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U.S. Geological Survey Global Change Research Program

ANALOG: A Program for Estimating Paleoclimate Parameters Using the Method of Modern Analogs

This report is preliminary and has not been reviewed for conformity with U.S. Geological Survey editorial standards (or with the North American Stratigraphic Code). Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

• UNIX analog.tgz
• Microsoft Windows analog.zip

Contents

• Background
• System requirements
• Operation
  • Run description file
    • verbose
    • basis and sample
    • distance
    • report
  • Data transformation file
    • ignore
    • new
    • arithmetic operations
• Input data formats
  • Tab-delimited ASCII
  • NAPD ASCII format
  • SPECMAP format
• Output data formats
• Error messages and warnings
• Programming notes
  • Additional file formats
• References
• Technical contact
• Appendix 1: Annotated list of included digital files
  • Source code
  • Executable code
  • Data bases
    • CLIMAP
    • NAPD
    • SPECMAP
  • Documentation

Initially the empirical relationship between climate and components of the sediment was determined using a multiple regression technique (Imbrie and Kipp, 1971). In these studies sea-floor sediments were examined to determine the percentage of various species of planktonic foraminifera present in them. Supposing that the distribution of foraminiferal assemblages depended strongly on the extremes of annual sea-surface temperature (SST), the foraminiferal assemblages (refined through use of varimax factor analysis) were regressed against the average SST during the coolest and warmest months of the year. The result was a set of transfer functions, equations that could be used to estimate cool and warm SST from the faunal composition of a sediment sample. Assuming that the ecological preference of the species had remained constant throughout the last several hundred thousand years, these transfer functions could be used to estimate SSTs during much of the late Pleistocene.

Hutson (1980) and Overpeck, Webb, and Prentice (1985) proposed an alternative approach to estimating paleoclimatic parameters. Their "method of modern analogs" revolved not around the existence of a few climatically-sensitive faunal assemblages but rather on the expectation that similar climatic regimes should foster similar faunal and floral assemblages. From a large pool of modern samples, those few are selected whose faunal compositions are most similar to a given fossil sample. Paleoclimate estimates are derived using the climatic character of only the most similar modern samples, the modern analogs of the fossil sample.

This report describes how to use the program ANALOG to carry out the method of modern analogs. It is assumed that the user has faunal census estimates of one or more fossil samples, and one or more sets of faunal data from modern samples. Furthermore, the user must understand the taxonomic categories represented in the data sets, and be able to recognize taxa that are or may be considered equivalent in the analysis.

ANALOG provides the user with flexibility in input data format, output data content, and choice of distance measure, and allows the user to determine which taxa from each modern and fossil data file are compared. Most of the memory required by the program is allocated dynamically, so that, on systems that permit program segments to grow, the program consumes only as many system resources as are needed to accomplish its task.

System requirements

• MS-DOS systems:
  • 80386 or compatible 32-bit CPU
  • 2 or more megabytes of extended memory
• Macintosh systems:
  • Macintosh System 7.0 or later
  • 2 or more megabytes of memory beyond what the system uses
• UNIX systems:
  • ANSI-conformant C language compiler

Blank lines in the run description file are ignored. Comments may be included by inserting the pound sign `#' anywhere on a line; the pound sign and all chararcters to the end of the line are considered part of the comment and are ignored by the program. Lines may begin with any number of spaces or tab characters to enhance the file's readability. Names and keywords can be in upper or lower case or a mixture, but under UNIX, file names must be given with the correct letter case, or the program won't find the files. File names should not contain braces (`{' or `}') since these indicate the grouping of items in the run description file.

The run description file consists of a sequence of keywords followed in some cases by file names or descriptive words. Items may be listed in any order, but the grouping described by braces below must be maintained. This keeps related information together. An example is shown in figure 1.

The following words are keywords, and cannot be used as the names of files:

        basis
        sample
        data
        transform
        meta
        distance
        report
        name
        closest
        verbose

The general form of the basis specification is

        basis {
            data file_name: format
            transform file_name
            meta file_name: format
            }

To include a data set in the analysis, give its group (basis or sample) followed by an opening brace, and specify the following information:

1. The keyword data, the name of the file containing the data, and (optionally) a description of the file's format. The colon, if present, must be followed by a space or tab, and the names must not contain spaces or tabs.
2. The keyword transform and the name of the file containing the transformation rules (explained below).
3. The keyword meta, the name, and format of the file containing meta data for the samples, using the same form as the data statement. At present, meta data is reported only for basis samples, so you don't need to specify a meta data file for fossil samples.

