EPA-600/3-86-019
A COMPUTERIZED SYSTEM FOR THE EVALUATION OF AQUATIC HABITATS
"ASED ON ENVIRONMENTAL REQUIREMENTS AND POLLUTION TOLERANCE
ASSOCIATIONS OF RESIDENT ORGANISMS
(DRAFT FINAL PROJECT REPORT)
by
Clyde L. Dawson
Ronald A. Kellenthal
Department of Biological S'ciences
University of Notre Dame
Notre Dame, Indiana 46556
CONTRACT NO. CR 810711-01-0
Project Officer
Phil Larsen
Corvallis Environmental Research Laboratory
Corvallis, Oregon 97330
CORVALLIS ENVIRONMENTAL RESEARCH LABORATORY
OFFICE OF RESEARCH AND DEVELOPMENT
U.S. ENVIRONMENTAL PROTECTION AGENCY
CORVALLIS, OREGON 97330
U.S. Environmenta , Coon Agencvmcy
Region 5, Library rn-
77 West Jackson Bou-.. ,-d 12th Ffcv5
Chicago, JL 60604-3590 -
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DISCLAIMER
This report has been reviewed by the Corvallis Environmental
Research Laboratory, U.S. Environmental Protection Agency, and approved
for publication. Approval does not signify that the contents necessar-
ily reflect the views and policies of the. U.S. Environmental Protection
Agency, nor does mention of trade names or commercial products consti-
tute endorsement or recommendation for use.
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AB STRACT
The Environmental Requirements and Pollution Tolerance (ERAPT)
information retrieval and analysis system can be used interactively to
predict and evaluate aquatic habitats and organism assemblages. ERAPT
computerized data bases contain 57,345 biological, physical, chemical,
and distributional characteristics drawn from 887 sources for 1 ,691
species of North American diatoms, blue-green algae, the insect orders
Ephemeroptera (mayflies) and Plecoptera (stoneflies) , the dipteran
family Chironomidae (midges), and the fishes of U.S. E.P.A. Region V
(North Central U.S.).
The system can predict environmental conditions from resident
organisms, develop lists of species likely to occur under specified
environmental conditions, identify organisms useful as indicators of
environmental change, and interpret the environmental causes of changes
in species composition. It can also be used to screen organism
identifications by identifying tolerance incompatabilities and
environmental associations.
The system was tested by comparing its prediction of environmental
conditions based on the dominant fish community with environmental
characteristics obtained from aquatic habitat surveys for 64 sites on
three river systems in Ohio. An overall successful prediction rate of
95% was achieved. Where disagreements between predicted and reported
environmental characterizations occurred, they almost always were among
very similar tolerance ranges or habitat types.
111
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CONTENTS
Page
Abstract iii
Acknowledgements vi
I. Introduction 1-1
Background 1-1
System Operation 1-5
Future Development 1-8
Literature Cited 1-10
II. Technical System Description II-l
ERAPT Data Organization II-l
CODES File II-l
RAW DATA File II-3
SOURCES File II-6
ERAPT System Programs II-6
STRIP II-9
INITPNTS II-9
XPADIN 11-11
DMERGE 11-11
EPAEDIT 11-13
MASK 11-13
ALIST 11-13
RUNOFF 11-16
UNMASK 11-16
ERAPT 11-16
III. ERAPT Examples III-l
Predicting Environmental Change by Faunal Change .... III-2
Subdividing Faunas by Environmental Conditions III-3
Evaluating Introduced Species III-4
Predicting Faunal Change by Environmental Change .... III-5
Finding Environmental Differences Among Species III-6
Identifying Indicator Organisms III-7
Identifying Species by Environmental Conditions III-8
Interpreting Environmental Causes of Faunal Change .. III-9
Relocating Endangered Species 111-10
Predicting Unrelated Faunal Assemblages III-ll
Using One Faunal Assemblage to Predict Another 111-12
Evaluating Temporal Environmental Change 111-13
IV. System Validation IV-1
Methods IV-1
Results and Discussion IV-1
IV
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V. ERAPT Retrieval and Analysis Program Operation V-l
Abbreviations and Syntax V-l
Program Command List V-2
Program Command Descriptions V-3
Program Messages V-20
VI. EPAEDIT Data Base Editor Program Operation VI-1
Abbreviations and Syntax VI-1
Program Command List VI-1
Program Command Descriptions VI-2
VII. System Access and Implementation VII-1
Hardware and Software Requirements VII-1
Accessing University of Notre Dame Computer System .. VII-1
Running the ERAPT Retrieval and Analysis Program .... VII-2
ERAPT System Commands Vll-3
VIII. ERAPT Retrieval Codes and Definitions VIII-1
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ACKNOWLEDGEMENTS
We are indebted to many individuals for their help and support
during this project. The staff of the Corvallis Environmental Research
Laboratory and Northrop Environmental Services provided many ideas and
suggestions for the development of ERAPT system programs and data files,
and assisted in the development and definition of the set of retrieval
parameters and codes used by the system. We are particularly thankful
for the assistance of Jack Gakstatter, Ronald Carton, Jim Giattina, Bob
Hughes, Phil Larsen, and Bill Sanville. Paul Short and Martin B. Berg
assisted in the accumulation and computer entry of Region V fish envi-
ronmental data and in the testing of system programs. Data for system
validation were supplied by the State of Ohio Environmental Protection
Agency with the assistance of Daniel R. Dudley and Chris Yoder.
Cornelius I. Weber of the Environmental Monitoring and Support Labora-
tory, Cincinnati, Ohio, deserves special thanks for his encouragement
and support of this project. He and Donald J. Klemm also provided pre-
publication copies of environmental requirements and pollution tolerance
characterizations for diatoms, blue-green algae, chironomids,
Ephemeroptera, and Plecoptera which were incorporated into ERAPT data
bases. The compilers of these data summaries, William M. Beck, Jr.,
Michael D. Hubbard and William L. Peters, Rex L. Lowe, Rebecca F.
Surdick and Arden R. Gaufin, and Sam L. V anLand ingham, deserve partic-
ular credit for accumulating this critical information. Finally, we are
indebted to the over 500 biologists whose research results have been
incorporated into the data bases used by the ERAPT system. It is only
through their dedicated efforts that this information is available to
the biological community.
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SECTION I
INTRODUCTION
The Environmental Requirements and Pollution Tolerance (ERAPT)
information retrieval and analysis system permits computerized pre-
diction and evaluation of habitat characteristics and organism assem-
blages. ERAPT System data bases contain 57 ,660 parameter values
representing environmental characterizations of 402 genera and 1,689
species of aquatic organisms in the diatoms, blue-green algae, the
insect orders Ephemeroptera and Plecoptera, the dipteran family
Chironomidae, and the fish species of U.S. Environmental Protection
Agency (E.P.A.) Region V (North Central U.S.). The environmental
characterizations used by the ERAPT system have been derived from 887
data sources, primarily from the published literature (Table 1). This
represents a mean of 34.1 environmental parameters for each species,
with 5.6 data sources per species and 4.2 species per genus.
Information for the environmental characterization of diatoms, blue-
green algae, chironomids , Ephemeroptera and Plecoptera are adapted from
the E.P.A. publications: EPA-670/4-74-005 , EPA-600/3-82-073 , EPA-600/4-
77-024, EPA-600/4-78-061 , and EPA-600/4-78-062 developed by the E.P.A.
Environmental Monitoring and Support Laboratory, Cincinnati, Ohio.
Characterization of Region V fishes was done as part of this project.
Background
Aquatic organisms long have been recognized as potentially useful
indicators of habitat conditions and water quality. This is due to
their ability to reflect conditions through time, to demonstrate the
effects of disturbances after the environment has returned to apparently
normal physical and chemical conditions, to integrate the effects of
many different environmental factors and their interactions simul-
taneously, and to provide a living context for considerations of envi-
ronmental quality. According to Sladecek (1973) , the study and use of
organisms as indicators of water quality began in Europe in 1848 with
investigations on environmental relationships of Trichoptera by F. A.
Koler.ati. While much of the early investigation of aquatic indicator
organisms concentrated on microorganisms, many other aquatic organisms
possess attributes which make them well suited as indicators of envi-
ronmental conditions. The basic requirements for indicator organisms
are that they must be sensitive to environmental changes and have life
spans and generation lengths which are appropriate for use in environ-
mental assessment, long enough to reflect intermittent or occasional
disturbances and short enough so that sensitive life stages may be
subjected to adverse environmental conditions.
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ERAPT DATA BASE TOTALS
Author s
Records
Genera
Species
Citations
BLGR
420
221
50
161
2,289
CHIR
34
306
74
232
529
DIAT
48
342
50
295
2,726
EPHE
200
459
60
399
1,207
FISH
56
446
82
243
971
PLEC
125
450
86
364
1,767
Total
887
2,224
402
1,691
9,489
Entries 4,364 8,156 5,510 6,806 24,824 7,685 57,345
Table 1. Summary totals for information in the ERAPT data bases.
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The association between certain aquatic organisms and aquatic con-
ditions has been known for a long time. The insect syrphid fly genus
Eristalis has been associated with conditions of profound organic
enrichment since ancient Greece (Clausen 1954). Anglers have associated
aquatic insects with habitats of game fish for hundreds of years
(Schwiebert 1973). Environmental classification schemes using
chironomids and other aquatic insects, such as those reviewed by
Brinkhurst (1974), have been available for at least 50 years.
Discussions of the use of invertebrates as indicators of river and
stream pollution are provided by Gaufin and Tarzwell (1952), Hynes
(1958), and Goodnight (1973).
Given this association and the knowledge that aquatic organisms
have been a fundamental component of aquatic habitat surveys, it is
surprising that organisms play a relatively minor role in aquatic
assessment. One reason may be the difficulties often encountered in
comparing and summarizing information obtained by different researchers.
This may be due to differences in organism identifications made by
inexperienced personnel, or to inconsistent methods of data collection,
analysis, or presentation. A second factor may be the many diverse
outlets for publication of these data. They often appear only in
progress and summary reports, receive little dissemination, and are
frequently omitted from standard abstracting and indexing publications.
Another factor is the great difficulty in developing quality control
procedures for organism identifications. This has resulted in great
variation in the quality and reliability of published associations
between organisms and specific environmental conditions.
Investigators who compile data on aquatic organisms from more than
one source have often found variation in pollution tolerance and envi-
ronmental requirements information at both the genus and species levels.
For example, in reviewing tolerances to decomposable organic wastes
published in the E.P.A. Biological Field and Laboratory Methods manual
(Weber 1973), Resh and Unzicker (1975) noted that 61 of the 89 genera
known from more than one species bad differing tolerance information for
the different species. While justifiably concluding that generic iden-
tification was wholly inadequate for water quality evaluation, they left
unanswered the question of how useful available data are at the species
level.
Environmental data and reports vary widely in quality and
reliability. Standardized methods for data acquisition and analysis and
quality control procedures are reasonably well established for most bio-
logical, chemical, and physical environmental data. However, the
association of specific organisms with these parameters rests on the
reliability of species identifications performed by investigators of
varying backgrounds, experience, and expertise. At present, the primary
quality assurance mechanism for organism identifications is the compe-
tence and dedication of individual researchers. While independent
verification of voucher specimens by taxonomic experts is possible, this
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is a procedure which, even on a small scale, is time consuming and
costly and, on a large scale, would significantly exceed our present
resource of taxonomic experts (Irwin et .al. 1973, Barr 1974, Edwards and
Grotta 1975).
Publications providing summary information on the environmental
relationships and tolerances of aquatic organisms are extremely useful
in identifying potential indicator organisms and in establishing
tolerance levels of organisms to specific environmental factors.
However, unless the reference publication survey is extremely exhaustive
or very selective, it may be difficult to establish useful trends among
the vast amounts of often contradictory information reviewed.
Some publications providing useful summary information on the
environmental requirements and pollution tolerances of aquatic organisms
are: Proceedings of the Third Seminar on Biological Problems in Water
Pollution (Tarzwell 1965) which includes discussions of environmental
requirements of freshwater algae, protozoa, Crustacea, annelids,
insects, and fish; a manual on biological field and laboratory methods
(Weber 1973) published by the E.P.A. which includes summaries of the
tolerances of freshwater invertebrates to decomposable organic wastes;
the appendix of Sladecek's (1973) water quality system monograph which
includes many tables of tolerances of aquatic species to a variety of
environmental conditions; a book on the pollution ecology of freshwater
invertebrates (Hart and Fuller 1974) which includes information on envi-
ronmental requirements for a number of invertebrate groups; general
treatments of biological methods for water quality assessment (e.g.,
Cairns and Dickson 1973; James and Evison 1979) and a series of U.S.
E.P.A. Environmental Monitoring and Support Laboratory (Cincinnati)
water quality profiles for diatoms (Lowe 1974), Chironomidae (Beck
1977), Ephemeroptera (Hubbard and Peters 1978), Plecoptera (Surdick and
Gaufin 1978), Trichoptera (Harris and Lawrence 1978), and blue-green
algae ( VanLandingham 1982). The U.S. Department of the Interior Fish
and Wildlife Service also has been actively developing habitat suit-
ability index models for fish and wildlife species (Schamberger et &1.
1982).
While these reports have helped to make environmental information
on aquatic organisms more accessible to biologists, much of the poten-
tial of this accumulated information still remains unexploited. This
may be due to the taxonomic organization and fixed tabular format of
these publications which limit the ways in which their data can be used.
For example, most of these publications are organized by taxa rather
than by environmental factors. This makes them difficult to use to
predict the presence of organisms in a specific environment. Also, it
is often difficult to determine which environmental requirements are
consistent within a genus or higher taxonomic level and which environ-
mental inconsistencies at the specific level could be due to errors in
data collection or identification.
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A computerized storage, retrieval and evaluation system for these
data has been developed to enhance their usefulness by allowing queries
based on taxonomic association, environmental parameters, or a
combination of these factors. Since the environmental information for
diverse taxonomic groups can be standardized, it is possible to answer
questions concerning biological communities and their environments. In
addition to being able to ask a variety of questions about requirements
of organisms and environmental conditions, a major application of this
system is the development of lists of taxa associated with specific
environmental conditions which can serve as reference communities for
environmental scientists. This system also can be used as a device for
scrutinizing environmental data by comparing the known tolerances of
organisms reported in monitoring and impact studies with the physical
and chemical characteristics of the habitats from which they were
collected. Discrepancies encountered in these comparisons are flagged
as potential errors in data collection or specimen identification.
Another quality control device possible with these data is comparison of
the known ecological parameters associated with combinations of taxa
reported to be collected together at individual sites. Inconsistencies
in the environmental requirements of these taxa also can be flagged as
potential errors in identification.
Operation
The ERAPT system consists of an integrated set of computer programs
for the storage, retrieval, and manipulation of environmental require-
ments and pollution tolerance information on aquatic organisms. It has
been developed for use on an IBM 370/3033 computer system at the
University of Notre Dame. Data are stored and manipulated as hierarch-
ically related environmental requirements and pollution tolerance
categories representing tolerance ranges to specific pollutants or
environmental conditions, geographic locations, general or specific
habitat characteristics, and periods of appearance, emergence, or
greatest abundance. At present the system uses 21 heading categories
(Biological - stage, abundance, optimal growth period, reproductive
season, reproductive behavior, feeding behavior; Chemical - hardness,
salinity, nutrients, degradable organics, pH, oxygen; Physical -
temperature, turbidity, current, general habitat, specific habitat,
bottom type; Geographic - ecosystem regions, political geography)
divided into 303 specific parameters. These categories and parameters
were adapted from a set developed by the Aquatic Biology Section,
Environmental Monitoring and Support Laboratory of the U.S. E.P.A.
(Cincinnati, Ohio) for use with macroinvertebrates and diatoms (Lowe
1974, Beck 1977) , and were expanded for fish and other aquatic organisms
as part of this project in collaboration with the staff of the E.P.A.
Corvallis Environmental Research Laboratory.
Data for ERAPT arc encoded on tabular forms which may be produced
by the system. These forms contain boxes which correspond to specific
parameters such as stage, feeding behavior, or tolerance to environ-
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mental conditions for an individual species from a single reference
source. Data are coded on the forms by marking those environmental
categories applicable to a particular species and environmental site or
study. The ERAPT system reads the tabular forms as digitized X-Y co-
ordinate values corresponding to each mark on a form. The computer then
determines the relative location of each mark with respect to the form
and stores this information with a list of environmental codes which
identify the various parameters. Location tolerance values are stored
by the program and used to eliminate ambiguous mark positions.
The digitized data are then standardized for the ERAPT system.
Since data entry forms may contain any subset of the environmental cate-
gories included in the data base, the category codes stored with the
digitized data are used to create a translation table which transforms
the data to correspond with the full environmental category table used
by the ERAPT system. During this process both direct and hierarchical
correspondences between categories are established. For example, one
set of data entry forms may contain the environmental category Meso-
saprobic, whereas another may divide this category into alpha and beta
ranges. During this step these parameters are hierarchically associated
so that a parameter shown at a lower level of the environmental category
hierarchy is included at all upper levels. There is no limit to the
number of levels in a hierarchy and no requirement that the number of
levels be consistent among parameters. For example, the heading
salinity is divided into 11 categories with the categories Mesohalobous
and Oligohalobous further subdivided into 2 and 3 parameters, respec-
tively. This structure permits the ERAPT system to store, manipulate
and use environmental information differing in precision without
sacrificing the most reliable data.
During the standardization process the data are packed into com-
puter memory locations as 1-bit word subsegments. This allows data to
be stored very efficiently in computer memory. It also permits simul-
taneous multi-factor comparisons of environmental conditions by the
computer. This greatly reduces processing time and costs4 increasing
the amount of information which can be processed and simplifying
analysis and retrieval of the data.
The next procedure is the creation of a searchable data base. At
this point the various components of the system are linked. The taxon-
omic categories arc hierarchically connected in a manner similar to that
described previously for environmental headings and parameters. This
enables queries at any level of the taxonomic hierarchy. The linking
operation involves the association and storage of memory addresses for
the taxonomic names, environmental headings and parameters plus their
definitions, author citations and references, environmental data, and a
series of 2 to 8-character abbreviations which are used in the query and
information retrieval process. The lowest taxonomic level directly
accessible by the system is subspecies. However, data from individual
sources are available to the system as an external file.
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The data normally used by the system consist of two summaries of
the information contained in the various reference sources for each
taxon. They are stored as strings of binary digits which correspond to
bit by bit iterative logical sums (OR) and products (AND) of parameter
fields for each non-zero heading category for each taxon. Logical sums
include all environmental parameters given by any source for each taxon
in the system. For example, if one investigator reported that a species
occurs in streams and another reported that the same species occurs in
both lakes and streams, the logical sum for the general habitat heading
category for that species would include both lakes and streams. The
logical product summary includes only those parameters indicated by all
sources containing environmental requirements or pollution tolerance
information within each heading category for a taxon. Therefore, each
product summary consists of those environmental parameters which are
consistently associated with a taxon in the system. For the general
habitat example given above, the product summary would show only lakes,
since it was the only parameter indicated by all sources of information
for the taxon. A summary of inconsistencies among investigators re-
porting information about any heading category for a taxon may be
obtained by calculating the logical difference (exclusive OR) between
the sum and product summaries. In this case parameters are only in-
cluded in the summary if there is inconsistent information for that
taxon within the data base. In the general habitat example, streams
would be considered an inconsistent parameter since one source used the
parameter and the other did not. For taxcnomic categories above
species, similar data summaries are maintained based on logical sums of
the information for all lower taxonomic levels. The system also main-
tains the number of data sources which were summarized for each taxon
and environmental heading category.
Information retrieval and analysis is accomplished using an inter-
active program. The program uses a simple command format for queries of
the data base. These may be used to predict groups of organisms having
a select set of environmental characteristics. Species may be evaluated
for consistency of associated environmental information, providing lists
of potential indicator?. Groups of organisms may also be defined using
abbreviated taxonomic names for characterization and evaluation.
Species or groups of species may be compared to determine the similar-
ities and differences in their environmental requirements. Information
may be selected by taxonomic level, number of sources, or groups of
environmental parameters.
Definitions of environmental retrieval codes are available during
program operation. A complete help facility is also included to provide
on line documentation on program commands and capabilities. A history
of the searches performed during the session may be obtained. Program
output can be formatted for different page widths and may include or-
ganism common names. Individual search statements or complete terminal
sessions may be saved and later recalled for use with data bases con-
taining information on other groups of organisms. The program can
retain an almost unlimited number of saved searches and can provide
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directories and lists of these upon request. The program will permit
customization for a variety of printing and nonprinting computer ter-
minals and can be directed to pause between output pages. Input may
come from sources other than a terminal to permit other programs to
interface directly with the system. Output may also be redirected to
files or to a high-speed lineprinter.
