and daily streamflow time series may be obtained from USGS gages near the study site or as the output of river system management models.

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