The group is delimited using braces so the program will know which transformation file and which meta data file go with each basis file. Only the data file specification is actually required; the other statements are optional but will typically be needed.

Figure 1. Information indicated in the run description file. The basis data files are shown as boxes on the left. The sample data files are shown on the right. Braces connect the raw, rule, and meta data files in the figure, but these are typically separate physical files on the disk. Results are output to the file OUTPUT.TXT, and the input data are echoed to the standard output device because verbose is specified in the run description file. This figure is available also as io.eps, an encapsulated PostScript file.

Example: To read the CLIMAP modern core-top data base as a basis, include the following text in the run description file:

        basis {
            data climap.raw: tab
            transform climap.rule
            meta climap.meta: tab
            }

        sample {
            data mycore.dat: tab
            transform mycore.rule
            }

where measure name is one of the following (the underscores must be included as shown):

        manhattan
        euclidean
        squared_euclidean
        canberra
        squared_chord
        squared_chisquared
        dot_product
        correlation
        jaccard
        sorensen

        report {
            output file_name: format
            closest number
            meta variable_name_1
            meta variable_name_2
            ...
            meta variable_name_n
            }

closest should be followed by an integer; if closest is not indicated, the value 1 is used.

meta should be followed by the name of a meta data variable, in which case the statement can be repeated, or by all if you want all of the meta data variables added to the output for each matching modern sample. If the meta data variable's name contains any spaces, you must replace them with underscores in this statement.

Example: The following report statement causes ANALOG to create a file called analog.out for the results, to list the ten modern samples most similar to each fossil sample, and to report for each such modern sample the meta data variables present in the CLIMAP core-top data base.

        report {
            name analog.out: tab
            closest 10
            meta Latitude_degrees
            meta Latitude_minutes
            meta Longitude_degrees
            meta Longitude_minutes
            meta SST_cool
            meta SST_warm
            }

Since the transformation file allows you to rearrange the taxa found in one file so that they are commensurate with those in another, there will generally be one transformation file for every raw data file in the analysis.

Figure 2. Use of transformation files to make data from two different input files commensurate. Data file A has the variables A,B,C, and D, which are typically the names of biological taxa. Data file B has variables C, Da, Db, and E. In order to calculate distance coefficients properly, the variables must be the same in each data set. The user determines that taxa C, D, and E are present in both data sets, and notes that taxon E is composed of both types A and B, while taxon D is composed of types Da and Db. For data file A, the counts of taxa A and B are combined to calculate the counts of taxon E. A and B themselves are then ignored since these taxa are not tabulated separately in data file B. Likewise, data file A does not break taxon D into the two parts Da and Db, while data file B does. So the rules for data file B specify the creation of taxon D from Da and Db, and Da and Db are subsequently ignored. Finally, both data sets are transformed (after the addition and deletion of variables) by conversion to proportions (divide by sum). This figure is available also as an encapsulated PostScript file.

The transformation file is interpreted much like the run description file; blank lines are ignored, comments are indicated with the pound sign, spaces or tabs may precede keywords and taxon names, and keywords are not case sensitive. Certain words are recognized as keywords, and should not be used as taxon identifiers:

        new
        add
        subtract
        multiply
        divide
        ignore
        all
        by

Three directives can be given in transformation files: ignore, new, and arithmetic operations.

ignore

        ignore Depth_(mbsf)
        ignore Indeterminates

        new new_name {
            add old_name_1
            add old_name_2
            ...
            add old_name_3
            }

Examples:

        new dupac {
            add N._dutertrei
            add Neogloboquadrina_pachyderma
            }
        new Tsuga {
            add Tsuga_canadensis?     # note included '?'
            add Tsuga_heterophylla    # and '_' replaces ' '
            add Tsuga_mertensiana
            }

It is not necessary to specify variables in any particular order. ANALOG will sort them alphabetically and will only compare taxa whose names match exactly. Even spaces before and after the names are considered when comparing names.

arithmetic operations

        multiply
        divide
        add
        subtract

        count
        sum
        ssq
        mean
        var
        sdev

multiply and divide may be followed by the word by; the by will be ignored. The number of arithmetic operations is not limited.

Example:

To obtain percentages from counts, use the statements

        divide by sum
        multiply by 100

Input data formats

• the first value on a line (i.e. the string consisting of all characters up to the first tab) contain the sample identifier, and
• the first line contain column headings, which are interpreted as taxon or meta data variable names.