Future Development
Use of environmental indicator organsims on a regional basis ap-
pears to be particularly promising. Assessment systems based on a sound
knowledge of a local fauna, such as that developed for Wisconsin by
Hilsenhoff (1977) , would seem to have a great probability for success.
Development of local or regional environmental data bases is within the
capabilities of the ERAPT system. This will be greatly facilitated by
development of microprocessor-based versions of the retrieval and
analysis programs. Microprocessor implementation of the ERAPT system on
computers such as the I.B.M. PC and the Apple Macintosh is feasible and
a prototype microcomputer version of the retrieval and analysis program
is currently being developed.
One of the most interesting capabilities of the ERAPT system is its
potential for screening environmental data. The ability to automatical-
ly detect apparent inconsistencies among the environmental tolerances of
different organisms said to be collected together at a given site can be
used both to flag errors in data collection and organism identifications
and to evaluate the reliability of environmental data bases. For
example, it would be possible to require that taxonomic experts confirm
the identifications of organisms found to have inconsistent environmen-
tal information. This would provide a cost effective means of evalu-
ating the quality of biological information. Where new environmental
associations of organisms are found, the data bases can be modified,
thereby eliminating future error flags for the taxa involved. It is
even possible, to use environmental characteristics as characters in
taxonomic keys for organism identification. This is most applicable to
computer based identification systems which permit users to skip missing
or uncertain key characters such as the AUTOKEY taxonomic identification
system for aquatic organisms (Hellenthal 1978).
Because the ERAPT system can accept output from other computer
programs, it can be interfaced with ongoing environmental data collec-
tion projects to automatically summarize and evaluate information and to
scan for probable changes in environmental conditions. Interfacing
programs can convert numerical environmental data and codes unique to
local or regional data collection projects so that they can be used with
the ERAPT system. Output from the ERAPT system also can be used by
other programs for environmental decision making and evaluation.
Sources of environmental information within the data bases also can be
evaluated. For example, it is possible to identify investigators who
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have provided environmental information which frequently contradicts
that supplied by other workers for the same organisms.
Because the ERAPT programs are independent of the kinds of data and
organisms which they can processs the system has many applications to
other areas of biological and environmental research. Alternate sets of
biological categories or environmental parameters can be developed
easily for terrestrial or marine environments or for microbial organisms
or higher vertebrate groups. The system also has direct application to
behavioral, physiological, and genetic organism information. Because of
the structure and internal organization of the data used by the system,
there is no limit to the amount of information which can be accumulated
or queried for each kind of organism contained within a data base.
System capacities are related only to the number of kinds of organisms
and data catagories which can be accessed and evaluated as a group, and
are easily modified within programs. There is also no limit to the
number of groups which can be developed and programs permit transfer of
search statements between organism groups if they have compatable data.
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Literature Cited
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environment. Assoc. Systeraatics Collections, Lawrence, Kans. ii +
30 p.
Beck, W. M., Jr. 1977. Environmental requirements and pollution
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Cincinnati, Ohio. EPA-600/4-77-024. 261 p.
Brinkhurst, R. 0. 1974. The benthos of lakes. St. Martin's Press, New
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Cairns, J. , Jr. and K. L. Dickson [Ed.J. 1973. Biological methods for
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Goodnight, C. J. 1973. The use of aquatic macroinvertebrates as
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Lowe, R. L. 1974. Environmental requirements and pollution tolerance of
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Support Lab., Cincinnati, Ohio. EPA-600/4-74-005. 334 p.
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pollution tolerance of Plecoptera. U.S. Environ. Protection
Agency, Environ. Monitoring and Support Lab., Cincinnati, Ohio.
EPA-600/4-78-062. 417 p.
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Third seminar. U.S. Public Health Serv. Publ. 999-WP-25. 424 p.
VanLandingham, S. L. 1982. Guide to the identification, environmental
requirements and pollution tolerance of freshwater blue-green algae
(Chanophyta). U.S. Environ. Protection Agency,Environ. Monitoring
and Support Lab., Cincinnati, Ohio. EPA-600/3-82-073. 341 p.
Weber, C. I. [Ed.]. 1973. Biological field and laboratory methods for
measuring the quality of surface waters and effluents. U.S.
Environ. Protection Agency, Nat. Environ. Res. Center, Cincinnati,
Ohio. EPA-670/4-73-001. Sections individually paged.
1-11
-------
SECTION II
TECHNICAL SYSTEM DESCRIPTION
EBAF.T Data Organization
The ERAPT system performs its search and analysis operations on data
bases derived from three types of data files. The CODES file type
defines the environmental retrieval codes used in compatible data bases
and establishes their order and hierarchical relationships. The RAW
DATA file type establishes the environmental retrieval and reference
codes and taxonomic names for a single group of organisms and contains
the environmental characteristics of the organisms derived from indi-
vidual references. A RAW DATA file need not use all of the categories
contained in a specific CODES file and may contain additional categories
applicable to alternative CODES files. A single data base, therefore,
may be used in conjunction with different CODES files to produce
different searchable data bases. The third required file type defines
the SOURCES of environmental information contained in a RAW DATA file.
The CODES and SOURCES files may contain upper and lower case characters
and are in a format which is compatible with the University of Waterloo
text-formatting program, SCRIPT. The RAW DATA file is not formatted for
direct text-processing and must contain only upper-case characters.
CODES file.
The CODES file defines the retrieval codes used by all ERAPT system
programs and establishes their hierarchical relationships (Figure 1).
Each entry must begin on a new line and must contain four components:
(1) a descriptive term or phrase; (2) a formal definition; (3) a
hierarchical position value and retrieval code; and (4) a list of data
bases which use the entry. A ' - ' sequence is used to separate the
descriptive word or phrase from its associated definition. If the
definition begins on a separate line, the ' - ' sequence must terminate
the line containing the descriptive phrase. There is no limit to the
length of the descriptive definition which may contain as many lines of
text as necessary. On a new line immediately following the definition
is the hierarchical position and retrieval code for the entry. This
line must begin with a left bracket, '[' (EBCDIC hexadecimal value AD),
and terminate with a right bracket, ']' (EBCDIC hexadecimal value BD).
The hierarchical position is represented by a three digit integer number
starting immediately after the left bracket. The hierarchical position
number is followed by a 1 to 6-character upper-case alphanumeric
retrieval code. The highest level categories are numbered '010' and
must have 2-character retrieval codes. This 2-character code will
appear as a prefix to all other codes for this category. All divisions
of a major category must have a level value greater than ten, with
II-l
-------
Figure 1. Codes file example.
.CC 7;.US ;.CE ;PHYSICAL CHARACTERISTICS OF HABITAT
.BR ;.US jGeneral Habitat -
General type of habitat.
[010GH]
(FISH, CHIR 10, DIAT 6, EPHE 8, PLEC 8, BLGR 6)
Marine - Characteristic of oceans and seas.
[020 MARINE]
(FISH, CHIR 43, DIAT 33)
Neritic - Occurring typically above continental shelf
(close to shore).
[030MANERI]
(FISH, BLGR 47)
Oceanic - Occurring typically over deeper regions of oceans.
[030MAOCEA]
(FISH, BLGR 48)
Estuary - Characteristic of estuaries and brackish water habitats.
[020ESTUAR]
(FISH, CHIK 44, DIAT 34, BLGR 45)
Lentic Systems - Characteristic of lakes or' ponds.
[020LENTIC]
(FISH, BLGR 39)
Lake - Characteristic of large inland bodies of standing water.
[030LELAKE]
(FISH, CHIR 45, DIAT 35, EPHE 33, PLEC 33)
Pond - Characteristic of small bodies of lentic water
with macrophytes covering most of bottom.
[030LEPOND]
(FISH, CHIR 46, DIAT 36, EPHE 34, PLEC 34)
Temporary Water - Characteristic of temporary lentic habitats.
[030LETEMP]
(FISH)
Littoral - Shallow margin of lake or pond associated with aquatic
vegetation.
[030LELITT]
(FISH, BLGR 46)
Limnetic - Free open water in lakes and ponds.
[030LELIMN]
(FISH)
Profundal - Bottom sediment of lakes below littoral zone, consisting
of exposed fine sediment free of vegetation.
[030LEPROF]
(FISH)
Benthic - Occurring on bottom of lentic habitats.
[030LEBENT]
(FISH, BLGR 38)
11-2
-------
larger level values used to designate greater subdivisions of the
retrieval code hierarchy. The last line of each record is used to
indicate which RAW DATA files use the retrieval code. RAW DATA files
are designated by upper case, 4-character codes. The program STRIP uses
these codes to produce data entry sheets. This record must start with a
left parenthesis, '(', followed by the codes for the data base names in
which the retrieval code will be used and must end with a right
parenthesis, ')'. Data base codes optionally may be followed by an
integer number, indicating the order they are to be placed on the coding
sheet. Multiple data base codes are separated by commas.
RAW DATA lilg.
The RAW DATA file contains lists of retrieval codes, authors, taxon-
omic and common names, and environmental data for a related group of
organisms (Figure 2). It consists of four sections: (1) the data base
name code and revision date; (2) the list of retrieval codes; (3) a list
of data source codes; and (4) taxonomic and common names plus environ-
mental data arranged by source. The first line of the data base must
contain the four character data base name in columns one to four and
optionally a date of the form 'MM/DD/YY' beginning in column six.
The second line contains a three digit integer in columns one
through three, indicating the number of category codes used in the data
base. The following lines contain the ordered category codes, left
justified, in eight 9character columns.
The line following the category codes should contain a three digit
integer, in columns one through three, indicating the number of source
codes in the data base. The source codes should begin on the next line,
left justified, in eight 9-character columns. If the number of source
codes is zero, this line should be blank. The first three characters of
the source code normally are author initials, or some other unique ab-
breviation of author initials or names. These characters are followed
by the last two digits of the year the article was published. The sixth
character is used to form unique codes if the first five characters
match existing sources, using the next available letter of the alphabet.
If the reference source differentiated environmental requirements by
life stage, the seventh character position may contain an 'A', 'J', '!'
or 'S' to indicate that associated data pertain to adult, juvenile,
larva or smolt life stages, respectively. Otherwise, the field is left
blank. The eighth character position is currently not used and should
be left blank.
The taxonomic list follows the list of author codes. Each taxonomic
entry must appear on a separate line. The first twenty characters are
for the scientific name. Columns 21-23 indicate the taxonomic level of
the name (Table 1). If this number is negative the next line will begin
the data section specific to this entry rather than another taxon.
Columns 24-51 are for the common name, when appropriate. The names must
be nested hierarchically, with each genus and species used only once.
11-3
-------
Figure 2. RAW DATA file example.
FISH 2/07/85
278
STEGGS STLARVA STJUVENI STSMOLT STADULT ABABUNDA ABCOMMDN ABUNCOMM
ABRARE . . . PGALB PGBC PGMAN PGNWT PGSAS PGYUK
7
BEC83 LEE80 SPW79 E&U74 TMB81 TMB81 A TMB81 J
OSTEICHTHYES 55BONEY FISHES
ACIPENSERIFORbES 45
ACIPENSERIDAE 35STURGEONS
ACIPENSER 25
FULVESCENS -15LAKE STURGEON
4 BEC83 SPW79 E&U74 TMB81
103 1 30 5 9 19 34 85 99100117118126128207212217219221224225228238
237243244245246269271273275277 2 12 5 9 19 33 34 85 91 97124134128
230 3 11 19 20 5 23 34 85 97126127128233 4 42 5 19 20 34 97 85113
115117124128144205207209212217219221223224225228230231232233234235237
243244245250251250246269271273275277
SCAPHIRHYNCHUS 25
ALBUS -15 PALLID STURGEON
2 SPW79 E&U74
15 1 7 5 9 20 33 34100230 2 4 5229230233
PLATORYNCHUS -15SHOVELNOSE STURGEON
4 BEC83 SPW79 E&U74 TMB81
93 1 37 5 19 34 99115113100125128117151217219221224225226228230232
231233234235237238239240241243244245246249250251253 2 4 5 19 34230
3 6 19 8 5 85 97233 4 38 5 8 34 99100113115125130144148217218
219221223224226228230231232233234235237238239240241243244245246249250
251253
POLYODONTIDAE 35PADDLEFISHES
POLYODON 25
SPATHULA -15PADDLEFISH
4 BEC83 SPW79 E&U74 TMB81
92 1 3n 5 919 24 34 35 38 39 97212217219224226228230231232233234
235237237238240241243244245246249250251269 2 11 5 19 35 24100125127
126 85110230 3 7 19 35 24 5 85 97233 4 32 5 9 98 99100 97127126
217218219221222224225228230231233234235237238240241243244245246249250
251
II-4
-------
75 Kingdom
70 Subkingdom
66 Superphylum
65 Phylum
60 Subphylum
56 Superclass
55 Class
50 Subclass
49 Infraclass
48 Cohort
46 Superorder
45 Order
40 Suborder
39 Infreorder
36 Superfamily
35 Family
30 Subfamily
28 Tribe
28 Sub tribe
26 Supergenus
25 Genus
20 Subgenus
16 Superspecies
15 Species
10 Subspecies
5 Race or Variety
Table 1. Codes for levels in taxonomic hierarchy.
II-5
-------
The data section, if present, has two parts: (1) the list of refer-
ences specific to the entry, and (2) the data specific to each refer-
ence. Both of these sections begin with a three digit integer indi-
cating the number of entries in each section, therefore, the data
section may span as many lines as is necessary to contain the informa-
tion. The section containing the author list is written in 9-character
columns with the first position position replaced by the number of
authors. The data line is written as twenty-four, 3-character columns.
The first integer indicates the number of integers remaining in the
section, the second indicates the source of the data to follow. The
next value represents the number of environmental codes obtained from
the source followed by additional integers corresponding to the posi-
tions of environmental parameters used in the table at the beginning of
the file. The source number, number of codes, and parameter list fields
are repeated for each source of information for the taxon.
SOURCES file
The SOURCES file is a list of author citations and their associated
reference codes (Figure 3). The citations are separated from each other
by a blank line. Each entry has five parts, terminated with a period:
(1) the list of authors; (2) the year; (3) the title; (4) the source of
the information; and (5) the source code and a list of codes for the
data bases in which it is used. Each of these parts should begin on
separate lines. The source and data base codes must be in upper-case
letters and begin with ' REF: '. This is followed by the author code
and a list of codes for the data bases in which the source is used,
separated by spaces.
ERAPT System Programs
The ERAPT system includes ten programs and four data files which
interact with one another as illustrated in Figure 4. Data may be added
to a data base interactively with the program EPAEDIT or by merging new
data contained in files with the program DMERGE. If a small amount of
data is to be added to a data base, then EPAEDIT would be preferred. If
a large amount of data is to be entered or data from another data base
are to be merged with existing data files then DMERGE may be used to
automatically update RAW DATA files. DMERGE will add environmental data
to any taxonomic entry in the data base, inserting new author codes into
the data base as necessary.
Data may be entered into a computer by many means, including optical
character readers, optical scanners, manual digitizers, and electronic
drafting tablets. The basic concept of these systems is similar. A
data form, which may be generated by the computer, is filled out by
hand. Entries on the form are read as coordinates and translated into
numbers which represent environmental codes. These data are then
converted into a format acceptable as input by the program DMERGE.
11-6
-------
Figure 3. SOURCES data file example.
Aggus, Larry R. and William M. Bivin.
1982.
Habitat Suitability Index Models: Regression Models Based on
Harvest of Coolwater Fishes in Reservoirs.
Fish and Wildlife Service. U.S. Department of the Interior.
FWS/OBS-82/10.25.
REF: A&B82 FISH
Bain, Mark B. and Jane L. Bain.
1982.
Habitat Suitability Index Models: Coastal Stocks of Striped Bass.
Fish and Wildlife Service. U.S. Department of the Interior.
FWS/OBS-82/10.1.
REF: B&B82 FISH
Becker, George C.
1983.
Fishes of Wisconsin.
The Universiy of Wisconsin Press.
REF: BEC83 FISH
II-7
-------
Figure 4. ERAPT System organization.
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II-8
-------
The program STRIP uses the CODES file to produce a text file which
is then processed by SCRIPT to produce data entry forms. Data entered
on these forms are digitized using an optical character reader, manual
digitizer, or an electronic drafting tablet. Although not totally auto-
mated, these three methods enable rapid and accurate data entry. If a
large amount of data is to be entered an optical scanner should be
considered. Forms for this type of entry are often used in automated
test scoring, where the data are represented as ovals, usually darkened
with a pencil. The advantages of this method are total automation and
speed since the whole form is read in a single pass. However,
developing and producing these forms in small quantities is expensive.
One method of data collection uses SCRIPT generated coding forms in
conjunction with a microcomputer. The coding sheet is defined to the
microcomputer, using the program INITPNTS, which makes a translation
table for the coding sheet.
After the translation table is produced, the program XPAD is used to
store data from the coding sheets as files on the microcomputer.
Taxonomic name and author information are entered from the keyboard and
the coordinate positions for environmental characteristics are
digitized. These data then are transferred to a main frame computer in
a format suitable for processing by the program DMERGE.
DMERGE is used on the main frame computer to combine new and exist-
ing data files. This final updated RAW DATA file should be compiled and
evaluated for errors using the program MASK before either of the
original data files is deleted. The program ALIST may be used to list
the updated RAW DATA file. The program UNMASK may also be used to list
the contents of the COMPILED DATA file. The program RUNOFF may be used
to list program or data files. Once the RAW DATA file has been compiled
and verified it can be used by the ERAPT retrieval and analysis program
as a data base.
STRIP
The program STRIP is used to generate coding forms for use in data
collection. The CODES data file is scanned by the program for the
information to be used in making the form. This information is written
to a file. This file and a file containing the initial formatting
commands are processed by the text-formatting program SCRIPT. The
result is the form in Figure 5.
INITPNTS
The program INITPNTS is used to enter environmental parameter codes
positions from a master coding sheet into the microcomputer. It
prompts for all necessary information, including the name of the output
file when all of the points have been entered. The corresponding envi-
ronmental parameter codes then are stored in a separate file in the same
order. The program will accommodate 400 codes and their coordinates.
II-9
-------
Figure 5. Coding form for environmental data.
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It only needs to be used once for the creation of a translation table
for each type of coding sheet.
XPADIN
The XPADIN program allows entry of data into the ERAPT system using
a graphics tablet digitizer. The program prompts for the name of a trans-
lation table file generated by INITPNTS. Then the name of the output
file is requested. After the translation table is loaded, the program
prompts for entry of the coding form boundaries. A coding sheet is
placed on the digitizer in the template and the first and last positions
on column one are marked with the stylus of the graphics tablet. Envi-
ronmental characteristics are entered into the microcomputer by drawing
horizontal lines next to the parameters on the form. If the mark entered
is acceptable it will be displayed on the screen. Ambiguous marks
result in visual and audible error messages and must be re-entered.
The scientific name is entered by marking the name spot on the tem-
plate. The scientific name and reference are entered via the keyboard
and control is returned to the graphics tablet digitizer. When entry of
coding form data is completed, the "page finished" spot on the graphics
tablet is marked. The form may be in two or three parts. If so, the
additional parts may be entered by marking the "page" spot on the gra-
phics tablet. Incorrect codes may be changed by marking the "delete"
spot on the template, and then entering the position of the new code.
Once generated, files containing new environmental information are
transferred to the main frame computer for input to the program DMERGE.
DMERGE
The program DMERGE merges a new data set (Figure 6) into an existing
data base, creating a new combined data base. Neither of the input data
files are changed.
The program reads original RAW DATA files from unit 10 , reads addi-
tional data from unit 12, and writes the merged file to unit 11. Units
1 and 2 are used as scratch space if the merger cannot be performed in a
single pass. Units 5 and 6 are allocated to the keyboard for input and
output.
During execution of the DMERGE program, the message "TERM NOT FOUND"
may appear, followed by a taxonomic name which appeared in the new data
file but was not present in the original RAW DATA file. The options are
ADD, CHANGE, or SAVE. SAVE ends the program without the addition of the
new taxonomic name or its associated data. ADD will insert a new
species and its associated data into the merged RAW DATA file. CHANGE
is used to modify a taxonomic name contained in the data file to be
merged with original RAW DATA file.
11-11
-------
Figure 6. DMERGE input data file example.
ESOX 025
NIGER -15
001 BEC83
010 1 8 5 9 10 24 28 29 50 55
ESOX 025
A^RICANUS -15
001 BEC83
012 1 11 5 7 9 21 24 25 30 42 48 55107
11-12
-------
The program can merge environmental data of up to 200 genera or
higher taxonomic levels and up to 800 species. An array is dimensioned
at 10,000 integers to serve as workspace for the program. If this space
is exceeded the current file is written to a scratch file and processing
is performed in passes. Therefore, there is no limit to the amount of
environmental data that can be merged into a data base. When all of the
data to be merged is processed, a printed message indicates that the
final processing pass is being made. When this step is complete the
output file is a new RAW DATA file; ready for verification and
compilation using the MASK program.
