PHABSIM
for Windows
User’s Manual and
Exercises
Midcontinent Ecological
Science Center
November 2001
Open File Report 01-340
U.S. Department of the
Interior
U.S. Geological Survey
Acknowledgments
This document evolved from IF310 course materials developed and revised numerous times since 1984.
Several individuals made significant contributions to the Windows� version of the software and this
version of the manual in the following order. All are employees of the Midcontinent Ecological Science
Center (MESC), U.S. Geological Survey (USGS), unless otherwise noted. Mr. John Bartholow wrote
early versions of the laboratory exercises. Mr. Ken Bovee provided revision and insight to habitat
suitability curve development and testing. Dr. Robert Milhous wrote the original PHABSIM programs.
He also wrote the PHABSIM Version 2 (DOS) reference manual with assistance from Ms. Marlys Updike
and Ms. Dianne Schneider (Milhous et al., 1989). Substantial portions of this text and of the Version 2
class text were taken or adapted from that earlier work. Dr. Thomas Hardy, Utah State University,
consolidated and expanded on earlier course materials to provide a working draft of the PHABSIM
Version 2 (DOS) class text under contract to the MESC. Substantial portions of the text in this document
(in all chapters and in the laboratory exercises) are adapted from that draft. Dr. Sam Williamson
contributed numerous insights into the techniques and strategy of habitat modeling and wrote the
descriptive text for those ideas. Mr. Jeff Sandelin designed and programmed the Windows� interface and
made numerous contributions to the text while employed under a support services contract. Ms. Julianne
Brown, also a support services contractor, performed extensive testing of the programs to ensure results
were correct and congruent with the previous version of the software. Mr. Jim Henriksen provided
numerous insightful review comments and text revisions while using the PHABSIM for Windows
programs. Dr. Terry Waddle supervised the design and testing of this software version. He also
contributed substantial new text material while editing this version of the manual and laboratory exercises
to reflect the overarching IFIM concept and the PHABSIM for Windows structure.
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Preface
A Brief History of PHABSIM
In the 1970’s a major change in terminology regarding maintaining streamflow to protect aquatic
organisms in streams was introduced. To some, the change was considered merely semantic. But to those
whose pioneering work led to the change, it was both substantive and significant. The change was from
common usage of the term “low flow” or “minimum flow” to the common usage of the term “instream
flow.” During the early 1970's, the Water Resources Research Catalog served as an index of most of the
ongoing research related to water resources, with each project identified by several key words. As late as
1975, the Catalog contained no research projects under the key words “instream flow,” while at the same
time, there were many studies using the key words “low flow.”
The typical description of the concept of “low flow” in those days was something like this:
“Water is taken out of the stream for a variety of uses, such as irrigated agriculture,
municipal and industrial. Low flow means that amount of water that must be left in the
stream for the fish. With anything less than the low flow, the fish will die.”
In a thoughtful piece published in the April 1991 edition of Rivers, Harvey Doerksen recalled how Don
Tenant, then an aquatic biologist for the State of Montana, described the shortcomings of the “low flow”
concept in human terms:
After many years, I still have a vivid recollection of a photographic slide that [Don
Tennant] showed as part of his presentation at a conference. It was a picture of a family
of perhaps half a dozen people crowded into a small bathroom. ... The point that Don
wished to make was simply this: in the short run, a population of fish in the stream can
make out quite well with an extreme low flow event, just as a family can tolerate the
closeness that comes with crowding into a small bathroom. Over extended periods,
however, the low flow could not be tolerated any better by a population of fish than
sustained proximity could be tolerated by a family in a crowded bathroom. And yet, that
very concept of maintaining a sustained low residual flow was the prevailing approach to
protecting fish habitat.
One of the serious problems with the “low flow” approach was that biologists distinguished only between
two relative conditions with respect to fish habitats: the level below which disaster would occur, and
everything else. However, other water users made incremental assessments of their need. An irrigation
district, for example, could project water quantity needs for any increment of irrigated acreage, but the
biologists at the time did not have the technology to do similar incremental assessments of the potential
impacts of various irrigated acreage scenarios.
In the late 1970's the U.S. Fish and Wildlife Service (FWS), through what then was its Office of
Biological Services, received funding from the Environmental Protection Agency (EPA) to establish the
Cooperative Instream Flow Service Group, which incorporated the combined talents of people from
several federal and state agencies. The Group’s central charge was to develop methods for quantifying the
biological effects of altered streamflows.
The result of a concerted effort on the part of the Instream Flow Group was the Instream Flow
Incremental Methodology (IFIM) (Stalnaker et al., 1995; Bovee et al., 1998), of which the Physical
Habitat Simulation System (PHABSIM) is a major component. This new technology was highly
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significant for at least two reasons. First, it allowed fishery biologists to negotiate acceptable flow levels
with other instream and out-of-stream water users from among a variety of possible scenarios, in the same
way that the other users had been doing for years.
Second, the change in the prevailing terminology from “low flow” to “instream flow use” meant that
biologists no longer were trying to find that magical flow level below which a stream should not be
dewatered. Instead, they were in a position to assert instream flow needs for fish habitats and other
environmental values. Furthermore, they could do so in terms of the seasonal life cycle needs of the fish
(or other aquatic organisms) over the annual hydrograph. This change was thus an instrument through
which fish and associated environmental values were viewed as legitimate water users among many,
instead of merely a residual, after the water users had been served.