Sample ID\tG. ruber\tG. sacculifer\tN. pachyderma
KNR110/43PC 0-2cm\t100\t50\t0
P1AR92B8 0-2cm\t0\t0\t200

1. Fossil sample identifier
2. Rank of the modern analog
3. Sample identifier of the modern analog
4. Distance between fossil sample and the modern analog
5. Meta data variables from the modern analog

Usage: ANALOG run_description_file_name

You neglected to enter the name of the run description file on the command line.

The name given is misspelled or the file is unavailable. If the file is the run description, which controls subsequent execution, the program does not continue. If the file is a raw or meta data file, the program tries to continue without that file's data.

The run description file is incomplete or there is an opening brace that has no corresponding closing brace.

The run description or transformation file contains a syntax error. This message appears when one of the following rules is broken:

• File name must follow data keyword.
• Format description must follow colon after file name if colon is present.
• File name must follow transform keyword.
• File name must follow meta keyword in basis or sample groups.
• File name must follow name keyword in report group.
• Meta variable name or keyword all must follow meta keyword in report group.
• Opening brace must follow basis, sample, or report keywords.
• Taxon name must follow ignore, new, or add in transformation file.
• Opening brace must follow taxon name in new statement of transformation file.
• Name following distance keyword must be a recognized distance measure.
• Number must follow closest keyword in report group.
• Number or keyword sum must follow arithmetic operator in transformation file; keyword by may appear between them.

Extraneous text appears where a keyword or closing brace should be. Check to see if you misspelled a keyword.

Warning: extra meta data at end of line ...

ANALOG counts the number of variables in a tab-delimited file by looking at the column headings. If there are fewer column headings than there are columns with data in them, the program notices the extra characters at the end of the line and informs the user that they exist. It then proceeds, ignoring the extra characters.

Warning: found temperature data but no numerical data for sample (name) ...

A sample ID for meta data must match exactly the ID for the same sample in the raw data file. If they do not, the program assumes that the two records refer to different samples. If the program encounters meta data for a sample for which it has no raw data or, after having read meta data, finds samples for which no meta data could be found, these warnings are issued.

Error: data card (number) refers to wrong core ...

The SPECMAP data is quite specific about the order of lines referring to an individual core. Similarly, the core identifier must be the same on the data cards as on the master card.

Warning: expected sample meta data, got (string) ...

NAPD ASCII format files must abide by specific guidelines for the arrangment of data. If these guidelines are not followed, ANALOG will be unable to continue. Meta data can be read only from the modern files (those whose extension is .m50). An attempt to read meta data from a fossil NAPD data file (extension .f70) will generate the warning indicating that the meta data could not be read.

Error: could not allocate ...

An attempt to allocate memory dynamically has failed. This indicates that there is not enough memory to read, interpret, or analyze the data. On some systems it may be possible to increase the amount of memory that is available to the program.

Warning: rule file (name) says to ignore (name), which isn't in (name)

These messages indicate discrepancies between the rule file and the data file. Where possible, ANALOG will continue, issuing a warning. Where it cannot proceed without additional information from the user, ANALOG issues an error message and stops.

If, after transformation, the sample data contains a taxon that is not present in the basis data, or vice versa, that taxon is ignored when computing the distance measure. A warning is issued because the condition may give misleading results even though the distance measures can still be calculated.

The named file could not be created. Instead, results will be directed to the standard output device.

It is possible to compile the Macintosh version so that it will run under Macintosh System 6. As distributed, System 7 is required because the program makes a call to PBCatSearch, a toolbox routine that locates a file by name on a Macintosh volume. If you replace the reference to Mac_fopen with the standard C fopen in the file input.c, and do not include the input file macfiles.c in the project, the program will run under System 6, but the data files must then reside in the same folder as the program.

An ancillary program called transpos is available for MS-DOS and UNIX systems. This program transposes the rows and columns of a tab-delimited text file. A typical use might be to get a list of column headings from a tab-delimited text file. Cut the first line from the tab-delimited text file, then run the program transpos, redirecting output to a disk file. The output will contain a list of column headings, one per line.