EPAEDIT
The program EPAEDIT is an interactive editor for a RAW DATA file.
The program has several functions: (1) add, delete, or replace data for
a source or sources; (2) display information by author, species or code;
and (3) search for information by species, common name or source code.
The program reads the RAW DATA file as unit 10 and the SOURCES files
unit 12. These files are not modified by the program. The revised RAW
DATA file it is written to unit 1. Units 5 and 6 are allocated to the
terminal for input and output.
MASK
The program MASK is used to standardize and compress a RAW DATA file
into a COMPILED DATA file. This permits searches across different data
bases as well as the taxonomic comparison and evaluation capabilities of
the retrieval and analysis program. As part of the compilation process,
information for each taxon from all sources is stored as two data sum-
maries (Figure 7). The OR summary contains the information reported by
any data source. The AND summary holds the information agreed upon by
all sources. The program uses units 5 and 6 for terminal input and
output. The CODES file is read from unit 10. The RAW DATA file to be
compiled is read as unit 12. Unit 11 is used for output if the program
results are written to a data file rather than to the line printer.
The MASK program produces only a list of summary statistics at the
terminal unless errors are detected in the RAW DATA file. Error mes-
sages produced by the MASK program begin with three asterisks and may be
preceded by system messages. Most are caused by read errors in the
input file. Therefore, a copy of the RAW DATA file may be helpful in
determining the specific problem which caused the error.
ALLSI
The program ALIST will produce a readable text file from a RAW DATA
file (Figure 8). The RAW DATA file is read from unit 10 and the text
file is written to unit 9. Unit 6 is used to write diagnostic and error
messages. The output file can be formatted and printed using RUNOFF.
11-13
-------
Figure 7. COMPILED data file.
Truncated to fit the page:
FILENAM5: FISH CREATED: 2/08/85 FROM INPUT FILE: 2/07/85
OSTEICHTHYES 55BONEY FISHES
ACIPENSERIFORJES 45
ACIPENSERIDAE 35 STURGEONS
ACIPENSER 25
FULVESCENS -1 SLAKE STURGEON
4040 200000401040 00000000000040 2040101000004000000
04401900 E000000000000306160001D80DC000060080156 A5DCFFE3F300045D40000
04401100A00000000000030210000010084000060080000000000000000000000000
SCAPHIRHYNCHUS 25
ALBUS -15 PALLID STURGEON
2020100000100010000000000000100000000000002000000
04400800E00000000000000212000000000000000000000000064000000000000000
04400800E00000000000000212000000000000000000000000060000000000000000
PLATORYNCHUS -15SHOVELNOSE STURGEON
4040200000300030000000000000302020001020004000000
04801000A000000000000302160001DOOA500000008900027DEFFFFF740000000000
04801000A000000000000002100001COOA0000000080000000040000000000000000
POLYODONTIDAE 35PADDLEFISHES
POLYODON 25
SPATHULA -15PADDLEFISH
4040200000303030000000000000400020000000004000000
04401080 BB000000000003021EOOAOOOOB8000000000002A7EEFFEFF700044000000
04401080900000000000000210000000098000000000000000040000000000000000
11-14
-------
Figure 8. ALIST output file
CHORDATA Phylum CHORDATES
CYCLOSTOMATA Class HAGFISHES AND LAMPREYS
PETROMYZONTIFORMES Order
PETROMYZONTIDAE Family LAMPREYS
ICHTYOMYZON Genus
BDELLIUM Species OHIO LAMPREY
Author: SPW79
ST-.LARVA ST-.ADULT RB:COMPLE RB-.LITHOP FB:PRPLAN FB:PARASI
GH:RIMEDI GHtRILARG BT:GRAVEL SH:NERIFF SH:NEOFFC PG:IL
Author: TMB81
ST:ADULT PTtSAPHOB GH:STSMAL GH:RIMEDI GH:RILARG CU:LIMNOB
CU:LIMNOP PG:PA PG:WV PG:AL PG:KY PG:TN
PG:IL PG:1N PG:OH
Author: LEE80
ST:JUVENI ST:ADULT GP:SUMMER FB-.PARASI GH:STREAM GH:RISMAL
GH:RIMEDI GH:RILARG ER:2110 ER:2210 ER:2510 PG:PA
PG:VA PG:WV PG:AL PG-.KY PG:SC PG:TN
PG : IL PG: IN PG : OH
CASTANEUS Species CHESTNUT LAMPREY
Author: BEC83
ST-.LARVA ST:ADULT RB:PHYTOP RB:XYLOPH FB:PRPLAN FB:PARASI
GH:LELAKE GHtSTLARG BTrSILT BT-.SAND BT:GRAVEL BT:COBBLE
BT:VEGETA SH:NERIFF CU-.INDIFF CU:RHEOPH PG:AL PG:KY
PG:MS PG:NC PG-.TN PG:IL PG:MI PG:MN
PG:WI PG:AR PG-.LA PG:OK PG:TX PG:IA
PG:KS PG:MO PG:ND PG:MAN
Author: SPW79
ST-.ADULT FB:PARASI GH:RIMSDI GH:RILARG PG:IL
Author: E&U74
ST:ADULT AB:UNCOMM FB:PARASI GH:STREAM GHrRISMAL PG:MN
Author: LEE80
FB:PARASI GH:LELAKE GH:RIVER ER:2110 ER:2210 ER-.2310
ER:2320 ER:2510 ER:2530 PG:AL PG:GA PG:KY
PG:MS PG-.NC PG:TN PG-.IL PG:IN PG-.MI
PG:MN PG:WI PG:AR PG:LA PG:TX PG: IA
PG-.KS PG:MO PG-.ND PG:ONT PG:MAN
11-15
-------
RUNOFF
The program RUNOFF is designed to format files for printing on the
line printer. The program reads the file to be formatted from unit 10
and writes the formatted file to unit 9, which is then sent to the
printer using the IBM utility program IEBGENER. Units 5 and 6 are used
for terminal input and output. The form type, form length, line
spacing, line numbering, print train, device and number of copies all
may be controlled using RUNOFF. RUNOFF is limited to printing fixed
length files of 80 columns.
The program UNMASK will produce a readable text file or printed copy
of a compiled data base (Figure 9). Units 5 and 6 are used for terminal
input and output. Unit 9 is used for line printer output. The CODES
file is read from unit 10 and a COMPILED DATA file is read from unit
12. Unit 11 is used for output if results are written to a data file
rather than to the line printer.
ERAPT
ERAPT is an interactive environmental information retrieval and
analysis program which uses information in any COMPILED DATA file. The
program is independent of the data base or codes file used. The program
reads the CODES file from unit 10. A COMPILED DATA file is read from
unit 12. Units 5 and 6 are used for terminal input and output and unit
9 is used for any output to the line printer. Unit 14 is used to access
HELP information on program commands, and NEWS notices. Unit 15 is used
for the storage and retrieval of saved searches. Unit 16 is used as a
temporary output file to store control information for the linepr inter
if an offline printout is requested.
Notices and command syntax descriptions are contained in a HELP file
so that thsi information may be changed without modifying the program.
The format of this file is shown in Figure 10. Lines beginning with an
'@' symbol are command definitions. The next 12 characters are the
command word followed by a three digit integer number. The first digit
indicates the number of lines in the syntax section, and the last two
digits the number of lines in the explanation. Several terms may have
the same definition if they follow one another on separate lines. When
counting lines, those beginning with an '@' symbol are ignored. If a
section is to be omitted a blank line should be in the file as in syntax
line for the command HISTORY. The NEWS section begins with 'tfBEGIN
NEWS' and terminates with '#END NEWS'. All of the intervening lines are
printed as the NEWS message.
The data used by the ERAPT program are stored in memory in a bit
mapped binary form to pack the information as efficiently as possible.
The data structure and linkages are illustrated in Figure 11. For each
taxonimoc entry in a data base the system maintains, the scientific
11-16
-------
Figure 9. UNMASK output file example.
NOTURUS
ELEUTHERUS
OR
AND
EXILIS
OR
AND
ST
OX
ST
GH
BT
TU
ER
PG
PG
PG
ST
SH
PG
2 AB 1
0 GH 3
: ADULT
: RIVER
: GRAVEL
:EULICH
:2200
:REG04
:REG05
:OK
-.ADULT
: NEK TON
:IL
PT
BT
AB
GH
BT
TU
ER
PG
PG
PG
AB
SH
MOUNTAIN
0 RB 0
0 TU 2
:UNCOMM
:RIMEDI
: BOULDE
:OLIGOL
:REG03
:GA
:IN
:MO
.UNCOMM
:2000
FB
CU
GH
GH
BT
CU
PG
PG
PG
GH
ER
> SLENDER
1 RB 0
0 TU 2
: UNCOMM
:DETRIT
:SAND
: NERIFF
.RHEOBI
:REG04
:IL
:OK
:PREDAT
.STREAM
:2200
FB
CU
RS
GH
BT
SH
ER
PG
PG
PG
FB
BT
ER
MADTOM
0 HA 0
2 ER 1
:LOTIC
:RILARG
: VEGETA
: RHEOPH
:PA
:KY
:OH
:LOTIC
:2200
MADTOM
1 HA 0
3 ER 1
: SPRING
:LOTIC
:GRAPEB
:NERUN
:2000
:AL
:IN
: RE GO 7
:PRINVE
: GRAPE B
:2210
SA
PG
GH
BT
SH
CU
PG
PG
PG
BT
ER
SA
PG
FB
GH
BT
SH
ER
PG
PG
PG
FB
BT
ER
0 NU 0
3
: STREAM
:SAND
: NEKTON
: RHEOBI
:VA
:NC
:REG06
: GRAPE B
:2210
0 NU 0
3
rPREDAT
: STREAM
: GRAVEL
rNEPOOL
:2200
:KY
:MN
:IA
:HERBIV
: GRAVEL
:2500
RC = 03
OR 0 PH 0
GH : STLARG
BT: GRAPE B
SH:NERIFF
ER:2000
PG:WV
PG:TN
PG:AR
BT: GRAVEL
PG:REG05
RC = 04
OR 0 PH 0
FB:PRINVE
GH:STSMAL
BT: COBBLE
SH:NEOFFC
ER:2210
PG:MS
PG:WI
PG:KS
FB:HEGRAZ
SH : NEKTON
ER:2510
11-17
-------
Figure 10. HELP file example.
(3INPUT 105
60UTPUT 105
TERMINAL/LINEPRINTER/UNIT ##
Redirects input or output to the terminal, lineprinter
or the unit specified by UNIT ##. The use of the unit
is not advised. If the Unit was not pre-allocated to
the program the program will err, this error cannot
be trapped so the program may quit running.
@HISTORY 101
Lists your search results in reverse chronological order.
@ECHO 101
ON/OFF
Turns on or off the echoing of search results.
#BEGIN NEWS
Updates for Version 8.0
The ability to work directly with binary data has been added
to the system. The command MASK produces binary masks
as its result, not searches. These masks may then be
used as the argument to a logical operator, like AND,
to produce a search or to combine two masks,
See HELP MASK for more details.
#END NEWS
11-18
-------
figure 11. ERAPT progran data structure and linkages.
| IDENTIFICATION [-p DATA |-fTAX GNOMIC LEVEL]RH1GHER TAXON1HIC LEVEL]
->TAXA
DATA f-|CONTRIBirrORCOUNTE|TOTAL REFERENCES[
luciug |-(oDATA|-| gpeciet
->
11-19
-------
name, taxonomic level, a pointer to the next higher taxonomic level, and
a pointer to a data record if data are present. The data record in-
cludes information on the number of sources used in accumulating infor-
mation for each environmental category and the total number of data
sources used, a pointer back to the taxonomic record, and an array of
binary environmental data. The pointers allow either taxonomic names or
environmental data to be searched.
The results of these searches are placed on a stack for later refer-
ence. Twenty search results may be kept on the stack at a time and they
may contain either lists of pointers to taxonomic entries or bit mapped
data representing environmental category information.
This allows search results to be either lists of species or envir-
onmental characteristisc of a habitat, and permits these two distinctly
different kinds of results to be compared or evaluated in subsequent
queries. For example, it is possible to define a list of species to the
system and request a list of their shared environmental requirements.
This environmental description may then be compared to those developed
for specific habitats or projected from alternative species
assembladges.
11-20
-------
SECTION III
ERAPT EXAMPLES
The following section provides a series of brief examples to
illustrate some of the features and uses of the ERAPT system. The user
would have entered the information on any line which begins with one of
the system prompts: '>', or 'MORE-/E>'. All other lines contain output
from the system. Scientific names entered on command lines have been
abbreviated to the fewest characters required by the system. All of
these examples are exact representations of ERAPT system input and
output.
The examples are divided into three parts: 1) the question to be
answered, 2) the list of ERAPT system commands and responses, and 3) a
running commentary on the right side of the page explaining the commands
used and search results.
III-l
-------
Predicting Environmental Change by Faunal Change
The fauna of a small stream has changed since a previous survey by the
addition of one new species and the loss of two previously existing
species. What might this indicate?
Consider only the information
XJIAUFY PH BT pH, and bottom type.
Enter the two lost species.
ES-AM ET-MLC/END
ESOX AMERICANOS
ETHEOSTOMA MICRCPERCA
SEARCH: 1 RECORDS: 2
X3CMPARE 1
PH2 BT2
AIL PH:AI*AIP BT:SAND BT:GRAPEB BT:GRAVEL BT:VEGETA BT:DETRIT
SEARCH: 2 MASK.
XXWPARE NOTR-CHAL
NOTROPIS CHALYBAEUS
PHI BT 1
ALLPH:ACIDOB PH:ACIDCP BT:SAND BT:VEGETA
SEARCH: 3 MASK.
S NOT 3
SEARCH: 4 MASK.
5PRINT
0 RECORDS.
2 NOT 3
SEARCH FROM OR SUMVttRY
SUM PH:AIKAIP BT:GRAPEB BT:GRAVEL BT-.DETRIT
JHEIP/DEFINE PH BT
PH: pH - Negative logarithm of hydrogen ion activity.
PH:ACIDOB Acidobiontic - pH < 5.5.
PH:AdDOP Acidophilous - pH 5.6-6.5.
PH-.NEUTRA Neutral - ph 6.6 - 7.5.
PH:AIKAJP Alkaliphilous - pH 7.6-8.5.
PH:AIKAIB Alkalibiontic - pH > 8.5.
PH:INDIFF pH Indifferent - Not pH dependent, found in both acid,
neutral, and alkaline waters.
BT: Bottom Type - Bottom requirements for satisfactory growth or reproduction.
BT:SILT Silt - Particle size 0.0039-0.0625 ran.
BT:SAND Sand - Particle size 0.0525-2.0 ran.
BT:GRAPEB Gravel or Pebble - Particle size 2.0-64.0 nrn.
BT:GRAVEL Gravel - Particle size 2.0-16 ran.
BT:PEBBLE Pebble - Particle size 16.0-64.0 mn.
BT:COBBLE Cobble or Rubble - Particle size 64.0-256.0 mn.
BT:BOUIDE Boulder - Particle size > 256.0 ran.
BT:BEDROC Bedrock or Claypan - Solid rock or clay bottom.
BT:VEGETA Vegetation - Bottom covered with aquatic vegetation.
BT:MUCK Muck - Bottom primarily composed of FPOM.
BT:DETRIT Detritus - Bottom primarily composed of (PCM.
Determine connon requirements
of the older species.
Determine characteristics of
the new species.
Determine the characteristics
of the older species which
are not shared by the new and
print the list of differences.
list definitions for all pH
and bottom type codes.
III-2
-------
Subdividing Faunas by Environmental Conditions
Samples were obtained from a river which consisted of a series of deep
pools connected by more shallow, riffle sections. Which species came
from which areas of the river?
5DEFTNE CAMP-ANCM H1DDCN-ALOS HYBOP-AES NCOROP-ATH NDTCR-DORS HYB-X-P
CAMPOSTCMA. ANCMALUM
KIDDCN AL060IDES
HYBOPSIS AESTIVALIS
NDTRCPIS ATOERINDIDES
NDTRCPIS DORSALIS
HYBCPSIS X-PUNCEAIA.
MDRE-/E>CAMP-CLIGO ETHE-MAC DORO-PETE/END
OWPOSTOMA. CL1GCLEPIS
ETHESTCMA. MACULATUM
DORC6CMA. PETEMENSE
SEARCH: 1 RECORDS: 9
>1 AND SHtCPOCL
SEARCH: 2 RECORDS: 6
XPRINT/COMK
6 RECORDS.
1 AND SHNEPOCL
SEARCH FRCM OR StMftRY
Define the list of species
found in the river.
Which species are from pools?
List the species which occur in
pools, including cannon names.
PETENENSE
HIODCN ALOSOIDES
CAMPCSTCMA. ANCMALUM
CAMPOSTO& OLIGOLEP1S
NOIRCPIS A3HERINOIDES
NOTRQPIS DORSALIS
>1 AND SHNERUT1
SEARCH: 3 RECORDS: 7
7 RECORDS.
1 AND SHNERIEF
SEARCH FRCM OR SUMftRY
IHREADFIN SHAD
OOLDEYE
CENTRAL STCNEROLLER
LARGESCALE STCNEROLLER
EMERALD SHINER
BIGMDUTH SHINER
Which species are from riffles?
List species which are found in
riffles including conmon names.
DORC6CMA. PETENENEE
HIODCN ALOSOIDES
CAMPOSTCMA. ANCMALUM
CAMPOSTCMA. OLIGCLEPIS
HYBCPSIS AESTA.VALIS
HXBCPSIS X-PUNCIAIA.
ETHESTCMA. JttCULAIUM
IHREADFIN SHAD
GCLDEYE
CENTRAL STONEROLLER
LARGESCALE STCNEROLLER
SkFlKIJIl CHUB
GRAVEL CHUB
SPOTTED DARTER
111-3
-------
Evaluating Introduced Species
What species might be good choices to stock in the following habitat?
5NCTT CURHECFH
SEARCH: 1 RECORDS: 253
>1 AND GHLEPOND BTVEGETA BTSAND BTG8AVEL EBPKPISC PGIL
SEARCH: 2 RECORDS: 16
>PRIOT/CC»CN
16 RECORDS.
1 AND GHLEPCND BTVEGETA BTSAND BTGRAVEL FBPRPISC PGIL
SEARCH FROM OR SUMftRY
Exclude those which need current.
The pond to be stocked is in
Illinois. The large pond
has a vegetated sand and
gravel bottom. The pond has
an abundance of small forage
fish but few piscivorous gane
fish.
List the species of game fish
which have these requirements
and include common names.
SALMD TRUTTA
SALVELMJS FONTTNALIS
ESCK AM3RICANUS
ESCK AhERICANUS VERMICULAIUS
SEMOTILUS ATROMACULATUS
ICTALURUS NEBULGSUS
ICIALIMJS PUNCTATUS
CULAEA INCONSTANS
LEPCMIS CYANELLUS
LEPOMIS GULOSUS
LEPCMIS MACRDCHIRLJS
MCRCPrERUS DCLCMEUI
hDLCRCFTERUS SALM)IDES
PCMCKIS ANNJLARIS
PCMKIS
PERCA FLAVESCENS
BROWN TROUT
BROCK TROUT
GRASS PICKEREL
CREEK CHUB
BROUN BULLHEAD
CHANNEL CATFISH
BROCK STICKLEBACK
GREEN SUNFISH
WARMDUTH
BLUEGILL
SMVLLM3UTH BASS
LARGEMDUTH BASS
VlfflECRAPPIE
BLACK CBAPPIE
YELLOW PERCH
II1-4
-------
Predicting Faunal Change by Environmental Change
If a forested area is to be cleared for farming, what will happen to the
existing fauna of the stream if this causes siltation?
»EFINE SAIM)-GAI SAIMD-TRUT SAIV-FCNT CLINO-FUND NOCCM-MLCR NOTRO-ARD Enter the present f auia.
SAIMD GAIRDNERI
SAIMD TRUTTA
SAIVEIINUS FCNTINAUS
CIINOSTOMUS FUNDULDIDES
NOCOffS MICROPOGON
NOTROPIS ARDENS
MDB&-/ESAMBIO-KJP ETHE-BUN ETHE-CAMU ETHE-FLAB PERG-EV/END
AMBLCPLJTES HJPESTRIS
ETHEOSTOMA BLENNIOIDES
ETHEOSTOMA. CAMJRUM
ETHEOSTCMA FLABEUARE
PERCINA EV1DES
SEARCH: 1 RECORDS: 11
X3CMPARE I/ALL List the environmental factors
ST11 AB 6 GP 1 RS10 RB 9 FB10 HA.1SA3NU1PH20X2 GHll cotnron to all of the species.