This change was not easy, nor did it occur overnight. In developing PHABSIM, the Instream Flow Group
drew on several developments in instream habitat assessment that were available at the time. Two
developments were of particular importance, the Washington Method (Collings et al., 1972) and the
univariate curve concept. The Washington Method provided the concept of mapping depth and velocity
conditions over gravel bars and applying binary suitability functions for salmon spawning in streams in
the Pacific Northwest. The area of a gravel bar suitable for spawning was evaluated at several measured
discharges by calculating the area having a suitability value of 1 for both depth and velocity. Approximate
suitable spawning area for unmeasured intermediate flows was estimated by interpolation.
Binary suitability functions (the observed condition is assigned a value of 0 or 1, unsuitable or suitable)
produced a value of 0 for some stream areas that, although not optimally suitable, were observed being
used by salmon. The use of a univariate suitability function, which ranked various depths or rates of flow
velocity on a 0 to 1 scale and allowed a smooth function covering the entire range of conditions, was
proposed by Waters (1976).
The Washington Method, even when modified to include the univariate curve approach, requires
numerous empirical measurements at different discharges. This limits the number of discharges for which
habitat can be evaluated and the number of study areas that can feasibly be evaluated with time,
manpower, and budget constraints.
The Instream Flow Group combined standard one-dimensional hydraulic simulation techniques with the
Washington Method and the univariate curve concept to produce PHABSIM. PHABSIM uses the
hydraulic simulation models to predict depth and velocity at unmeasured flows using basic physical and
engineering principles that were standard practice in the 1970’s. The resulting software suite multiplied
surface area for a section of stream by the univariate suitability curve values for depth, velocity, and
channel condition to arrive at a habitat index called Weighted Usable Area.
This software suite was first implemented on Control Data Corporation mainframe computers accessed by
terminals connected over telephone lines. The software consisted of numerous small piecemeal programs
that were cost-effective to develop and use in the mainframe environment. Numerous small files were
required for data input and numerous output files were produced. This placed a major burden on users of
the software to manage large numbers of files with often similar (but slightly different) contents. It also
produced a legacy of program names such as IFG-4.
During 1984 and 1985 the PHABSIM program suite was moved to microcomputers. A basic menu-driven
interface for the PHABSIM program was developed in 1989. The PHABSIM Version 2 (DOS) (Milhous
et al., 1989) programs were distributed until September 2000 as the standard version of PHABSIM
software.
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With the advent of the Windows graphical user interface, it became evident that the PHABSIM program
suite would serve a wider audience if input data and model results could be displayed graphically during
an application of the software. Development of the Windows interface for PHABSIM fulfills
commitments made to the U.S. Fish and Wildlife Service in the mid-1990’s. Two principle goals were
pursued while developing PHABSIM for Windows: (1) to keep the functionality of all core programs and
retain backward compatibility to PHABSIM Version 2, and (2) to simplify the bookkeeping and
calibration processes. We sought to both improve clarity of the various options for each program and
graphically display the results of applying each program. The ability to view plots of model results during
the calibration and option selection processes greatly speeds up calibration and increases understanding of
the effects of selecting various habitat simulation options.
To ensure the quality of PHABSIM for Windows, extensive testing and comparison with the DOS-based
PHABSIM Version 2 was performed. Several data sets were run through both versions and all options of
all programs were run and compared. In addition, both English and metric units were tested to ensure that
entire analyses could be reliably conducted in metric units. Our emphasis was on retaining the full set of
PHABSIM analytical functions and extensively testing the programs rather than on adding program
enhancements.
Use of This Document
This document is a combined self-study textbook and reference manual. The material is presented in the
general order of a PHABSIM study placed within the context of an IFIM application. The document may
also be used as reading material for a lecture-based course. This manual provides documentation of the
various PHABSIM programs so every option of each program is treated.
This text is not a guidebook for organization and implementation of a PHABSIM study. Use of
PHABSIM should take place in the context of an IFIM application. See Bovee et al. (1998) for guidance
in designing and performing a PHABSIM study as part of a larger IFIM application.
The document concludes with a set of 12 laboratory exercises. Users are strongly encouraged to work
through the laboratory exercises prior to applying the software to a study. Working through the exercises
will enhance familiarity with the programs and answer many questions that may arise during a PHABSIM
analysis.
Changes Between PHABSIM Version 2 and PHABSIM for Windows
The first obvious change between PHABSIM Version 2 (DOS) and PHABSIM for Windows is use of the
Windows graphical user interface and development of the necessary interface programs. The graphical
user interface program now includes considerably more code than the analytic al core programs.
Additional benefits of developing an extensive interface program include the following: file management
is largely done by program; users no longer need to keep track of file names and the risk of removing a
file needed at a later step has been essentially eliminated and each study site is kept in a separate, user-
specified, project directory, reducing the risk of confusing project files.
In developing this version of PHABSIM, certain decisions were made regarding the structure of
PHABSIM data and analyses. All cell definitions now match the data gathering approach taught in the
IF305 field techniques course. The cell definition distinctions HABTAE and HABTAV have disappeared
and all HABTAV options are now included in HABTAE. Thus, there is no HABTAV program. For
consistency, HABTAM cell definitions also match those used in HABTAE. The 100 cell per cross section
limit has been eliminated so an unlimited number of cells may be defined for each cross section.
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