Additional file formats

The actions taken by the new read functions may be complex. Briefly, the read function is given a pointer to a data base structure, whose members include the information specified in the run description file. If p is the pointer passed to the read function, then raw data are read from p->raw.filespec; the variable names are stored in p->raw.name_buffer; pointers to the names are stored in p->raw.name, and the number of raw variables is stored in p->raw.count. Raw data for each sample are stored in the arrays p->sample[n].raw. The meta data must be read likewise from p->meta.filespec, the number of variables in p->meta.count, the names in p->meta.name_buffer, and pointers to the names in p->meta.name. Meta data values are stored as strings in the array p->sample[n].meta_buffer, and pointers to those strings are stored in p->sample[n].meta. See the code in input.c for details.

Adding another output format is essentially the same, but is less complex, because the output data are simpler in form. See the code in results.c for clues.

References

• Hutson, W.H., 1980, The Agulhas current during the Late Pleistocene: Analysis of modern faunal analogs: Science, v. 207, p. 64-66.
• Imbrie, J., and Kipp, N., 1971, A new micropaleontological method for quantitative paleoclimatology: Application to a late Pleistocene Caribbean core: in Turekian, K.K. (ed.), The Late Cenozoic Glacial Ages, Yale University Press, pp. 71-181.
• Overpeck, J.T., Webb, T. III, and Prentice, I.C., 1985, Quantitative interpretation of fossil pollen spectra: Dissimilarity coefficients and the method of modern analogs for pollen data: Quaternary Research, v.23, p. 87-108.
• North American Pollen Database, Illinois State Museum, Springfield, Illinois, USA, and National Geophysical Data Center, Boulder, Colorado, USA.

        Peter N. Schweitzer
        Mail Stop 918, National Center
        U.S. Geological Survey
        Reston, VA 20192

        Tel: (703) 648-6533
        FAX: (703) 648-6560
        email: pschweitzer@usgs.gov

Makefile

Make description file for UNIX.

analog.h

Data structures and constants used in the program.

analog.c

Main program source code.

distance.c

Distance measure calculation.

error.c

Error and warning output. Modify this file if you want more sophisticated handling of error and warning messages.

input.c

Interpretation of the input data. Modify this file to read files in formats that are not already supported.

macfiles.c

Macintosh code to locate input files by name anywhere on the system.

parse.c

Interpretation of the run description file.

results.c

Output of results for each sample.

rules.c

Interpretation of the data transformation files.

ANALOG.EXE

MS-DOS executable code, requires DOS4GW.EXE

DOS4GW.EXE

Rational Systems, Inc. DOS-extender. This enables the 32-bit MS-DOS program ANALOG.EXE to execute.

analog.hqx

Macintosh executable file, encoded using BinHex 4.0.

CLIMAP

world.fauna

The core top data base received from Brown University, corrected.

changes.fauna

Changes made to world.fauna to fix typos in core identifiers.

world.sst

The meta data file received from Brown University, corrected.

changes.sst

Changes made to world.sst to fix typos in core identifiers.

cc_meta.c

Program to convert world.sst to be readable by ANALOG as tab- delimited ASCII.

cc_raw.c

Program to convert world.fauna to be readable by ANALOG as tab- delimited ASCII.

climap.meta

CLIMAP core top data base meta data file in tab-delimited ASCII format. Includes core locations and SST values taken from published atlases.

climap.raw

CLIMAP core top data base raw data file in tab-delimited ASCII format.

climap.rule

List of taxa from climap.raw; modify this file to create an appropriate transformation file for climap.raw.

run_description

Example run description file for reading in the CLIMAP core top data base. As distributed, this file lacks a sample statement, so no analysis is actually carried out. But it can be modified to analyze a set of fossil samples by adding one or more sample statements.

NAPD

modern.m50

The modern samples of the North American Pollen Database.

taxa.m50

A list of taxon names from modern.m50; modify this list to create an appropriate transformation file.

run_description

A sample run description containing commands to read modern.m50.

SPECMAP

specmap.070

Text file describing the format of specmap.071 and specmap.072.

specmap.071

Modern Atlantic core-top data base.

specmap.072

Fossil samples. These lack meta data.

test_specmap

A sample run description containing commands to read specmap.071 and specmap.072.

analog.tex

Source code for this document, in LaTeX.

analog.ps

PostScript version of this document.

index.html

This HTML document.

io.gif

Figure 1, in Graphic Interchange Format (GIF).

io.pict

Figure 1, in Macintosh PICT format.

io.eps

Figure 1, in encapsulated PostScript.

rule.gif

Figure 2, in Graphic Interchange Format (GIF).

rule.pict

Figure 2, in Macintosh PICT format.

rule.eps

Figure 2, in encapsulated PostScript.

bin | data | src

Directories for this document.

Maintained by Peter Schweitzer

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