Bill SH10 TE 7 1U11 CU11 ERll PG11
AND ST:ADULT GP:SUtt£R FB:PREDAT HA:SLIGHT SA,:EURYHA. NU:OLCGOT
PH:ACIDCP PH:NEU1RA PHrAlKAIP PH:INDIFF OX:EUOXXP OX-.bESOXX
GH:DdnC GH:STREAM SH:NEKTCN ER:2000 ER:2200 ER:2210
PG:REG03 PG:VA PG:REGm PG:KX PG:NC PG:1N
PG:REGC5 PG:OH
SEARCH: 2 hftSK.
»EIP DEFINE HASLIGHT SAEURYHA OX List the definitions for
HA: Hardness - Hardness of water measured as mg/1 CaCCB. HASLIGHT, SAEURYHA and all
HA:SLIGHT Slightly Calcareous - Total hardness 20-100 wg/l CaCCB. codes for dissolved oxygen.
SA: Salinity - Dissolved salt concentration for habitat.
SA:EURYHA Euryhalinous - Occurs under broad raige of salt
concentrations. (CHIR 15, DIAT 19 , BIGR 30)
OX: Oxygen - Dissolved oxygen requirements for reproduction and
growth.
OX:EUOXYP Euoxyphilous - High oxygen concentration, (2 > 7.5 mg/1.
(saturated)
OX:MESOXY Mesoxyphilous - Moderate oxygen concentrations, 02 5.0-7.5 mg/1.
OX:OLIGOX Oligoxyphilous - laa oxygen concentrations, C2 2.5-5.0 mg/1.
OX:ANOXYP AnoxyphiLous - Facultative anaerobic, C2 < 2.5 mg/1.
>i AND BTSILT Which of the current fauna
SEARCH: 3 RECORDS: 2 caa tolerate silt?
*RIKT Print the silt tolerant
species.
2 RECORDS.
1 AND BTSILT
SEARCH FROM OR SUMARY
AlffiLOPLTTES HJPESTRIS ETHEOSTOMA. FLABELLARE
III-5
-------
Finding Environmental Differences Among gpecies
Two closely related species rarely occur together.
factors distinguish between them?
XyWJFY DELZTE ST PG RS AB HI
DEUTCNG...
What environmental
XXWPARE LEPCH-GBB LQ>CM->EGAlVDIFFERENCE
upcms GIBBOSJS
LBPCMIS hEGALOTlS
KB2FB2GH2BT2SH2TE1TU2CU1
DIF FB:HEEBIV FBrHEGBAZ FBtHEBROW FB:OMNIVO GH:LELHT GH:RB£DI
BT:GRAPEB BTrGRAVEL BTzDETRIT SH:NEOFPC
IEPCMIS GBBCBUS
NCTT BT:GRAPEB BT:GBAVEL
IEPCMIS JEGALCOIS
NCT FB-.HERBIV FBrHEGBAZ FBrHEBROW FBrCMNIVO GH:LELITr GHtRIMEDI
BTtDEIRIT TE:hESOm TE-.MMJGH CU:LIMCB
Prevents information on stage
political geography,
reproductive season, abundance
or ecoregion from being
considered.
Compare the two species
for differences
The factors which differ
between the species.
Factors not characteristic of
1/apPnU.S gibbosus.
Factors not characteristic of
qealotis.
111-6
-------
Identifin Indicator Organisms
A construction project along a river may cause it to become silted.
Which species might be good indicators of changing turbidity for
monitoring the river?
5DEFINE NOT-STRA NOT-FLAV CAT-CAT H10-TER LEP-OSS HXP-NIG MICRO-FUNG
NOTROPIS STRAMDEUS
NOTURUS FLATUS
CATOSTOMUS CATOSTOMUS
HIDDON TERGISUS
LEPIS03TEUS GBSEUS
H5DPBNTELIUM NIGKLCANS
MICROPTERUS PUNCTULATUS
MORE-/END > MCKO-CAR MCK-DUQ PERO-MACRO ETHE-ZCN COTT-BAIR/END
M3H06TOMA CARINATUM
MCKOSTOtt. DUQUESNEI
PERCINA. >ttCRDCEPHALA
ETHEX3BTOJA ZCNALE
COTTUS BAIBDI
SEARCH: 1 RECORDS:
>1 AND TUEULICH
SEARCH: 2 RECORDS:
52 NOT BTSILT
SEARCH: 3 RECORDS: 8
>3 EVAL BT TU
SEARCH: 4 RECORDS: 3
CA1DSTOMUS CATOSTOMUS
BTrGBAPEB BT:GRAVEL TU:EULJCH
KECROFTERUS PUNCIUlArUS
BT:GRAPEB BTrGRAVEL TU:EULICH
PERCINA mCROCEPHALA RC:
BT:GRAPEB BT:GRAVEL BT:BOUIJ)E TUtEULICH
Enter a list of species.
12
12
RC: 6
RC:
3 RECORDS.
3 EVAL BT TU
SEARCH FROM OR SUMMARY
CATOSTOMUS CATOSTOMUS
MLCROPTERUS PUNCTULMUS
PERCINA I^CROCEPHALA
Make sure that they are all
found in clear water.
Remove those that would
tollerate silt.
Find potential indicators
for turbidity and bottom type.
List of species and
requirements.
List the species and their
cotitnon names.
LCNGNOSE SUCKER
SPOTTED BASS
LCMGHEAD DARTER
III-7
-------
Identifying Species by Environmental Conditions
Some specimens collected as part of an environmental monitoring study
can be identified only to genus. Given a general knowledge of the
habitat characteristics and geographic location, what species are
likely?
>AND PGOi BRAND BTCRAVEL GHLELAKE SHNSNEAR TEMESOTH
SEARCH: 1 RECORDS: 23
>1 FIND NOTRCPIS/COMH
Nomopis orawuius COMH SHINER
NCHRCPIS DORSALIS BIGM3UTH SHINER
NOTRCPIS HJDSCNIUS SPOTIAIL SHINER
RC: 6
RC: 6
RC: 5
Enter what is known about the
habitat.
Of the 36 possible species of
Natropis only these three are
found in the habitat
previously described.
III-8
-------
Interpreting Environmental Causes of Fauna,! Change
A species has reappeared in a habitat where it has not been collected
for many years. What might the return of this species indicate?
XJUALDY BT SH IE TU CU Consider only physical
information: bottom type,
specific habitat, tanperature,
turbidity, and current.
5FIND NOm-AT/SUtfCOtCN List all of the information
NOTOCPIS ATHERINOIDES QERALD SHINER RC: 5 on the Bierald shirer.
BT2SH3TE1TO4CU2
SUM BTrSAND BT:GRAPEB BT:GRAVEL BT:MJCK SH:NEKTCN SH:NEHJN A comparison between these
SH:NEPCOL SH:NECFEC SH-.NEPEU TEihESOTH TEt^bEDI TU:EUL1CH factors and the current data
TU:M5SCLI IU:POLYL1 OhLIMOP should show any changes.
II1-9
-------
Relocating Endangered Species
A rare species is found only in a small section of one river system. Due
to changing environmental conditions this species may be lost if it cannot
be relocated. Do other species have similar environmental requirements?
What environmental characteristics must a potential relocation site have?
XJIALIFY BTSHPG
XXWPARE NOTUR-T
NuTIUBUS TRAUTMANI
BT 1 SH 1 PG 1
AND BT:SILT BT:SAND BT:GRAPEB BT:GRAVEL BT:PEBBLE BT-.BOJLDE
BT:VEGETA SH:NEK10N Sl:NERIFF SHNEEUN PG:FEGD5 PG:CH
SEARCH: 1 MASK.
5AND 1
SEARCH: 2 RECORDS: 2
>PRINI/CCMMCN
2 RECORDS.
AND1
SEARCH FRCM OR SWtttRY
Only consider information on
bottom type, specific habitat,
and political geography.
Find the characteristics of
BatePffi tTfflirwmi and find
all species which have
identical requirements.
Print the 2 species found
with their common names.
KHNICH1HYS CATARACTAE
NOTURUS TRAUTMANI
LCNGNDSE DACE
SCIOIDMADTCM
XJIALDY RESET
QUALIFICATION SET TO ALL.
XXMPARE2
ST2AB1RS1RB1
PG2
AND ST:ADULT AB:RARE
FB: SIMPLE FB:LIIHOP
GH:LELAKE GH:LOTIC
GH-.RIVER GH:RIS>ttL
BT-.PEBBLE BT:BCUIDE
TE:>ESOTH TE:hELOW
TU:POLYLI CU:RHEOBI
PG:OH
SEARCH: 3 MASK.
FB1GH1BT2SH2TE1TU1CU2ER2
RS:SPRING
FB:PREDAT
GH: STREAM
BT:SILT
BT:VBGETA
TE:MEMSDI
ER:2000
RS:SUM^ER
FB:PRINVE
GH:STSMAL
BT:SAND
SH-.NEKTCN
TU:EULICH
ER:2200
RS:AUrUMN
FB:PRPLAN
GH:STMEDI
BTzGRAPEB
SH:NERIFF
TU:^ESOLI
ER:2210
RB:CCMPLE
GH:LENTIC
GH:STLARG
BT:GRAVEL
SH:NERJN
TU:OLIGOL
PG:REOD5
Reset for all information.
Compare the species found
to be identical to the
Scioto madton to determine
what requirements they share.
I11-10
-------
Predicting Unrelated Faunal Assemblages
Given the environmental characteristics of a stream habitat, predict
the fish and mayfly communities likely to be present.
ERAPT FISH
E.R.A.P.T. DATABASE INFORMATION RETRIEVAL PROJECT.
> SAVE snaa
BEGIN SEARCH SIEE#1
> AND GHSTKEAM PHAIKALP TEMSCTH TUEULICH PGFECD5
SEARCH: 1 RECORDS: 13
>END
SEARCH ENDED
> PRINT
13 RECORDS.
AND GHSTREAM PHAIKALP TEMESCflH TUEULICH PGREG05
SEARCH FROM OR SUMftRY
SAIM) GAIRDNERI SALVELINUS FCNTINALIS
ESOX A>ERICANUS ESOX AtERICANUS VERMICULATUS
ESOX LUCIUS NJIROPIS CORNUTUS
SEMOTILUS ATRCMACULATUS LEPOMIS MACHRCCH3EUS
MICROPTERUS DOLOMIEUI MICROPTERUS SALMDIDES
POMOXIS NIGRCMACULATUS ETHECSTOMA MICROPERCA
PERCA FLAVESCENS
>END
A SEARCH WAS SAVED TO A TEMPORARY DATA FILE. TO SAVE THIS FILE
ENTER A FILE NAtC (1-8 CHARACTERS) OR ENTER A AND THE
THE DATA SET WILL BE DELETED. > SAVELB
ERAPT EPHE SA( SAVELB)
E.R.A.P.T. DATA BASE INFORMATION RETRIEVAL PROJECT.
>EXEC STTE#1
*CLEAR
DATA STACK CLEARED - READY FOR SEARCH 1.
*AND GHSTREAM PHAIKALP TEMESOTH TUEULICH PGREGD5
SEARCH: 1 RECORDS: 9
*END SriE#l
SEARCH ENDED
> PRINT
9 RECORDS.
AND GHSTREAM PHAIKALP TEMESOTH TUEULICH PGREGD5
SEARCH FROM OR SIMMY
ARTHROPLEA BIPUNCIATA BAETISCA BAJKOVI
CLOEON RUBROPICTUM EPEORUS VTTREUS
EPHERON ALBUM HEXAGENIA ATROGAUDATA
HEZAGENIA MJNDA PARAIJcPTOPHLEBIA MIT.T.TS
SIPHLGNURUS QUEBECENSIS
>END
Save the following lines as
search STTE#1
Enter the habitat description.
Stop saving STTE#1.
Print the species.
A new library must be created
to keep the search that was
saved.
Enter the Mayfly data base
using the SaveFile SAVELB.
Recall the save statements.
List the species that have
the sane requirements as the
fish species.
III-ll
-------
Using One Fauna1 Assemblage to Predict Another
A group of fish species is known to occur together at a site under
investigation. What stonefly species are predicted to occur in this
habitat based on the environmental characteristics associated with the
fish?
ERAPT FISH SAVEFTLB(SAVELB)
E.R.A.P.T. DATA BASE INFORMATION RETRIEVAL PROJECT.
> QUALIFY PH GH TE TU
> COMPARE ESOX-AM MICRO-SAL ETHEO-MIC/KEEP/END
ESOX AMERICANUS
MICRCFrERUS SAIM)IDES
EIHEGSTOMA MICRCPERCA
KEEPING FISfflOl
PH3 GH3 TE3 TO 3
AND PH:AIKALP GH:LENTIC GH:LELAKE GH:LEPCND GH:LELITr GH:LOTIC
GH:STREAM TE:MESOIH TU:EULICH
SEARCH: 1 M4SK.
>END
ERAPT PLEC SAVE(SAVELIB)
E.R.A.P.T. DATA BASE INFORMATION RETRIEVAL PROJECT.
>CATALCG
CATALOG CF LIBRARY FILE:
SITE#1
FISHD01 «EEP>
2 FILES IN LIBRARY.
> GET FISTOOl
MDRE-/END >
MDRE-/END >
SEARCH: 1 MASK.
SEARCH ENDED
>AND 1
SEARCH: 2 RECORDS: 1
> PRINT
Access the retrieval progran
and request the use of a
SaveFile library called
Only consider information on
pH, general habitat,
temperature, and turbidity.
Compare the fish species
found in the lake for their
similarities and KEEP the
result.
The similarities are stored
in a search called FISTO01.
List the files contained in
the SaveFile library.
Get the result of the
comparison of the fish
species.
One species has the same
requirements as the fish
Print this stonefly.
1 RECORDS.
>ttSK/C PHAIKALP GHLENTIC GHLELAKE GHLELITT GHLOTIC
SEARCH FROM OR StMftRY
GHSTREAM TEMESOTH
PARAGNETINA MEDIA
>END
II1-12
-------
Evaluating Temporal Environmental Change
To evaluate environmental change in a river over time, an initial list
of species is to be saved for comparison with any subsequent changes in
the faunal composition of the habitat.
ERAPT FISH
E.R.A.P.T. MIA BASE INFOfrftTICN RETRIEVAL PROJECT.
> SAVE smtf2
BEGIN SEARCH SHB//2
Specify that all of the commnd
lines which follow are to be
saved as a search called
SIIE#2 until the END command
is entered.
> DEFINE ESO-L HXBO-AM NOIR-DO NOOR-SPI CAT-CCMM NOTE-CR
ESCK LUCIUS
HXBCPSIS AtBLCPS
NCURCPIS DORSALIS
NOTRCPIS SPILOETERUS
CATOSTCMUS OCMERSCNI
NOTEMIGCNUS CRYSOEUCAS
MDKG-/END > ICTA-1CB LEP-*£G LEP-MLC MtCRr-SAL PERO-FL
ICTALURUS NEBULOGUS
Enter the names of the
species found at Site #2.
LEPCMIS MECROXPHUS
MICRCPTERUS SALMDIDES
PERCA. FLAVESC3ENS
MDRE-/END > ETHEH»A ETHE-SPEC PERC-^ftC/END
EIHECSTCMA. GBACILE
ETHEOBTCMA. SPECTABILE
PERCINA. MACROCEPHALA
SEARCH: 1 RECOKDS: 14
>END SITE#2
SEARCH ENDED
> COMPARE 1
STL4 AB 8 PT 2 RS11 RB11 FB14 HA1SA5PH5CK4GH14 BH4
SH14 TE 8 TU14 CU 8 ER14 PG4
AND ST: ADULT PTrFACULT FB:PREDAT FB:PRINVE HA:MDDERA GH:LOTIC
GH:STREAM SH:NE3CDDN SH-.NEPOCL TE:bESOm ER:2000 ER:2200
ER:2210 PG:REGD5
SEARCH: 2 MM3K.
>END
Include /END operand to term-
inate the definition of species.
Stop saving lines into the
file SIT£#2.
Compare the defined species
and list their similarities.
111-13
-------
SECTION IV
VALIDATION
Methods
Survey data for verification of the ERAPT system were obtained from
the State of Ohio Environmental Protection Agency for 64 sites from 20
rivers, streams, and tributaries in the Cross Creek and Yellow Creek,
Blanchard River, and Tuscarawas River systems in southeastern and north-
western Ohio. For each site a list of fish species and abundances and
descriptive information on the habitat was provided. This included the
dissolved oxygen, temperature, pH, turbidity, bottom type, and general
and specific habitat characteristics of most sites, with current,
degradable organics, and pollution information provided for a few of
the sites.
The five numerically dominant species at each site were entered into
the ERAPT system and used to predict local environmental conditions.
These species accounted for at least one half of the total fishes col-
lected and, therefore, were taken to be representative of the environ-
mental conditions present within the habitat sampled. The ERAPT
system's Compare function was used to identify the environmental charac-
teristics common to each fish community. This information was used for
comparison with the environmental description of each habitat.
Habitat characterization information for each collecting site was
transformed into ERAPT environmental parameter codes directly from field
survey forms. These data then were compared with the environmental
descriptions predicted by the system from the associated dominant fish
community for each category of environmental characteristic. The com-
pared data were considered to be in agreement if they shared common
environmental parameters. For example, a general habitat predicted by
the fish assemblage as lake or large river was considered to be in
agreement with a habitat characterized as either large river or lake.
Likewise, a community predicted bottom type of gravel was considered to
be in agreement with a habitat characterized as gravel, sand, and silt.
Results and^ Discussion
In comparing 300 environmental characteristics obtained from field
survey forms to those predicted by the ERAPT system from the dominant
fish community, 285 showed agreement for an overall successful pre-
diction rate of 95% (Tables 1-2). The successful prediction rates for
the Cross Creek and Yellow Creek, Blanchard River, and Tuscarawas River
systems were 95%, 97%, and 93%, respectively. There was 100% agreement
between predicted and observed characterizations for temperature,
current, and degradable organics in all three river systems. Those
IV-1
-------
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IV-2
-------
River Systems
DOg *g/I
Temperature
pH
Current
Turbl dl ty
General Habitat
Bottom type
Organl ce
Specific Habitat
Pollution
Croea & Yellow TUB care* as Blanchard Total
No. of No. of No. of No. of
Sites Agreement Sites Agreewent 8|teB Agreement SI tea Agreement
13
18
18
2
22
34
33
-
31
-
100%
100%
81%
100%
82%
100%
97%
-
97%
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5
6
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3
2
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10
3
10
2
100%
100%
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80%
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90%
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100%
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22
5
32
62
59
3
57
2
96%
100%
86%
100%
88%
98%
95%
100%
95%
100%
Table 2. Results of ERAPT system validation study.
IV-3
-------
environmental parameters not in complete agreement between observed and
predicted characterizations were: general habitat (98%), dissolved
oxygen (96%) , specific habitat and bottom type (95%) , and pH and
turbidity (88%).
Turbidity and pH showed the lowest agreement between the predicted
and observed values because of discrepancies in the characterization of
sites in the Cross Creek and Yellow Creek system. The only other dif-
ferences between reported and predicted results for this river system
were for site 1 of Yellow Creek, which the ERAPT system predicted to be
a large stream with a sand and gravel bottom, but which was reported to
be a small river with a silt bottom.
Discrepancies in the results of turbidity comparisons may be due to
the seasonal nature of turbidity in rivers. Conditions of high turbi-
dity may have their greatest impact on specific life stages , and fishes
may be insensitive to relatively turbid conditions during some portions
of the year. The main disagreement in turbidity occurred over a three
mile stretch of Cross Creek where three adjacent sampling sites were
characterized as being more turbid than that predicted by the dominant
fish community. This also could have been the result of recent environ-
mental change which had not yet been expressed in the fish population
through a sensitive life stage.
Reported and predicted values for pH differed at three sites in the
Cross Creek and Yellow Creek system. In each case the reported pH was
lower than that predicted by the dominant fish community. At two of the
sites the fish assemblage predicted pH values of greater than 8.5,
whereas field data indicated pH ranges of 8.1 to 8.5 and 7.3 to 7.8. At
the third site the fish community predicted pH values in excess of 5.5,
but the field data indicated a pH range of 2.8 to 4.0. These results
also suggest changing environmental conditions which are not reflected
yet in the fish community.
Four discrepancies between observed and predicted habitat charac-
terizations were found from separate sites in the Tuscarawas River
system. The specific habitat of one site was described as a run,
whereas the ERAPT system predicted a pool habitat from dominant fish
community. Another site was reported to have a depth of 0.45 m which
fell just outside of the predicted range of 0.5 to 2.0 m. The other two
sites were reported to have silt and clay bottoms instead of the pre-
dicted bottom type of sand.
Sites in the Blanchard River system showed only two disagreements
between reported and predicted environmental characterizations. At one
site in which the dissolved oxygen concentration was reported to be 2.1
to 5.0 ppm, the ERAPT system predicted levels of greater than 5.0 ppm.
At another site the system predicted a water depth of 1.0 to 2.0 m, as
opposed to the reported depth of 0.85 m.
IV-4
-------
While there were some disagreements between predicted and reported
environmental characterizations, they almost always were among very
similar tolerance ranges or habitat types. In addition, only one site
which discrepancies between the observed and predicted characterizations
of more than one kind of environmental parameter. This was site number
1 of Yellow Creek where there were minor disagreements in both specific
habitat and bottom type. Overall, ERAPT system predictions of habitat
characteristics from the dominant fish assemblages closely approximated
the information obtained from field surveys at all of the sites
evaluated.
IV-5
-------
SECTION V
ERAPT PROGRAM
The ERAPT program offers a broad range of retrieval and analysis capa-
bilities for use in environmental assessment. These include the ability
to characterize environmental conditions from resident organisms, to
identify organism assemblages from environmental conditions, to predict
changes in the biological community resulting from environmental change,
and to identify environmental change for change in the species
composition of a habitat.
Abbreviations and_ Syntax
The scientific names may be abbreviated by the fewest letters to make
them unique. Esox lucius may be abbreviated ES-L. If a combination is
not unique the first matching entry will be used in DEFINE or COMPARE or
all matching entries will be listed in the case of the FIND command.
The commands may be abbreviated with the fewest letters to make them
unique. FIND may be abbreviated F but CLEAR must be CL. As a rule, the
first two characters of all commands are sufficient.
All parameters which begin with a slash, /, are position independent and
completely optional. Only the first character after the slash is re-
quired and it is the only character that is checked, therefore /DEFINE,
/DEFINITION, /DEF, and /D are all synonymous.
The 2-8 character environmental retrieval codes may not be abbreviated.
Code lists and definitions may be obtained through the help command.
Throughout this section several conventions are used in the command
syntax.
Braces {}. Mutually exclusive parameters are enclosed in braces, {}.
Brackets []. Optional parameters are enclosed in brackets, [].
Slashes /. All options are preceded by a slash, /. The option is
ended with a blank space or another option.
Numeral Signs #. All numeric parameters are represented using number
sign, #, with each symbol representing a digit. A parameter with
a range from 0 to 99 would be shown as ## whereas a range of
0 to 9 would be a #.
Characters XX. The symbol XX is used for two character category codes
like PG, political geography. In the case of the QUALIFY command
any 2 to 8 character code may be used.
V-l
-------
Arrows <>. The symbols <> are used to represent keys on the terminal.
is the enter or return key.
Examples:
OUTPUT {TERMINAL LINEPRINTER UNIT ## FILE ##}
One of these parameters must follow the command
OUTPUT but only fine, may be used.
PRINT [##] [/OFFLINE] [/COMMON]
All parameters are optional and may be used separately.
The first is expected to be a 1 or 2 digit number, the
others are the parameters /OFFLINE and /COMMON.
QUALIFY {[ON]
[OFF]
[RESET]
[ADD XX ... XX:XXXXXX]
[DELETE XX ... XX:XXXXXX]
[XX ... XXrXXXXXX]}
There are 6 valid parameters. Only one of the 6 may be
used on a command line at any time. Three are single
word parameters: ON, OFF, and RESET; 2 have parameters
of their own which must be present: ADD XX ... XX and
DELETE XX ... XX; and the sixth parameter is just a
list of 2 to 8 character category codes. A valid
example would be QUALIFY DELETE PG BTrGRAVEL BT:SAND.
Program CQmm.an.rf List
The following is a list of the ERAPT information retrieval system com-
mands and syntax. This information can be obtained from the
ERAPT program by typing HELP followed by any command.
HELP The help command lists all the commands which can be used in
the ERAPT program:
Example:
HELP
HELP IS AVAILABLE ON THE FOLLOWING COMMANDS:
?
COMPARE
END
GET
LINEPRINTER
NOT
QUALIFY
TERMINAL
WIDTH
1
AND
DEFINE
EVALUATE
HELP
LEVEL
OR
RESET
TIME
XOR
ENTER HELP
&
CATALOG
DIFFERENCE
EXECUTE
HISTORY
MASK
OUTPUT
SAVE
USE
'COMMAND'.
"*
CLEAR
ECHO
FIND
INPUT
NEWS
PRINT
SOURCES
WAIT
V-2
-------
Program Command Descriptions
The following pages are similar to the output obtained by
typing 'HELP CommandName'.
AND: AND REQUIRED: AN SYNONYMS: &
PURPOSE:
AND searches the data base for all organisms which
have the environmental parameter(s) specified or will
combine two searches to produce a list of organisms
or characteristics common to both lists.
SYNTAX:
[##] AND {[##] [XX:XXXXXX]} {[/CONTINUE] [/END]}
EXPLANATION:
/CONTINUE allows multiple lines to be entered.
/END ends the continuation.
EXAMPLE:
AND PG-.IN PG:HI
The result will be those organisms in the data
base which are found in both Indiana and
Hawaii.
3 AND PG:IN PG:OH BT:SAND
The result will be those organisms in search
3 which also occur in IN and OH and prefer a
bottom type of sand.
4 AND 5
The result will contain those organisms which
were in both search 4 and search 5.
RELATED COMMANDS: OR, NOT, XOR, DIFFERENCE, &, |, ~
CATALOG: CATALOG REQUIRED: CA
PURPOSE:
Lists the names of the search files in the savefile
library. See the ERAPT command for more information
on the savefile. CATALOG lists two types of files:
those generated from the SAVE command and those by
the /KEEP option on COMPARE. The types are displayed
to the right of the name as either or .
If /SAVE is specified only the SAVE files will be
listed. If /KEEP then only the KEEP files are
listed. If a file name, FileName, is included its
contents will be listed.
V-3
-------
SYNTAX:
CATALOG [/SAVE][/KEEP][FileName]
NOTE: The CATALOG may not be used in a saved search and a
warning message will be displayed if it is entered.
EXAMPLE:
XJATALOG
CATALOG OF LIBRARY FILE:
FISH001
OHIOEPA
OHIOEPA2
FISH002
4 FILE(S) IN LIBRARY.
The file types are listed in the right
column.
RELATED COMMANDS: SAVE, EXECUTE, GET, COMPARE/KEEP
CLEAR: CLEAR REQUIRED: CL
PURPOSE:
This clears search memory. The next search will
be 1. This is needed before a SAVE command.
The results of all searches cannot total more than
1000 and the highest allowable search number is 20.
If either of these limits is reached you will not be
allowed to continue searching until the CLEAR command
is issued.
SYNTAX:
CLEAR
COMPARE: COMPARE REQUIRED: CO
PURPOSE:
Compares 1 or more species or search results and
returns the categories found in any species, /SUM; the
categories found to be common to all species, /ALL;
or categories which differ between the species, /DIF.
/KEEP may be used to store the result of a
comparison.
SYNTAX:
COMPARE {[GNS-lSPP] ... GNS-[SPP]] [[«] ... ##]} [/KEEP]
[/ALL] [/DIF] [/SUM] {[/CONTINUE] [/END]}
V-4
-------
EXPLANATION:
/CONTINUE allows multiple line input, /END terminates
multiple line input. /SUM prints the sum, /ALL the
product, /DIF the difference (default is to print the
logical product, /ALL). A search will be saved
having the same characteristics for each type of
comparison specified except /DIF which does not
result in a search. If the search is being saved,
the record written to the library will be MASK/C
followed by the category codes. If a single species
is entered the search will contain those organisms
which have the same environmental parameters as that
species (if SAVE/LITERAL is used the species entered
will be saved, not the result). /KEEP will save the
results of a comparison in a separate file in the
library. This option is not allowed in conjunction
with SAVE and if used it will cause an error message.
EXAMPLES:
COMP ESOX-AMERICANUS ESOX-M/A/D
This will compare Esox americanus to the
first species of Esox which begins with an
'M'. The similarities, /A, and the
differences, /D, between the two species will
be listed and a search will result containing
all similar characteristis.
COMP ESOX-AMERICANUS/A
This will list the categories which all
references for Esox americanus reported and
save these categories as a search.
COMPARE ESOX-AMERICANUS/C
ESOX-MASQ
ESOX-NI/A/D/E
This will compare the 3 species listed and
list their similarities, /A, and differences,
/D. A search will be result containing
characteristics common to all 3 species.
COMPARE 1 2
This will compare the species in search 1 and
search 2. Their similarities will be listed
and saved as a search statement.
COMPARE 1 ESOX-L
This compares the organisms in search 1 with
Esox lucius. Their similarities will be
listed.
RELATED COMMANDS: GET, DEFINE, FIND, CATALOG
V-5
-------
DEFIHE: DEFINE REQUIRED: DE
PURPOSE:
Allows a list of species to be entered into the
computer. The result is a search which contains the
species which were entered.
SYNTAX:
DEFINE Genus-species ... Genus-species {[/CONTINUE] [/END]}
EXPLANATION:
The list needs to be entered followed by /END. The
/CONTINUE option is the default, input is continued
on multiple lines until the /END is encountered.
RELATED COMMANDS: COMPARE
DIFFERENCE: DIFFERENCE REQUIRED: DI SYNONYMS: XOR
PURPOSE:
Compares two search results and returns a list
containing the species or categories which were in
one list or the other but not in both lists.
SYNTAX:
## DIFFERENCE ##
NOTE:
If the first list is omitted the default would be to
use the entire data base, identical to NOT ##
RELATED COMMANDS: AND, OR, NOT, XOR, &, |, ~
ECHO: ECHO REQUIRED: EC
PURPOSE:
Causes statements read from a saved file to be
displayed at the terminal.
SYNTAX:
ECHO {ON OFF}
EXPLANATION:
Turns on or off the printing of search statements
read from a library file. Default condition is ON.
EHD: END REQUIRED: EN
PURPOSE:
Exits the program or ends a current SAVE.
V-6
-------
SYNTAX:
END
NOTE:
If 2 SAVE commands are issued without an intervening
END, an END command for the first SAVE will be issued
automatically by the program before the second SAVE
is begun. Nesting or recursion of SAVE is not
allowed.
RELATED COMMANDS: SAVE
EVALUATE: EVALUATE REQUIRED: EV
PURPOSE:
EVALUATE is designed to find groups of organisms
which could potentially be used as indicators of
environmental conditions.
SYNTAX:
[XX] EVALUATE XX [##] [XX XX XX ##] {[/FULL][/SHORT]}
EXPLANATION:
XX is any two-character category code.
## is the minimum number of sources (default=l).
/FULL = Full listing (default), /SHORT = Short list.
A full listing will include all of the entries and
the categories which were found to be consistent. A
short listing will include only the taxa.
EXAMPLE:
EVALUATE BT CU 2 SH GH 3
This will find all organisms which have a
minimum of 2 sources for information on
bottom type and current and a minimum of 3
sources for information on specific habitat
and general habitat. All organisms listed
will have complete agreement of all of the
references in these areas.
EXECUTE: EXECUTE REQUIRED: EX
PURPOSE:
Executes the search from the savefile.
SYNTAX:
EXECUTE SearchName
V-7
-------
EXPLANATION:
You will be prompted for the 'SearchName' if it is
omitted. If you wish to end the command at this
point just type a carriage return .
NOTE:
You are not permitted to execute a saved search while
saving a search. This eliminates the possibility
that a search might call itself and become an
infinite loop.
RELATED COMMANDS: GET, SAVE, CATALOG
FIND: FIND REQUIRED: F
PURPOSE:
Used to locate information on a taxon or group of
related taxa. Common names may be listed with
scientific names. Summaries of information about the
taxa may also be listed.
SYNTAX:
## FIND [TAXON:][T1][-T2] {[/FULL] [/ALL] [/SUM]}
[/COMMON]
EXPLANATION:
TAXON: ORDER,FAMILY,GENUS OR SPECIES (DEFAULT=GENUS)
Tl = The taxonomic name at the level specified by
TAXON:
-T2 - The next lower taxonomic name. The dash must
be included.
/FULL = Full listing (/ALL/SUM),
/ALL = All entries common to the references for the
: organism,
/SUM = All entries from any reference for the
organism.
/COMMON will list the common names as well as the
scientific names.
If the summaries agree, only the SUM summary is
printed.
Use underscore for blanks, if necessary.
EXAMPLES:
FIND FAMILY:ESOCIDAE-ESOX/F
All information for the family Esocidae genus
Esox will be listed.
FIND G:ESOX-LUCIUS/C
The reference count and the common name will
be listed for the species Esox lucius.
V-8
-------
F ESO-/C
The scientific and common names and reference
count will be printed for all genera and
species within the genera which have the
first three letters 'ESO'.
RELATED COMMANDS: COMPARE
GET: GET REQUIRED: G
PURPOSE:
To recall the result of a COMPARE/KEEP from the
library file.
SYNTAX:
GET Name
EXPLANATION:
You will be prompted for the 'name' if it is omitted.
If you wish to end the command type carriage return,
, rather than a name. A comparison which has
been saved in this manner does not contain the CLEAR
command and therefore does not reset the search stack.
NOTE:
You are not allowed to GET a file while you are
saving a search.
RELATED COMMANDS: EXECUTE, CATALOG, COMPARE/KEEP
HELP: HELP REQUIRED: HE SYNONYMS: ?
PURPOSE:
Prints information for the COMMAND, category or code
listed.
SYNTAX:
HELP [[COMMAND]!/SYNTAX]] [/DEFINE!XX:XXXXXX]]
EXPLANATION:
If the option, /SYNTAX, is used, only the command
syntax is listed. /DEFINE will list the categories
used in the ERAPT system. If a category or code is
listed, the /D option must be used. Help on
categories will list all information on the category
and all codes in the category. Help for a code will
list the category and the one code. Multiple codes
and categories may be entered but may not exceed one
80-character line.
V-9
-------
EXAMPLES:
HELP
This will list all the commands.
HELP DEFINE
This will list all of the information on the
DEFINE command.
HELP BT GHLOTIC PH/DEFINE
This will list all of the categories for
bottom type, BT, and for pH, and provide
definitions for the codes and it will list
the definition for general habitat lotic,
GHLOTIC.
HISTORY: HISTORY REQUIRED: HI
PURPOSE:
Lists all searches and the number of records found
from your current search back through the first
search.
SYNTAX:
HISTORY
INPUT: INPUT REQUIRED: IN
PURPOSE:
Redirects input from the terminal, lineprinter, or
the unit number specified by UNIT ##.
SYNTAX:
INPUT {TERMINAL UNIT ## FILE ##}
NOTE:
The use of the unit number option is not advised. If
the unit was not pre-allocated to the program, the
program will err when a write or read is made to or
from the unit. This error can not be trapped, so the
program will stop abnormally.
RELATED COMMANDS: OUTPUT
LEVEL: LEVEL REQUIRED: LE
PURPOSE:
Returns the taxonomic level which is the highest taxon
to be searched for or sets the highest acceptable
taxon to return from logical operations: AND, OR, NOT,
XOR. The default is species.
SYNTAX:
LEVEL [Taxon]
V-10
-------
EXPLANATION:
Taxon is the taxonomic level to which you wish your
searches restricted. It may be species, genus,
family, or order.
EXAMPLES:
LEVEL
This will return the current setting for the
taxa to be searched.
LEVEL GENUS
This will set the level to find only genera
and all taxonomic levels lower than genus,
i.e. species and subspecies, when the logical
operators are used.
LIMKPRINTER: LINEPRINTER REQUIRED: LI
PURPOSE:
Sets the width of the LINEPRINTER.
SYNTAX:
LINEPRINTER [WIDTH {WIDE NARROW}]
EXPLANATION:
If WIDTH is omitted the next time WIDTH is called it
will affect the LINEPRINTER. If WIDTH is included,
you must include either WIDE, 132 columns, or NARROW,
72 columns.
RELATED COMMANDS: TERMINAL, WIDTH
MASK: MASK REQUIRED: M
PURPOSE:
Defines a search containing a set of category codes
to be used in logical operations with other searches.
SYNTAX:
MASK [XX-.XXXXXX] {[/CONTINUE} [/END]}
EXPLAINATION:
Use /CONTINUE if more than one line is needed define
the desired characters. You will be prompted for
more input until /END is entered.
V-ll
-------
NEWS: NEWS REQUIRED: NE
PURPOSE:
Lists the notices and differences in this revision.
SYNTAX:
NEWS
EXAMPLE:
NEWS
CHANGES SINCE V6.03
The TIME command will now print the CPU time left in
the logon session if the ON or OFF parameters
are omitted.
CHANGES SINCE V6.02
The help command has been changed, now enter HELP
to get a list of the commands (many of which
have been changed for the better). HELP
followed by a command will list its syntax and
give an explanation of its function.
HOT: NOT REQUIRED: NOT SYNONYMS: ~
PURPOSE:
Finds all organisms which do not have the category or
categories listed. If used on two search numbers
then the species or categories in the first, not in
the second, are returned.
SYNTAX: [##] NOT {[##] lXX:XXXXXX]} {[/CONTINUE] I/END]}
EXPLANATION:
/CONTINUE may be used to enter more than one line of
parameters. You will be prompted for more lines
until you enter /END on a line.
EXAMPLE:
NOT PG-.IN
All organisms not found in Indiana
3 NOT 4
The result is all entries in search three
which are not in search four.
RELATED COMMANDS: AND, OR, XOR, DIFFERENCE, &, |, ~
V-12
-------
OR: OR REQUIRED: OR SYNONYMS: |
PURPOSE:
Lists all organisms which have any of the categories
listed or combines two searches.
SYNTAX:
[##] OR {[##] [XX:XXXXXX]} {[/CONTINUE] [/END]}
EXPLANATION:
/CONTINUE may be used to enter more than one line of
parameters. You will be prompted for more lines
until you enter /END on a line.
EXAMPLE:
OR PG:IN BT:SAND
The result is any organism which is either
found in Indiana or over a bottom type of
sand.
3 OR 4
The result will be those entries in either
search three or four.
3 OR PG-.IN
The result will be all entries in search
three and all entries found in IN.
RELATED COMMANDS: AND, NOT, XOR, DIFFERENCE, &, |, ~
OUTPUT: OUTPUT REQUIRED: OU
PURPOSE:
Redirects output to the terminal, lineprinter, or the
unit number specified by UNIT ##.
SYNTAX:
OUTPUT {TERMINAL LINEPRINTER UNIT ## FILE ##}
EXPLANATION:
The use of the unit number option is not advised. If
the unit was not pre-allocated to the program, the
program will err when a write or read is made to or
from the unit.
The first time information is sent to the line
printer you will be prompted to enter your name and
mailing address so that the printout that you
generate can be sent to you. When you end the search
session you will be prompted for confirmation before
your printout is sent to the lineprinter.
V-13
-------
EXAMPLE:
OUTPUT LINEPRINTER
All search results will go to the line
printer until OUTPUT TERMINAL is used.
RELATED COMMANDS: INPUT
PRIBT: PRINT REQUIRED: P
PURPOSE:
Prints search ## to the output device.
SYNTAX:
PRINT [##] [/COMMON] [/OFFLINE]
EXPLANATION:
Defaults to the last search. Prints to the device
you have set for output, normally your terminal.
/COMMON lists the common names and the scientific
names in the printout.
Print is sent to the lineprinter if /OFFLINE is
specified.
EXAMPLE:
PRINT/C
Prints the last search with the common names.
PRINT 3
Prints search 3 at the terminal, or if output
is redirected to the lineprinter, the search
will be printed on the lineprinter.
PRINT 2 /OFFLINE
Prints search 2 to the lineprinter.
QUALIFY: QUALIFY REQUIRED: Q
PURPOSE:
It is used to suppress the printing of categories in
a listing produced by the FIND or COMPARE commands.
SYNTAX:
QUALIFY {[ON]
[OFF]
[XX ... XX-.XXXXXX]
[ADD XX ... XX:XXXXXX]
[DELETE XX ... XX:XXXXXX]
[RESET]}
V-14
-------
EXPLANATION:
XX is any category code (two to eight characters).
ON causes the last qualification list to be used
when output is produced by FIND or COMPARE. OFF
causes all categories to be printed. Qualify (Q)
followed by no options toggles ON and OFF and prints
the status as it changes. RESET sets the qualify
list to all categories (default condition). Q XX YY
would set the list to print only the codes specified
by XX and YY. Q ADD ZZ would now add the category
ZZ to the list that would be printed. Q DEL XX takes
XX out of the list so now only YY and ZZ would be
printed.
EXAMPLES:
QUALIFY DELETE PG
Now when a full list is printed the regions,
states, and provinces will not be printed.
QUALIFY ADD PGREG05 PGIN PGOH PGWI PGMN PGMI PGWI
Now if Region 5 or the states in Region 5
are present they will be printed.
RESET RESET REQUIRED: RE
PURPOSE:
Resets the parameters for the commands USE, INPUT,
OUTPUT to their default values: USE AND, INPUT
TERMINAL, OUTPUT TERMINAL.
SYNTAX:
RESET
SAVE: SAVE REQUIRED: SA
PURPOSE:
Used to save a series of commands into a library for
later use.
SYNTAX:
SAVE FileName [/LITERAL]
V-15
-------
EXPLANATION:
Saves a search named 'FileName' in the savefile.
/LITERAL saves statements as they are typed. The
major difference between this and the SAVE without
the option is that, in the former case the results of
COMPARE statements are saved, whereas with this
option the COMPARE statement with the list of species
is saved. All SAVEs are ended by END.
NOTES:
Not all statements are saved. The statements
saved are those which affect searches: AND, OR,
NOT, CONSISTENCY, COMPARE, END, INPUT, OUTPUT, and
FIND. If /LITERAL is included all statements are
saved as they are typed, except EXECUTE and CATALOG.
When a SAVE is started if the memory was not cleared
by the CLEAR statement, a warning will be printed
and the memory will be cleared.
If a duplicate FileName is found in the library you
will be prompted to rename this SAVE.
If a search is being saved and you save a new one,
the old search will be ended.
RELATED COMMANDS: CATALOG, EXECUTE, GET, COMPARE/KEEP
SOURCES: SOURCES REQUIRED: SO
PURPOSE:
Sets the minimum number of sources to be considered
in all searches after this command is issued (default
is 1).
SYNTAX:
SOURCES ##
EXAMPLE
SOURCES 5
Only organisms which have 5 sources will be
considered when searching the data base.
TERMINAL: TERMINAL REQUIRED: TE
PURPOSE:
Sets the width of the TERMINAL.
SYNTAX:
TERMINAL [WIDTH {WIDE NARROW}]
V-16
-------
EXPLANATION:
If WIDTH is omitted the next time WIDTH is called it
will affect the TERMINAL. If WIDTH is included, you
must include either WIDE, 132 columns, or NARROW, 72
columns.
RELATED COMMANDS: LINEPRINTER
TIME: TIME REQUIRED: TI
PURPOSE:
TIME prints the time you have left in the time
sharing session. Or it can be used to determine how
much time a statement takes to execute.
SYNTAX
TIME {[ON] [OFF]}
EXPLANATION:
TIME ON displays the CPU time of searches as they
execute. TIME OFF (default) turns off this feature.
This is the default. TIME prints the CPU time
remaining for the logon session in seconds.
USE: USE REQUIRED: US
PURPOSE:
Selects the data summary to be searched. Searches
from the AND summary consider information common to
all sources for each organism. Searches from the OR
summary use all available information on each
organism.
SYNTAX:
USE {AND OR}
EXPLANATION:
All searches and comparisons made after this will use
the summary which was chosen. The OR summary is the
default. Use of the AND summary may substantially
reduce the amount of information available during
searches.
EXAMPLE:
USE AND
After this, when a search is performed, the
information examined will be the information
upon which all authors agreed for each
species.
V-17
-------
WAIT: WAIT REQUIRED: WA
PURPOSE:
WAIT changes the number of lines displayed on your
terminal, to prevent information from scrolling off
the top of a Video Display Terminal.
SYNTAX:
WAIT {['«] [ON] [OFF]}
EXPLANATION:
Causes the terminal to wait after ## lines for the
user to enter a to terminate a listing or
a to continue listing. The default is 20
lines. WAIT OFF lists without stopping, WAIT ON
restores last wait value used.
WIDTH: WIDTH REQUIRED: WI
PURPOSE:
To change the number of columns which are displayed
on your terminal or printer at the lineprinter.
SYNTAX:
WIDTH {WIDE NARROW}
EXPLANATION:
A WIDTH must be specified: use WIDE, 132 columns, or
NARROW, 72 columns. The device affected is the last
device changed (default is terminal). See TERMINAL
or LINEPRINTER.
RELATED COMMANDS: TERMINAL, LINEPRINTER
XOR: XOR REQUIRED: X SYNONYMS: DIFFERENCE
PURPOSE:
Compares two search results and returns a list
containing the species or categories which were in
one list or the other but not in both lists.
SYNTAX:
## XOR ##
NOTE:
If the first list is omitted the default would be to
use the entire data base, identical to NOT ##
RELATED COMMANDS: AND, OR, NOT, DIFFERENCE, &, |, ~
V-18
-------
?: ? REQUIRED: ? SYNONYMS: HELP
PURPOSE:
An alternative form of help.
SYNTAX:
Refer to HELP
&: & REQUIRED: & SYNONYMS: AND
PURPOSE:
An alternative form of AND.
SYNTAX:
Refer to AND
RELATED COMMANDS: AND, OR, NOT, XOR, DIFFERENCE, |, ~
|: | REQUIRED: | SYNONYMS: OR
PURPOSE:
An alternative form of OR.
SYNTAX:
Refer to OR
RELATED COMMANDS: AND, OR, NOT, XOR, DIFFERENCE, &, ~
~: ~ REQUIRED: ~ SYNONYMS: NOT
PURPOSE:
An alternative form of NOT.
SYNTAX:
Refer to NOT
RELATED COMMANDS: AND, OR, NOT, XOR, DIFFERENCE, &, |,
V-19
-------
Program Messages
SEARCH LIST DOES NOT EXIST, RE-ENTER-
This message was caused by typing a search number which has not
yet been done. Re-enter the number of the desired search. The
remainder of the command has not been discarded and will be
processed when a valid number is entered.
COMMAND CANNOT BE USED IN PRESENT CONTEXT.
A command was typed which was not used in a way understandable
by the programs command interpreter.
MORE/E->
If you have included the /CONTINUE option on a command you will
be prompted with this message to enter more lines or to enter
/END to execute the command that you have entered. If you use
the COMPARE command and forget to enter any species, you will be
prompted with this message automatically.
ERROR - LIST DOES NOT EXIST.
The search number specified on the right side of an AND, OR, or
NOT did not exist. The line was discarded and must be
re-entered.
SEARCH HAS NO CODES FOR THIS DATA BASE.
All of the codes which were entered are not in the data base and
the search will result in zero entries. This is a warning, and
may appear if searches are run between data bases using the
result of the COMPARE command.
STACK OVERFLOW - CAN'T CONTINUE, CLEAR STACK.
This is caused when the results of your searches exceed 1,000
entries or if you attempt to run more than 20 searches. To
correct this situation type CLEAR.
ERROR IN OPTION - ASSUMING SHORT LISTING
An option other than /FULL was entered. The search
will proceed as if no option was entered.
ERROR - INVALID OPTION IGNORED.
An option was entered on the FIND command which could not be
interpreted. The option was discarded and execution will
continue.
V-20
-------
NOTHING TO FIND? - RE-ENTER LINE.
FIND was entered without a taxonomic name. The command has
stopped and it must be re-entered correctly.
CAN'T FIND 'GENUS-SPECIES'.
The entry you tried to find does not exist in the data base.
The name, in apostrophes, was the name which was searched for.
NO NEWS AVAILABLE.
There is no news section in the help file. If the HELP command
does not work, there is a problem which should be reported to
us.
ENTER USE PARAMETER-
The USE command was entered without the AND or the OR parameter.
One of the two must be entered. If a bad parameter was entered
this message will prompt you to enter a valid parameter. A
cancels this command.
BAD SYNTAX OR TERM.
An unidentified term was entered after the USE command.
NOT A VALID USE PARAMETER.
A command was entered after USE but it was not AND or OR.
ENTER TERMINAL/FILE ## -
INPUT was entered without specifying TERMINAL or UNIT ##.
ERROR - 'xxxxxxx' NOT A DEVICE.
The name entered after INPUT or OUTPUT was not a device:
TERMINAL, LINEPRINTER, or a UNIT ##.
CAN'T READ FROM LINEPRINTER.
LINEPRINTER is an output device only.
ENTER TERMINAL/LINEPRINTER/FILE ## -
OUTPUT was entered without specifying TERMINAL, LINEPRINTER, or
a valid UNIT ##.
ERROR - SOURCES MUST BE FOLLOWED BY NUMBER.
V-21
-------
The SOURCES command was entered without specifying the number of
sources to be consided. The command is discarded and the
sources are unaffected.
NOT A VALID WAIT OPTION.
The WAIT command was entered with an incorrect option. The valid
options are ON, OFF or a number. The line is discarded.
ENTER WIDTH(WIDE/NARROW)-
WIDTH was entered without either WIDE (132 columns) or NARROW
(72 columns). One of these terms must be entered.
UNRECOGNIZED WIDTH OPTION.
An option was entered after the WIDTH command which is invalid.
The only valid options are WIDE or NARROW.
ERROR - PRINT OPTION IGNORED.
An option other than /OFFLINE or /COMMON was entered on the
PRINT command and was discarded. The command will execute.
ENTER FILE NAME, OR TO CANCEL-
SAVE was entered without a search name. A name must be entered.
If a is entered then the command is canceled.
NOTICE - SAVE ENDED LAST SEARCH.
If you were saving a search and have typed save again, the
current search will be ended and a new search will be started.
LIBRARY MEMBER FileName EXISTS - RENAME MEMBER.
The name you want to use is already in use, the search will need
a new name. You will be prompted to provide a new name.
WARNING - STACK LEVEL IS NOT 1, IT WILL
BE RESET, TO CONTINUE, TO CANCEL->
The search memory must be at 1 to begin saving searches. If
you do not type a the memory will be cleared and the search
will be started.
WRITE ERROR IN LIBRARY FILE.
This error should not occur. You will need to contact us if it
does.
V-22
-------
ERROR - SEARCH MAY NOT BE EXECUTED DURING SAVE.
This warning is printed if you attempt to execute a saved search
while saving a search. This prevents you from executing the
search that you are saving.
ENTER FILE NAME-
You are being prompted for the name of the saved search you wish
to execute. If you enter an incorrect name or a blank line the
library of searches will be cataloged for you.
CAN'T FIND FileName IN LIBRARY.
The name of the search you wish to execute does not exist. A
catalog of the library will be printed for you.
ERROR - CATALOG MAY NOT BE EXECUTED DURING SAVE.
Just a warning message to prevent a CATALOG during a search.
The CATALOG would cause the file to be damaged if it were
performed during a SAVE, so it is not allowed.
NO FILES IN LIBRARY.
The library file contains no saved searches.
ERROR - CAN'T FIND SPECIES, RE-ENTER LINE:
ERROR AT:XXXXXXXX
The COMPARE or DEFINE command has not been able to interpret
your input line. The error is listed in the line after the
colon. The line that has been printed out has been discarded
and you will now be prompted for more information with the
prompt MORE/E->.
CAN'T FIND Genus-Species.
The COMPARE or DEFINE command could not locate the species
listed and was discarded. The remainder of the line will be
processed, and you will be prompted for more input, giving you
an opportunity to correct the error.
ENTER YOUR NAME AND MAILING ADORESS(3 LINES FOR ADDRESS)
NAME>
ADR1>
ADR2>
ADR3>
The first time offline output is specified you will be prompted
V-23
-------
for the information listed above. It is necessary so that your
printout can be sent to you. The computer will use the first 30
characters of each line.
ENTER TO CONTINUE, TO CANCEL.
The number of lines specified in the WAIT command has been
listed on your screen. This gives you the opportunity to
inspect the output printed thus far or to cancel a listing if
desired.
ERROR - CATEGORY 'XX' IS INVALID.
The category entered is not correct and the term will be
discarded.
ERROR - CODE 'XXrXXXXXX' IS NOT VALID.
The code is not valid and the term will be discarded.
ERROR - '/X' IS NOT A VALID OPTION.
The option which you have selected is not valid and it will be
discarded.
ERROR - COMMAND 'XXXXXXXXXXXX' IS AMBIGUOUS.
The command that has been entered does not contain enough
letters to determine which of several commands it might be. The
line will be discarded.
ERROR - 'XXXXXXXXXXXX' IS NOT A COMMAND.
The line entered is not recognized as a command and it is
discarded.
ERROR - OPTION 'XXXXXX' IS AMBIGUOUS.
The option on the QUALIFY command contains too few characters to
evaluate. The line is discarded.
ERROR - 'XXXXXX' IS NOT AN OPTION.
The option specified is not valid and will be discarded.
BAD TAXON, ASSUMING GENUS.
The taxonomic level you specified is not supported in the FIND
or LEVEL command.
ERROR - THIS COMMAND MAY ONLY BE USED ON TWO SEARCH STATEMENTS.
V-24
-------
The XOR or DIFFERENCE must only be used with search statements
and category codes are not allowed.
NOTHING TO PRINT - SEARCH DOES NOT EXIST.
Print was used on a search number that did not exist.
Error esages fro* run time errors beyond the control of the user.
If any of the following messages appear we need to be informed
so that they may be corrected.
FATAL ERROR - DATA SPACE EXCEEDED.
WARNING - DATA FILE IS TOO LARGE.
This error will appear only if the data file was too large to
load completely. Some of the data will not be searchable.
ERROR - EOF ENCOUNTERED IN CODES.
ERROR - GETCID FUNCTION HAS READ PAST EOF
V-25
-------
SECTION VI
EPAEDIT PROGRAM
The EPAEDIT program is an interactive editor for ERAPT RAW DATA files.
It can be used to add, delete, or replace environmental data, sources,
and taxonomic entries and search for and display environmental
information by scientific or common name or data source.
Abbreviations .and. Syntax
All commands and parameters may be abbreviated as single characters and
each argument of a command must be separated by a blank space. If a
blank must be included in a compound argument, then an underscore
character is used to represent the blank space. Since all operands may
be abbreviated as single characters, their order is critical. In
general, the command and its first argument must be included. The user
will be prompted for any remaining information that is necessary.
Throughout this manual several conventions are used in the command
syntax.
Braces {}. Mutually exclusive arguments are enclosed in braces, {}.
Brackets [ J. Optional arguments are enclosed in brackets, [ J.
Numeral Signs #. All numeric arguments are represented using a
number sign, #, with each symbol representing a digit. An
argument with a range from 0 to 99 would be shown as ##
whereas a range of 0 to 9 would be #.
Arrows <>. The symbols <> are used to represent keys on the
terminal. is the enter or return key.
Apostrophes ". All variable information is shown enclosed in
apostrophes. Apostrophes should not be used when this
information is entered.
Program Commands
The editor uses the following commands: Add, Bottom, Citation, Delete,
End, Find, Help, List, New, Replace, Show, Top. The command description
and examples are listed alphabetically. All entered lines must be ended
by pressing .
VI-1
-------
Program Cpnmnand Descriptions
Add: Add is used to incorporate additional information from a pre-
viously defined data source into a taxon. You will be prompted to
enter environmental codes. To quit entering codes enter a blank
line by typing .
Add {Author ['Source-code']}
(Codes ['Source-code')}
Author: Key word to indicate that a new source is to be added.
The 'Source-code' must exist in the data base and may not
exist in the record which is being modified.
Codes: Key word to indicate that data is to be added to a source
which exists both in the data base and in the record.
'Source-code' is a 1 to 8 character code indicating the reference
source which is stored in the SOURCES file.
The command will prompt for the category codes to add with the
message 'Code: '. Category codes may be entered on the line
followed by a . Prompting will continue until a blank
line is entered.
Bottom: Bottom is used to go to the end of the data file.
Citation: Citation is used to list the source for the keyword entered
after the command. If no keyword is entered then the last keyword
is used.
Citation 'Source-code'
'Source-code' is a 1 to 8-character code indicating the reference
which is to be retrieved from the SOURCES data file. The code
does not have to match any code in the file exactly. If the
letter L is entered then the citation returned will begin with the
letter L. If Citation is entered again without any 'Source-code'
then the next citation beginning with an L will be displayed.
VI-2
-------
Delete: Delete is used to delete a taxonomic entry or source and its
associated data, or a data value from the data base.
Delete {Taxa}
{Author} ['Source-code']}
{Code} ['Source-code' ['Category-code'JJ}
Taxa: Indicates that the entire record and all information
associated with it will be deleted. The entry is not
deleted immediately, but is marked for deletion by
changing its level to 100. When the data editing is
finished the new file will not contain this record. If a
record was accidently marked for deletion the record may
be restored by replacing its level information with the
proper taxonomic level.
Author: Indicates that a source is to be removed as well as all
of its data. If the 'Source-code' is not entered you
will be prompted for it. If all sources are to be
deleted it is easier to replace the taxonomic level with
a positive value. This will have the same effect as
deleting all of the sources.
'Source-code' is a 1 to 8-character code indicating the
reference which is stored in the SOURCES file.
Code: Indicates that a 'Category-code' within one 'Source-code'
is to be removed. If either of these two arguments is
omitted you will be prompted for it.
'Category-code' is a 1 to 8-character code indicating the
environmental category.
End: End is used to terminate an editing session. The data with the
editing changes may be saved or discarded. If no changes are made
then the data will not be saved.
End
{Save}
{Quit}
Save: Used to indicate that a new copy of the data base is to
be written out to a file specified by the OUTFILEO
argument on the editing command. The default file name
is R.DEPAEDIT.SAVE. This file may not be re-edited until
it is renamed and stored in the Partitioned dataset.
Quit: Used to indicate that no new data set will be written out,
thereby discarding all changes that have been made.
VI-3
-------
Find: Find is used to locate a species by its common or scientific name
or to locate a source. All searches begin with the present
position in the data base. If Find is entered without any
arguments then the last Find is repeated until the bottom of the
data base is reached.
Find {Taxa 'Taxonoraic-name'}
{Name 'Scientific-name'}
{Author 'Source-code'}
Taxa: Indicates that the next parameter will be a taxonomic
name, and the first occurence of that name should be
located. The 'Taxonomic-name' is searched by assuming
that the characters entered are the first characters in
the name, i.e. if the characters ES are entered then
Eaox will be found, but evides will not be found.
Name: Indicates that the next parameter will be a common name
or a portion of a common name, and that the next name
containing this sequence will be located. The sequence
of characters may occur anywhere in the name.
Author: Indicates that the next parameter will be a source code,
and the first occurence of that code will be located.
Help: Help is used to obtain information on the use of commands.
Help ['Command-name'J
List: List is used to list a range of lines in the data base.
List # Line indicated.
# # Lines within the range of #-# in the order indicated.
* # Lines forward beginning with the current position.
+# Lines forward beginning with the current position same
as * #.
-# Lines backward from the current position.
New: New is used to add a new reference to the source table. No
sources may be added until their codes are inserted in the source
table. The source data base still needs to be updated with the
reference information.
New ['Source-code']
'Source-code' is a 1 to 8-character code indicating the reference
which is stored in the SOURCES file.
VI-4
-------
Replace: Replace is used to change any parameter in the data base. The
code or source to be replaced must be unique within a record.
Replace {Taxa ['Taxonomic-name'J}
{Name ['Common-name']}
{Level ['level-number']}
{Author t'Old-Source-code' ['New-Source-code'J ]>
{Code ['Source-code' ['Old-code' ['New-code'JJ ]}
Taxa: Allows for a taxonomic name to be changed without
affecting its data.
Name: Allows replacement of the common name.
Level: Allows the level of an entry to be changed. The levels
are represented by their numeric codes. Frequently used
levels are: Genus, 25; Species, 15; Subspecies, 10. The
level of an entry may be changed to remove it from the
deletion list. If a taxon was marked for deletion it
will have a level of 100. If all of the information for
a taxon is to be deleted, the sign of the level must be
changed to positive.
Code: Allows the replacement of single category codes.
Show: Show is used to display information for a taxonomic level.
Show {Authors}
{Codes}
{Author 'Source-code'}
{Code 'Category-code'}
Authors: List all sources for a species. If the optional argument
'Source-code' is included then only the data for that
source is shown.
Codes: Display all sources and their associated codes. If the
optional argument 'Category-code' is included, then all
sources who reported that code will be displayed.
Top: Top is used to go to the beginning of the data file.
VI-5
-------
SECTION VII
SYSTEM ACCESS AND IMPLEMENTATION
Hardware and Software Requirements
The ERAPT Retrieval and Analysis System was developed for an IBM
370/3033 computer system at the University of Notre Dame. This system
uses the MVS (multiple virtual storage) operating system, with extended
TSO (time sharing option). The minimum region size requirement for
running interactive ERAPT system programs is 512K. All main frame
programs in the ERAPT system are written in the FORTRAN 77 Language and
have been compiled using the IBM VSFORTRAN compiler. In the interest of
program portability, IBM extensions to the ANSI FORTRAN 77 Language
have been avoided.
Programs for entry of environmental data for the ERAPT system were
developed for the Radio Shack TRS-80 Color Computer running under the
Extended BASIC Operating System Version 1.0 with 32 K of RAM. A Radio
Shack TRS-80 X-PAD digitizing table, interfaced with the Color Computer
was used to input environmental data from standard forms. All
microcomputer programs were written in the TRS-80 Extended Disk BASIC
language.
Accessing University of Notre Dame Computer System
The ERAPT retrieval and analysis system can be accessed on the
Univerity of Notre Dame computer system from ASCI computer terminals
over telephone lines at 300 or 1200 baud. The Notre Dame computer may
also be accessed through the Telenet telecommunications network. The
computer is generally available from 8:00 AM until 2:00 AM, Monday
through Friday, 8:00 AM to midnight Saturday, and after 4:00 PM on
Sunday, Eastern Standard Time. For information on how to establish a
Notre Dame Computer account or technical assistance on the ERAPT system
contact R. A. Hellenthal (Phone 219-239-7255).
To logon to the Notre Dame Computer dial 219-283-2411 and wait for
the computer to answer with a carrier signal. When accessing the system
at 300 baud an "@" symbol will usually appear at the terminal when a
connection to the computer has been established. No connect symbol will
appear when the system is accessed at 1,200 baud. After a connection
with the computer has been established, wait about 5 seconds and then
press the zero key. After a few seconds, the message, "ENTER LOGON-"
should appear at the terminal. Respond to this by typing:
LOGON tsoid ID(0212)
VII-1
-------
followed by pressing the RETURN key. "Tsoid" represents a valid account
number for the University of Notre Dame computer. As part of the logon
operation you should receive a message indicating that you have been
attached to the Biology Command Library. The ERAPT may now be entered
following any "READY" system response.
Running the ERAPT Retrieval and Analysis Program
The ERAPT command is used to initiate the ERAPT retrieval and
analysis program. Only the basic options required for program execution
are described below. More detailed information on the operation and
syntax of this command are provided in the section on ERAPT System
Commands. In the following command descriptions, parameters not
displayed in apostrophes must be entered as they appear, text displayed
in apostrophes is replaced by an appropriate name or operand , and
information displayed in brackets is optional. Neither brackets nor
apostrophes may be entered as part of the command.
Syntax:
ERAPT 'database' [Savefile('name') ] '
'database' - the ERAPT data base to be used in search and
evaluation operations. The following
databases are currently available:
FISH - Fishes of E.P.A. Region 5
BLGR - Blue-green algae
CHIR - Chironomidae (midges)
DIAT - Diatoms
EPHE - Ephemeroptera (mayflies)
PLEC - Plecoptera (stoneflies)
tSavefile('name') ] - an optional parameter which specifies
the 'name' of a file to be used for the
storage and retrieval of saved searches. If
the SAVEFILE operand is omitted and a search
is saved you will be prompted to enter a name
for this file. The file name must begin with
a letter, may not be more than 8 characters
long, and may not contain punctuation marks
or special symbols.
VII-2
-------
Example:
ERAPT FISH SAVEFILE(SEARCH)
The ERAPT program will be run and the fish data base will be
accessed. The library SEARCH will be used to store and execute
search expressions.
ERAPT FISH
The ERAPT program will be run and the fish data base will be
searched but no search library will be attached.
ERAPT System Commands
The following commands are used to execute the ERAPT system programs
on an IBM 370/3033 computer system running the Time Sharing Option
(TSO). These TSO commands provide a variety of run time options for the
ERAPT programs and provide an interface between the user and resources
available to the computer. The main operations which the TSO command
lists perform are the allocation of files necessary to run the programs;
the loading and execution of the ERAPT programs; the writing and sub-
mission of background jobs, in OS/V S2 MV S Job Control Language (JCL) , to
perform various tasks such as printing files on the line printers; and
the response to errors during the process of interpreting the commands.
ERAPT
The ERAPT command runs ERAPT program, controls the allocation of
the data base files, and submits any offline output as a batch job using
the IBM system utility program IEBGENER.
Syntax: ERAPT Database SavefileC'Filename') Lines(#) Copies(#) Update
Myprog Mydata Mycodes Prefix('Tsoid') Ppn('Tsoid') Clist
Required: Database
Defaults: Lines(2) Copies(l)
Arguments:
Database: Four character name for the file to be searched. The
file is expected to be a member of the partitioned data
set ERAPT.SRCH(Database) on either the user's account
or the default library account specified by PrefixO.
Savefile('Filename'): Indicates the name of the file to attach
into which information is saved. The file is created on
the user's account with a 'SRCH' suffix.
VII-3
-------
Lines(#): Maximum number of lines that the line printer will
print. The number indicates thousands. The default value
of 2 therefore will allow 2000 lines to be printed on the
line printer.
Copies(#): The number of copies of offline output that will be
produced.
Update: Uses the latest version of the system which may or may
not be the same as the current version in the library
account specified by PrefixO. This version is stored
in the account Ppn().
Myprog: Specifies that the account needed to find the program is
the user's.
Mydata: Specifies that the data file SRCH.DATA(database) resides
on the user's account and is to be used rather than the
data in the library account.
Mycodes: Specifies that the file ERAPT.DATA( RECODE) is to be
found on the user's account rather than in the library.
PrefixO: Specifies the default library prefix.
Ppn(): Specifies the default development account where the
program resides if Update is specified.
Clist: Will turn on CONLIST, SYML1ST, MESSAGE, and LIST to aid in
debugging the command file.
RUNOFF
The RUNOFF command runs the program RUNOFF and then uses the system
utility program IEBGENER to produce a copy of the data set on the line
printer. Special output forms and marginal line numbers may be
requested.
Syntax: RUNOFF File FormO PrefixO Fcb() LinesO LinectO Spinwriter Tn
CopiesO Clist
Required: File
Defaults: Form( STD) Pref ix(UserlD) Copies(l) Fcb() LinesO) Linect(O)
Arguments:
File: Fully qualified file name including extension. Prefix is
specified using the Prefix option if it is other than the
logon account.
FormO: Specifies the form to be used for the printout.
Fcb(): Specifies form spacing. VPPP V=lines/inch PPP=lines/page.
PrefixO: Specifies the default prefix.
LinesO: Maximum number of lines to print in thousands.
LinectO: Number of lines before a form feed is sent to the
printer. This should be left at zero since RUNOFF issues
form feed characters as needed.
VI1-4
-------
CopiesO : The number of copies of offline output that will be
produced.
Spinwriter: Specifies that the output is to be routed back to the
user's terminal.
Tn: Specifies the use of the TN (upper-lower case) print train
for the printer.
Clist: Will turn on CONL1ST, SYMLIST, MESSAGE, and LIST to aid in
debugging the command file.
EPAEDIT
The EPAEDIT command allows the EPAEDIT program to be run through
TSO and controls the file allocations.
Syntax: EPAEDIT File Outfile('Filename') Prefix('Tsoid') Clist
Required: File
Defaults: Outfile(R.DEPAEDIT.SAVE)
Arguments:
File: Four character name for the file to be searched. The
program allocates two files based on this name. The
first file is the actual data base ERAPT.DATA(FileFORM)
and the second is ERAPT.DATA(FileAUTH) containing the
reference information. Both of these files reside on the
prefix specified by PrefixO.
Outfile(): Specifies the file which will be written if End Save
is used to terminate the program. The command will not
allow an existing data file to be re-written.
PrefixO: Specifies the default library prefix.
Clist: Will turn on CONL1ST, SYMLIST, MESSAGE, and LIST to aid in
debugging the command file.
VII-5
-------
SECTION VIII
ENVIRONMENTAL RETRIEVAL CODES
BIOLOGICAL CHARACTERISTICS
Stage - Stage or stages to which source of data refers. [OlOSTl (FISH,
CHIR 1)
Eggs - Source data refers to egg stage. [020EGGS] (FISH, CHIR 1)
Larvae - Source data refers to larval stage or young of year fishes.
[020LARVA] (FISH, CHIR 2)
Juvenile - Source data refers to juvenile stage. 1020JUVENI] (FISH)
Smolt - Source data refers to smolt stage. [020SMOLT] (FISH)
Pupa - Source data refers to pupal stage. [020PUPA] (CHIR 3)
Adult - Source data refers to adult stage. [020ADULT] (FISH, CHIR
4)
Abundance - Typical abundance of adults. [010AB] (FISH)
Abundant - Expected in most habitats within its range and often
the dominant species; expected in all collections.
[020ABUNDA] (FISH)
Common - Expected in many habitats of its range but present in
moderate numbers; usually collected. [020COMMON]
(FISH)
Uncommon - Only occasionally present in habitats within its
geographic range or present in small numbers; often not
collected. [020UNCOMM] (FISH)
Rare - Occurs only in small number of habitats within its geographic
range, but sometimes may be abundant in those habitats.
[020RARE] (FISH)
Pollution Tolerance - Tolerance to decomposable organics. tOlOPT]
(FISH, CHIR 5, DIAT 4, EPHE 3, PLEC 3, BLGR 2)
Saprophilic - Usually in organically polluted waters but also in
clean waters. [020SAPHIL] (FISH, CHIR 20, DIAT 25,
EPHE 11, PLEC 11, BLGR 12)
Facultative - Wide tolerance to organic pollution. [020FACULT]
(FISH, CHIR 21, EPHE 12, PLEC 12)
Saproxenous - Usually in clean waters but also in organically
polluted [020SAXENO] (FISH, CHIR 22, DIAT 26, EPHE 13,
PLEC 13, BLGR 13)
Saprophobic - In water that has not been exposed to organic
pollutants. 1020SAPHOB] (FISH, CHIR 23, DIAT 27, EPHE
14, PLEC 14, BLGR 14)
Optimal Growth Period - Season of optimal growth. [010GP] (FISH, DIAT
8, BLGR 8)
Winter - Optimal growth in winter. [020WINTER] (FISH, DIAT 51, BLGR
60)
VIII-1
-------
Spring - Optimal growth in spring. [020SPRING] (FISH, DIAT 52, BLGR
61)
Summer - Optimal growth in summer. [020SUMMER] (FISH, DIAT 53, BLGR
62)
Autumn - Optimal growth in autumn. [020AUTUMN] (FISH, DIAT 54, BLGR
63)
Reproductive Season - Period of reproduction or sexual maturity.
[010RS] (FISH, CHIR 12, EPHE 10, PLEC 10)
Winter - Reproduction or sexual maturity in winter. [020WINTER]
(FISH, CHIR 61, EPHE 45, PLEC 45)
Spring - Reproduction or sexual maturity in spring. [020SPRING]
(FISH, CHIR 62, EPHE 46, PLEC 46)
Summer - Reproduction or sexual maturity in summer. [020SUMMER]
(FISH, CHIR 63, EPHE 47, PLEC 47)
Autumn - Reproduction or sexual maturity in autumn. [020AUTUMN]
(FISH, CHIR 64, EPHE 48, PLEC 48)
Reproductive Behavior - [01ORB] (FISH)
Complex - Prepare nest or tend eggs. [020COMPLE] (FISH)
Simple - No nest preparation or tending of eggs. [020SIMPLE] (FISH)
Lithophil - Rocks or gravel preferred. [020HTHOP] (FISH)
Phytophil - Plants preferred. [020PHYTOP] (FISH)
Peliphil - Sand, silt, or mud preferred. [020PELIPH] (FISH)
Xylophil - Wood or debris preferred. [020XYLOPH] (FISH)
Pelagophil - Eggs released in open water. [020PELAGO] (FISH)
Speleophil - Holes, cavities, or burrows preferred. [020SPELEO]
(FISH)
Internal - Internal fertilization. [020INTERN] (FISH)
Polyphil - No preferred substrate. [020POLYPH] (FISH)
Feeding Behavior - [010FB] (FISH, CHIR 13, EPHE 11,PLEC 11)
Predator - Feeds primarily on animals. [020PREDAT] (FISH, CHIR 65,
EPHE 49, PLEC 49)
Piscivore - Feeds primarily on fish. [030PRPISC] (FISH)
Invertivore - Feeds primarily on macroinvertebrates.
[030PR1NVE] (FISH)
Planktivore - Feeds primarily on microinvertebrates.
[030PRPLAN] (FISH)
Herbivore - Feeds primarily on plants. [020HERBIV] (FISH, CHIR 66,
EPHE 50, PLEC 50)
Grazer - Feeds primarily on aufwuchs. [030HEGRAZ] (FISH)
Browser - Feeds primarily on macrophytes. [030HEBROW] (FISH)
Omnivore - Regularly feeds on both plants and animals. [0200MNIVO]
(FISH, CHIR 67, EPHE 51, PLEC 51)
Scavenger - Regularly feeds on non-living animal matter.
[020SCAVEN] (FISH, CHIR 68, EPHE 52, PLEC 52)
Detritivore - Typically feeds on nonliving plant material.
[020DETRIT] (FISH)
Shredder - Feeds on coarse particulate organic matter.
[030SHREDD]
Collector - Feeds on fine particulate organic matter.
[030COLLEC]
VIII-2
-------
Parasite - Feeds on host organisms for food, sometimes resulting in
the death of the host. [020PARASI] (FISH)
CHEMICAL CHARACTERISTICS OF HABITAT
Hardness - Hardness of water measured as mg/1 CaC03. [010HA] (FISH)
Non-calcareous and Acid - Total hardness < 20 mg/1 CaC03.
[020NONCAL] (FISH)
Slightly Calcareous - Total hardness 20-100 mg/1 CaC03. [020SLIGHT]
(FISH)
Moderately Calcareous - Total hardness 100-200 mg/1 CaC03.
[020MODERA] (FISH)
Highly Calcareous - Total hardness > 200 mg/1 CaC03. [020HIGHLY]
(FISH)
Salinity - Dissolved salt concentration for habitat. [010SA] (FISH,
CHIR 3, DIAT 3, BLGR 4)
Poly- or Euhalobous - Marine forms, salt concentration > 30,000
mg/1. [020POLEUH] (FISH, BLGR 22)
Polyhalobous - Salt concentration > 40,000 mg/1. [030POPOLY]
(FISH, CHIR 11, DIAT 10)
Euhalobous - Marine forms, salt concentration 30 ,000-40 ,000
mg/1. [030POEUHA] (FISH, CHTR 12, DIAT 11)
Mesohalobous - Brackish-water forms, salt concentration 500-30,000
mg/1. [020MESOHA] (FISH, CHIR 13, DIAT 12, BLGR 23)
Alpha Mesohalobous - Alpha range, salt concentration 10,000-
30,000 mg/1. [030MEALPH] (FISH, DIAT 13, BLGR 24)
Beta Mesohalobous - Beta range, salt concentration 500-10,000
mg/1. [030MEBETA] (FISH, DIAT 14, BLGR 25)
Oligohalobous - Freshwater forms, salt concentrations < 500 mg/1.
[0200LIGOH] (FISH, CHIR 14, DIAT 15, BLGR 26)
Halophilous - Stimulated by small amounts of salt, range 150-500
mg/1. [0300LPHIL] (FISH, DIAT 16, BLGR 27)
Haline Indifferent - Tolerates small amounts of salt, range
50-150 mg/1. [0300LINDI] (FISH, DIAT 17, BLGR 28)
Halophobous - Does not tolerate small amounts of salt, < 50
mg/1. [0300LPHOB] (FISH, DIAT 18, BLGR 29)
Euryhalinous - Occurs under broad range of salt concentrations.
[020EURYHA] (FISH, CHIR 15, DIAT 19, BLGR 30)
Nutrients - Characteristic nutrient concentrations. [OlONU] (FISH, CHIR
4, DIAT 2, EPHE 2, PLEC 2, BLGR 3)
Hypereutrophic - Characteristic of extreme eutrophic conditions:
total P > 100 ug/1, inorganic N > 1500 ug/1, organic N
> 1200 ug/1. [020HYPERE] (FISH, BLGR 16)
Eutrophic - High nutrient concentrations: total P 30-100 ug/1,
inorganic N 500-1500 ug/1, organic N 700-1200 ug/1.
[020EUTROP] (FISH, CHIR 16, DIAT 6, EPHE 7, PLEC 7,
BLGR 17)
VIII-3
-------
Mesotrophic - Moderate nutrient concentrations: total P 10-30 ug/1,
inorganic N 300-650 ug/1, organic N 400-700 ug/1.
[020MESOTR] (FISH, CHIR 17, DIAT 7, EPHE 8, PLEC 8,
BLGR 18)
Oligotrophic - Low nutrient concentrations: total P 5-10 ug/1,
inorganic N 200-400 ug/1, organic N 200-400 ug/1.
[0200LIGOT] (FISH, CHIR 188, DIAT 8, EPHE 9, PLEC 9,
BLGR 19)
Ultraoligotrophic - Extremely low nutrient concentrations: total P
< 5 ug/1, inorganic N < 200 ug/1, organic N < 200 ug/1.
[020ULTRAO] (FISH)
Dystrophic - Rich in huraic materials. [020DYSTRO] (FISH, CHIR 19,
DIAT 9, EPHE 10, PLEC 10, BLGR 20)
Eurytrophic - Indifferent to inorganic nutrient content.
[020EURYTR] (FISH, BLGR 21)
Degradable OrganicB - Typical association with degradable dissolved
organics. [0100RJ (FISH, DIAT 4, BLGR 2)
Polysaprobic - Zone of degradation and putrefaction, 02 < 1 mg/1.
[020POLYSA] (FISH, DIAT 20, BLGR 7)
Mesosaprobic - Zone where oxidation of organic load is proceeding,
[020MESOSA] (FISH) 02 1-3 mg/1. (DIAT 21, BLGR 8)
Alpha Mesosaprobic - Alpha range of pollution, nitrogen as amino
acids. [030MEALPH] (FISH, DIAT 22, BLGR 9)
Beta Mesosaprobic - Beta range of pollution, nitrogen as ammonia
compounds. [030MEBETA] (FISH, DIAT 23, BLGR 10)
Oligosaprobic - Oxidation of biodegradables complete, high
inorganics, 02 > 3 mg/1. [0200LIGOS] (FISH, DIAT 24,
BLGR 11)
pfl - Negative logarithm of hydrogen ion activity. [010PH] (FISH, CHIR
2, DIAT 1, EPHE 1, PLEC 1, BLGR 1)
Acidobiontic - pH < 5.5. [020ACIDOB] (FISH, CHIR 5, DIAT 1, EPHE
1 , PLEC 1 , BLGR 1)
Acidophilous - pll 5.6-6.5. [020ACIDOP] (FISH, CHIR 6, DIAT 2, EPHE
2, PLEC 2, BLGR 2)
Neutral - ph 6.6 - 7.5. [020NEUTRA] (FISH, CHIR 7, DIAT 3, EPHE 3,
PLEC 3)
Alkaliphilous - pH 7.6-8.5. [020ALKALP] (FISH, CHIR 8, DIAT 4, EPHE
4, PLEC 4, BLGR 4)
Alkalibiontic - pH > 8.5. [020ALK.ALB] (FISH, CHIR 9, DIAT 5, EPHE
5, PLEC 5, BLGR 5)
pH Indifferent - Not pH dependent, found in acid, neutral, and
alkaline waters. [020INDIFF] (FISH, CHIR 10, BLGR 3,
EPHE 6, PLEC 6)
Oxygen - Dissolved oxygen requirements for reproduction and growth.
[0100X] (FISH, CHIR 6, EPHE 4, PLEC 4)
Euoxyphilous - High oxygen concentration, 02 > 7.5 mg/1. (saturated)
[020EUOXYP] (FISH, CHIR 24, EPHE 15, PLEC 15)
Mesoxyphilous - Moderate oxygen concentrations, 02 5.0-7.5 mg/1.
[020MESOXY] (FISH, CHIR 25, EPHE 16, PLEC 16)
VIII-4
-------
Oligoxyphilous - Low oxygen concentrations, 02 2.5-5.0 mg/1.
[0200LIGOX] (FISH, CHIR26, EPHE 17, PLEC 17)
Anoxyphilous - Facultative anaerobic, 02 < 2.5 mg/1. [020ANOXYP]
(FISH, CHIR 27)
PHYSICAL CHARACTERISTICS OF HABITAT
General Habitat - General type of habitat. tOlOGH] (FISH, CHIR 10, DIAT
6, EPHE 8, PLEC 8, BLGR 6)
Marine - Characteristic of oceans and seas. [020MARINE] (FISH, CHIR
43, DIAT 33)
Neritic - Occurring typically above continental shelf (close to
shore). [030MANERI] (FISH, BLGR 47)
Oceanic - Occurring typically over deeper regions of oceans.
[030MAOCEA] (FISH, BLGR 48)
Estuary - Characteristic of estuaries and brackish water habitats.
[020ESTUAR] (FISH, CHIR 44, DIAT 34, BLGR 45)
Lentic Systems - Characteristic of lakes or ponds. [020LENTIC]
(FISH, BLGR 39)
Lake - Characteristic of large inland bodies of standing water.
[030LELAKE] (FISH, CHIR 45, DIAT 35, EPHE 33, PLEC 33)
Pond - Characteristic of small bodies of lentic water with
macrophytes covering most of bottom. [030LEPOND]
(FISH, CHIR 46, DIAT 36, EPHE 34, PLEC 34)
Temporary Water - Characteristic of temporary lentic habitats.
[030LETEMP] (FISH)
Littoral - Shallow margin of lake or pond associated with
aquatic vegetation. [030LELITT] (FISH, BLGR 46)
Limnetic - Free open water in lakes and ponds. [030LELIMN]
(FISH)
Profundal - Bottom sediment of lakes below littoral zone,
consisting of exposed fine sediment free of vegetation.
[030LEPROF] (FISH)
Benthic - Occurring on bottom of lentic habitats. [030LEBENT]
(FISH, BLGR 38)
Lotic Systems - Characteristic of lotic systems. [020LOTIC] (FISH,
BLGR 43)
Stream - Characteristic of small flowing waters: width < 20.0 m,
maximum depth < 2.0 m, low flow < 100 CFS. 1030STREAM]
(FISH, CHIR 48, DIAT 38, EPHE 36, PLEC 35)
Small Stream - width 0-2.7m, maximum depth 0-0.5m, low flow
< 1 CFS. [040STSMAL] (FISH)
Medium Stream - width 2.7-7.5 m, maximum depth 0.5-1.0 m,
low flow 1-10 CFS. [040STMEDI] (FISH)
Large Stream - width 7.5-20.0 m, maximum depth 1.0-2.0 m,
low flow 10-100 CFS. [040STLARG] (FISH)
VIII-5
-------
River - Characteristic of larger flowing waters: width > 20.0 m,
maximum depth > 2.0 m, low flow > 100 CFS. [030RIVER]
(FISH, CHIR 47, EPHE 35, PLEC 36)
Small River - width 20.0-54.0 m, maximum depth 2.0-4.0 m,
low flow 100-1000 CFS. [040RISMAL] (FISH)
Medium River - width 54.0-148.0 m, maximum depth 4.0-8.0 m,
low flow 1000-10,000 CFS. [040RIMEDI] (FISH)
Large River - width > 148.0 M, maximum depth > 8.0 m, low
flow > 10,000 CFS. [040RILARG] (FISH)
Intermittent Flow - Flowing only part of year. [030INTERM]
(FISH)
Interrupted Flow - Flow passes underground at some point or
points. [030INTERU] (FISH)
Canopy Cover - Characteristic of stream with canopy covering.
[030CANOPY] (FISH)
Open - Characteristic of stream without canopy covering.
[0300PEN] (FISH)
Spring - Characteristic of springs and seepages. [020SPRING] (FISH,
CHIR 49)
Cool spring - Occurring in cool springs and seepages.
[030SPCOOL] (FISH, BLGR 41)
Hot Spring - Occurring in hot springs. [030SPHOT] (FISH, BLGR
42)
Sulphurous Spring - Occurring in sulphurous springs.
[030SPSULF]
Aerophilous - Characteristic of non-submerged habitats. [020AEROPH]
(DIAT 39, BLGR 44)
Wetland - Characteristic of bogs, swamps or marshes. [020WETLAN]
(FISH, BLGR 40)
Bog - Occurring in areas characterized by bog vegetation (e.g.,
Sphagnum) [030WEBOG] (FISH)
Swamp - Occurring in standing or slowly flowing water among
woody macrovegetation. [030WESWAM] (FISH)
Marsh - Occurring in standing or slowly flowing water among
herbaceous macrovegetation. [030WEMARS] (FISH)
Eurytopic or Euryecious - Occurring in wide variety of habitats or
environments. [020EURYTO] (BLGR 49)
Other General Habitats - Characteristic of other or unspecified
aquatic habitats. [0200THER] (CHIR 50, DIAT 40, EPHE
37, PLEC 37, BLGR 50)
Bottom Type - Bottom requirements for satisfactory growth or
reproduction. [010BT] (FISH)
Silt - Particle size 0.0039-0.0625 mm. [020SILT] (FISH)
Sand - Particle size 0.0625-2.0 mm. [020SAND] (FISH)
Gravel or Pebble - Particle size 2.0-64.0 mm. [020GRAPEB] (FISH)
Gravel - Particle size 2.0-16 mm. [030GRAVEL] (FISH)
Pebble - Particle size 16.0-64.0 mm. [030PEBBLE] (FISH)
Cobble or Rubble - Particle size 64.0-256.0 mm. [020COBBLE] (FISH)
Boulder - Particle size > 256.0 mm. [020BOULDE] (FISH)
VIII-6
-------
Bedrock or Claypan - Solid rock or clay bottom. [020BEDROC] (FISH)
(FISH)
Muck - Bottom primarily composed of FPOM. [020MUCK] (FISH)
Detritus - Bottom primarily composed of CPOM. [020DETRIT] (FISH)
Specific Habitat - Specific type of habitat. [010SH] (FISH, CHIR 11,
DIAT 7, EPHE 9, PLEC 9, BLGR 7)
Planktonic - Suspended in water. [020PLANKT] ( BLGR 51)
Euplanktonic - Normally suspended, distribution current
dependent. [030PLEUPL] (DIAT 41, BLGR 52)
Tychoplanktonic - Normally periphytic, but often suspended.
[030PLTYCH] (DIAT 42, BLGR 53)
Nektonic - Free swimming. [020NEKTON] (FISH)
Riffle or rapid - characteristic of relatively shallow, white,
turbulent or broken water. [030NERIFF] (FISH)
Run - characteristic of relatively deep, fast-moving water.
[030NERUN] (FISH)
Pool - characteristic of relatively deep, slow-moving or ponded
waters. [030NEPOOL] (FISH)
Off channel - characteristic of sloughs, backwaters, oxbows,
tempory ponds, or temporary channels. [030NEOFFC]
(FISH)
Benthic - characteristically found on or near the bottom of a
river or a stream. [030NEBENT] (FISH)
Pelagic - characteristically found in the water column as
opposed to in or on the substrate. 1030NEPELA] (FISH)
Nearshore - characteristically close to the shore or on shallow
bars of medium to large rivers. [030NENEAR] (FISH)
Periphytic - Occurring on substrate or submerged objects (Aufwuchs).
[020PERIPH] (DIAT 43, BLGR 54)
Epibenthic - Occurring on, but not penetrating substrate.
[030EPIBEN] (CHIR 51, EPHE 38, PLEC 38)
Embenthic - Occurring in substrate (penetrating). [030EMBENT]
(CHIR 52, EPHE 39, PLEC 39)
Epipelic - Occurring on or in mud and silt. [030EPIPEL] (CHIR
53, DIAT 44, EPHE 40, PLEC 40, BLGR 55)
Episabulic - Occurring on or in sand. [030EPISAB] (CHIR 54,
EPHE 41, PLEC 41)
Epilithic - Occurring on or under rocks. [030EPILIT] (CHIR 55,
DIAT 45, EPHE 42, PLEC 42, BLGR 56)
Endolithic - Growing into rocks. [030ENDOLI]
Epixylous - Occurring on or burrowing into wood. [030EPIXYL]
(CHIR 56, DIAT 46, EPHE 43, PLEC 43)
Epizooic - Occurring on or within animals. [030EPIZOO] (CHIR
57, DIAT 47)
Epiphytic - Occurring on or within plants. [030EPIPHI] (CHIR
58, DIAT 48, EPHE 44, PLEC 44, BLGR 57)
Attached - Normally sessile. [030ATTACH] (CHIR 59, DIAT 49)
Unattached - Normally free living and capable of locomotion.
[030UNATTA] (CHIR 60, DIAT 50)
VII1-7
-------
Other Specific Habitats Occurring in other or unspecified specific
habitats. [0200THER] (FISH, BLGR 58)
Retreat Builder - Builds retreat. [020RETREA]
Case Maker - Builds case. [020CASEMA]
Free Living - Does not build case or retreat. [020FREELI]
Temperature - Temperature requirements for satisfactory growth,
development, or reproduction. [010TE] (FISH, CHIR 7,
DIAT 9, EPHE 5, PLEC 5, BLGR 9)
Euthermal - Warm-water forms, temperature usually > 30 C.
[020EUTHER] (FISH, CHIR 28, DIAT 55, EPHE 18, PLEC 18,
BLGR 64)
Mesothermal - Temperate-water forms, temperature usually 15-30 C.
[020MESOTH] (FISH, CHIR 29, DIAT 56, EPHE 19, PLEC 19,
BLGR 65)
Low Mesothermal - temperature usually 15-20 C. [030MELOW]
(FISH)
Medium Mesothermal - temperature usually 20-25 C. [030MEMEDI]
(FISH)
High Mesothermal - temperatures usually 25-30 C. [030MEHIGH]
(FISH)
Oligothermal - Cold-water forms, temperature usually 0-15 C.
[0200LIGOT] (FISH, CHIR 30, DIAT 57, EPHE 20, PLEC 20,
BLGR 66)
Low Oligothermal - temperature usually 0-5 C. [0300LLOW] (FISH)
Medium Oligothermal - temperature usually 5-10 C. [0300LMEDI]
(FISH)
High Oligothermal - temperature usually 10-15 C.
(FISH)
Stenothermal - Temperature range < 5 C.
DIAT 58, EPHE 21, PLEC 21,
Metathermal - Temperature range 5-15 C.
DIAT 59, EPHE 22, PLEC 22,
Eurythermal - Temperature range > 15 C.
DIAT 60, EPHE 23, PLEC 23,
Turbidity - Characteristic turbidity of habitat.
EPHE 6, PLEC 6)
Eulichtophilous - Characteristic of low turbidity, clear water, <
100 JTU. [020EULICH] (FISH, CHIR 34, EPHE 24, PLEC 24)
Mesolichtophilous - Water generally clear, but occasionally clouded,
100-300 JTU. [020MESOLI] (FISH, CHIR 35, EPHE 25, PLEC
25)
Oligolichtophilous - Characteristic of high turbidity, murky water,
> 300 JTU. [0200LIGOL] (FISH, CHIR 37, EPHE 27, PLEC
27)
Polylichtophilous - Occurring at wide range of turbidity.
[020POLYLI] (FISH, CHIR 36, EPHE 26, PLEC 26)
Current - Current characteristics of habitat. [OlOCU] (FISH, CHIR 9,
DIAT 5, EPHE 7, PLEC 7, BLGR 5)
Limnobiontic - Characteristic of standing waters only. [020LIMNOB]
(FISH, CHIR 38, DIAT 28, EPHE 28, PLEC 28, BLGR 32)
[0300LHIGHJ
[020STENOT] (FISH,
BLGR 67)
[020METATH] (FISH,
BLGR 68)
[020EURYTH] (FISH,
BLGR 69)
[010TU] (FISH,
CHIR 31,
CHIR 32,
CHIR 33,
CHIR 4,
VIII-8
-------
Limnophilous - Usually in standing water, but may be in running
water. [020LIMNOP] (FISH, CHIR39, DIAT 29, EPHE 29,
PLEC 29, BLGR 33)
Current Indifferent - Common in both standing and flowing waters.
[020INDIFF] (FISH, CHIR 40, DIAT 30, EPHE 30, PLEC 30,
BLGR 34)
Rheophilous - Usually in running water, but may be in standing
water. [020RHEOPH] (FISH, CHIR 41, DIAT 31, EPHE 31,
PLEC 31, BLGR 35)
Rheobiontic - Characteristic of running water only. [020RHEOBI]
(FISH, CHIR 42, DIAT 32, EPHE 32, PLEC 32, BLGR 36)
GEOGRAPHIC DISTRIBUTION
Ecosystem Regions - Bailey ecoregions. [010ER] (FISH)
Polar Domain - 1000. 10201000] (FISH)
Tundra Division - 1200. [0301200] (FISH)
Arctic Tundra Province - 1210. [0401210] (FISH)
Bering Tundra Province - 1220. [0401220] (FISH)
Brooks Range Province - ML210. [040Ml220] (FISH)
Subarctic Division - 1300. [0301300] (FISH)
Yukon Parkland Province - 1310.' [0401310] (FISH)
Yukon Forest Province - 1320. [0401320] (FISH)
Alaska Range Province - M1310. [040M1310] (FISH)
Humid Temperate Domain - 2000. [0202000] (FISH)
Warm Continental Division - 2100. [0302100] (FISH)
Laurentian Mixed Forest Province - 2110. [0402110] (FISH)
Columbia Forest Province - M2110. [040M2110] (FISH)
Hot Continental Division - 2200. [0302200] (FISH)
Eastern Deciduous Forest Province - 2210. [0402210] (FISH)
Subtropical Division - 2300. [0302300] (FISH)
Outer Coastal Plain Forest Province - 2310. [0402310]
(FISH)
Southern Mixed Forest Province - 2320. [0402320] (FISH)
Marine Division - 2400. [0302400] (FISH)
Willamette Puget Forest Province - 2410. [0402410] (FISH)
Pacific Forest Province - M2410. [040M2410] (FISH)
Prairie Division - 2500. [0302500] (FISH)
Prairie Parkland Province - 2510. [0402510] (FISH)
Prairie Brushland Province - 2520. [0402520] (FISH)
Tall-grass Prairie Province - 2530. [0402530] (FISH)
Mediterranean Division - 2600. [0302600] (FISH)
California Grassland Province - 2610. [0402610] (FISH)
Sierran Forest Province - M2610. [040M2610] (FISH)
California Chaparral Province - M2620. [0402620] (FISH)
Dry Domain - 3000. [0203000] (FISH)
VIII-9
-------
Steppe Division - 3100. [0303100] (FISH)
Great Plains Short-grass Prairie Province - 3110. [0403110]
(FISH)
Palouse Grassland Province - 3120. [0403120] (FISH)
Intennountain Sagebrush Province - 3130. [0403130] (FISH)
Mexican Highlands Shrub Steppe Province - 3140. [0403140]
(FISH)
Rocky Mountain Forest Province - M3110. [040M3110] (FISH)
Upper Gila Mountains Forest Province - M3120. [040M3120]
(FISH)
Colorado Plateau Province - P3130. [040M3130] (FISH)
Wyoming Basin Province - A3140. [040M3140] (FISH)
Desert Division - 3200. [0303200] (FISH)
Chihuahuan Desert Province - 3210. [0403210] (FISH)
American Desert Province (Mojave-Colorado-Sonoran) - 3220.
[0403220] (FISH)
Humid Tropical Domain - 4000. [0204000] (FISH)
Tropical Savanna Division - 4100. [0304100] (FISH)
Everglades Province - 4110. [0404110] (FISH)
Rainforest Division - 4200. [0304200] (FISH)
Hawaiian Islands Province - M4210. [040M4210] (FISH)
Cultural Ecosystems - Initiated and maintained by man - 9000.
[0209000] (FISH)
Croplands - Perennial production - 9100. [0309100] (FISH)
Urban or Industrial - Areas dominated by construction, roads and
buildings - 9200. [0309200] (FISH)
Political Geography - Geographic distribution using US EPA regions,
states, and provinces. [010PG] (FISH, CHIR 14, EPHE
12, PLEC 12)
Region 1 (NE-N) - Northeastern US states. [020REG01] (FISH, CHIR
69, EPHE 53, PLEC 53)
CT - Connecticut. [030CT] (FISH)
ME - Maine. [030ME] (FISH)
MA - Massachusetts. [030MA] (FISH)
Nil - New Hampshire. [030NH] (FISH)
RI - Rhode Island. [030RI] (FISH)
VT - Vermont. [030VT] (FISH)
Region 2 (NE-C + PR) - Northeastern US states and other. [020REG02]
(FISH, CHIR 70, EPHE 54, PLEC 54)
NJ - New Jersey. [030NJ] (FISH)
NY - New York. [030NY] (FISH)
PR - Puerto Rico. [030PR] (FISH)
Region 3 (NE-S) - Middle Atlantic US states. [020REG03] (FISH, CHIR
71, EPHE 55, PLEC 55)
DE - Delaware. [030DE] (FISH)
MD - Maryland. [030MD] (FISH)
PA - Pennsylvania. [030PA] (FISH)
VA - Virginia. [030VA] (FISH)
WV - West Virginia. [030WV] (FISH)
VIII-10
-------
Region 4 (SE) - Southeastern US states. [020REG04] (FISH, CHIR72,
EPHE 56, PLEC 56)
AL - Alabama. [030AL] (FISH)
FL - Florida. [030FL] (FISH)
GA - Georgia. [030GA] (FISH)
KY - Kentucky. [030KY] (FISH)
MS - Mississippi. [030MS] (FISH)
NC - North Carolina. [030NC] (FISH)
SC - South Carolina. [030SC] (FISH)
TN - Tennessee. [030TN] (FISH)
Region 5 (W Great Lakes) - Western Great Lakes US states.
[020REG051 (FISH, CH1R 73, EPHE 57, PLEC 57)
IL - Illinois. [030IL] (FISH)
IN - Indiana. [030IN] (FISH)
MI - Michigan. [030MI] (FISH)
MN - Minnesota. [030MN] (FISH)
OH - Ohio. [0300H] (FISH)
WI - Wisconsin. [030WI] (FISH)
Region 6 (SC) - South Central US states. [020REG06] (FISH, CHIR Ik,
EPHE 58, PLEC 58)
AR - Arkansas. [030AR] (FISH)
LA - Louisiana. [030LA] (FISH)
NM - New Mexico. 1030NM] (FISH)
OK - Oklahoma. [0300K] (FISH)
XX - Texas. 1030TX] (FISH)
Region 7 (C) - Central US states. [020REG07] (FISH, CHIR 75, EPHE
59, PLEC 59)
IA - Iowa. [030IA] (FISH)
KS - Kansas. [030KSJ (FISH)
MO - Missouri. [030MO] (FISH)
NE - Nebraska. [030NE] (FISH)
Region 8 (Rocky Mt.) - Rocky Mountain US states. [020REG08] (FISH,
CHIR 76, EPHE 60, PLEC 60)
CO - Colorado. [030CO] (FISH)
MT - Montana. [030Ml] (FISH)
ND - North Dakota. [030ND] (FISH)
SD - South Dakota. [030SD] (FISH)
UT - Utah. [030UT] (FISH)
WY - Wyoming. [030WY] (FISH)
Region 9 ( SW + Hi, Gu) - Southwestern US states and other.
[020REG09] (FISH, CHIR 77, EPHE 61, PLEC 61)
AZ - Arizona. [030AZ] (FISH)
CA - California. [030CA] (FISH)
GU - Guam. [030GU] (FISH)
HI - Hawaii. [030HI] (FISH)
NV - Nevada. [030NV] (FISH)
VIII-11
-------
Region 10 (NW'+Ak) - Northwestern US states. [020REG10] (FISH,
CHIR 78, EPHE 62, PLEC 62)
AK - Alaska. [030AK] (FISH)
ID - Idaho. [030ID] (FISH)
OR - Oregon. [0300R] (FISH)
WA - Washington. [030WA] (FISH)
Region 11 - Eastern Canadian provinces. [020REG11] (FISH, EPHE 63,
PLEC 63)
NB - New Brunswick. [030NB] (FISH)
NF - Newfoundland. [030NF] (FISH)
NS - Nova Scotia. [030NS] (FISH)
ONT - Ontario. [0300NT] (FISH)
PEI - Prince Edward Island. [030PIE] (FISH)
QUE - Quebec. [030QUE] (FISH)
Region 12 - Western Canadian provinces and territories. [020REG12]
(FISH, EPHE 64, PLEC 64)
ALB - Alberta. [030ALB] (FISH)
BC - British Columbia. [030BC] (FISH)
MAN - Manitoba. [030MANJ (FISH)
NWT - Northwest Territories. [030NWT] (FISH)
SAS - Saskatchewan. [030SAS] (FISH)
YUK - Yukon Territory. 1030YUK] (FISH)
U.S. Environmental Protection Agency
Region 5, Library (H.-i?]) ncy
77 West Jackson Boulevard, 12th Float
Chicago, IL 60604-3590
VTII-12
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