ProfitPress Mega CDROM2 Shareware Freeware (MSDOS)(1992)(Eng)

home *** CD-ROM | disk | FTP | other *** search

/ ProfitPress Mega CDROM2 …eeware (MSDOS)(1992)(Eng) / ProfitPress-MegaCDROM2.B6I / APPS / STATISTI / MVSP2.ZIP / MVSP.DOC < prev next >

Wrap

Text File | 1990-11-13 | 60.0 KB | 1,189 lines

_______________________________________________________ MMMMMMMMMMMM VV VV SSSSSSSS PPPPPPPP MM MM MM VV VV SS PP PP MM MM MM VV VV SSSSSSSS PPPPPPPP MM MM MM VV VV SS PP MM MM MM * VVV * SSSSSSSS * PP * _______________________________________________________ S H A R E W A R E ----------------- A MultiVariate Statistics Package for the IBM PC and Compatibles (C) Copyright Warren L. Kovach, 1986-1990 Institute of Earth Studies University College of Wales Aberystwyth, Wales SY23 3DB U.K. BITNET/JANET address: WLK @ ABERYSTWYTH.AC.UK CompuServe: 100016,2265 CIX: warrenk Ver. 2, October, 1990 This program is being distributed as user-supported software. If you find this program to be of value, a voluntary contribution (UKL40 or US$75 suggested) would be appreciated. - MVSP Ver. 2 -- Users Manual Page 2 ACKNOWLEDGEMENTS In the four years since I first released MVSP, I have received countless letters about this program, many with some very useful suggestions and comments. I have considered all of these and have incorporated most into this new version. My thanks go to all of those who have sent in comments. Special thanks go to John Birks (Bergen, Norway), Geoffrey King (Pickering, Yorkshire, England), and Lou Maher (Madison, Wisconsin, USA) for numerous comments on both the old and new versions of the program. I am indebted to Chris Meachem (Berkeley, California, USA) and Joe Felsenstein (Seattle, Washington, USA) for allowing me to distribute PLOTGRAM, the dendrogram plotting program, with MVSP. Very special thanks go to my wife, Catherine Duigan, for numerous suggestions for improvements in the program, help in designing this manual and the cover, assistance in the distribution of MVSP, and for putting up with many hours of computer-widowhood. Warren L. Kovach Berllan-Ber, Abermagwr, Wales September, 1990 This manual and the accompanying program are protected by international copyright laws; (C) Copyright 1986-1990 Dr. Warren L. Kovach. This manual and the accompanying computer program may not be reproduced except as outlined in the section below entitled "Limited User Licence". MVSP Ver. 2 -- Users Manual Page 3 TABLE OF CONTENTS Acknowledgements................................................2 Introduction....................................................4 The User Supported Concept......................................4 Limited User Licence............................................5 Installation....................................................6 Automatic Installation........................................6 Manual Installation...........................................7 Compatibility with Old Versions of MVSP.......................7 General Use of Program..........................................8 Menus.........................................................8 Entering and Editing Text.....................................9 Menu Options....................................................9 A-F: Statistical Procedures...................................9 M: Manipulate Data...........................................10 S: Change Drive or Sub-directory.............................10 Q: Quit MVSP.................................................10 P: Change Program Defaults...................................10 MVSP Data Editor...............................................11 Entering Data Labels.........................................11 Entering Data................................................12 Editing Labels and Data......................................12 Saving Data Matrix...........................................12 Utilities......................................................13 Reformat.....................................................13 Sortdata.....................................................13 Plotgram.....................................................14 Disclaimer.....................................................16 Future Plans...................................................17 80x87 Support..................................................18 References.....................................................19 Registration Form..............................................21 MVSP Ver. 2 -- Users Manual Page 4 INTRODUCTION MVSP is a package of common multivariate statistical procedures widely used in many areas of biology and geology, as well as other fields. These procedures include principal components analysis (PCA), principal coordinates analysis (PCO), correspondence analysis (CA; also called reciprocal averaging), distance or similarity measures, hierarchical cluster analysis, and diversity indices. This program provides a great deal of flexibility in the analyses, but is simple to use. Options for different forms of these analyses can be chosen from menus and these settings can be saved for future use. Most analyses can be run with as few as half a dozen keystrokes. One possible drawback to ease of use is that some users may be very tempted to take a "black box" approach to using these statistics, feeding in numbers and coming up with "The Answer". I must strongly warn the users of this program that statistics can be DANGEROUS! All these procedures make assumptions about the data and have restrictions on what they can and cannot do. If these assumptions and restrictions are violated, the results could be meaningless. I urge you to become familiar with the methods before you use this program. This manual contains a list of references that I have found very useful in understanding these techniques. In particular, Sneath & Sokal (1973), Gauch (1982), Pielou (1984), and Davis (1986) are very well written and give very clear discussions of these techniques. The manual distributed with the full registered version of this program, MVSP Plus (see next section), also contains many suggestions about the use of these procedures. I am always interested to see how MVSP is being used. I would appreciate receiving reprints of any papers you have published in which MVSP was used for data analysis. Thank you! THE USER SUPPORTED CONCEPT This software package is being distributed under the user supported concept. In case you haven't run across this software phenomenon, the following is a brief discussion of it's tenets. User supported software is an experiment in "grass-roots" software distribution and development. Andrew Fluegelman, one of the pioneers of this phenomenon in the microcomputer world, expressed it this way: 1) The value and utility of software is best assessed by the user on his or her own system, under actual working conditions. 2) The creation of new and useful software should be supported by the computing community. 3) Copying and sharing of software that you have found useful should be encouraged, rather than restricted. User supported programs are freely distributed to the computing MVSP Ver. 2 -- Users Manual Page 5 community, through the network of electronic bulletin board services, local computer user groups, word of mouth, and networks of friends with similar interests. The user support comes in two forms: The user is encouraged to evaluate the program, suggest any changes in the program that would be useful, and recommend the program to others if it is worth recommending. The user is encouraged to support further programming efforts through a voluntary monetary contribution to the program author. User supported means that you don't have to pay outrageous prices for a program without getting a chance to test drive it first to see if it really meets your needs. User supported means that if you decide that this program is worth supporting, then you support it voluntarily, for a reasonable cost, and without the hassles of copy-protection and the high cost of advertising. You are encouraged to copy and distribute the MVSP Shareware version of this program. If you find this program to be useful, a voluntary contribution to the author (UKL40 or US$75; dollar - price may change due to exchange rate fluctuations) would be appreciated. In return for the contribution, you will receive: An enhanced version of MVSP (MVSP Plus) that will be able to analyze very large matrices, with the size only limited by the amount of memory and disk space available (up to 750x750). MVSP Shareware is limited to 100x100 matrices. A version of MVSP that is compiled to use the 80x87 math co- processor chip. A complete printed manual. Priority for help with problems. Notification of future versions of MVSP and special deals on upgrades. An order form is appended to this manual. This program is copyrighted, and no price may be charged for this program by any person other than the author (Warren L. Kovach). MVSP Shareware may be distributed freely and a nominal fee may be charged for distribution costs, such as for the media and postage and handling, as long as this fee does not exceed UKL5 or US$10. - LIMITED USER LICENCE There are two versions of MVSP 2.0. MVSP Shareware can be freely copied and distributed as long as no price is charged other than for the cost of media, postage, and handling, not to exceed UKL5 - or US$10 (see section on User Supported Concept above). MVSP Plus is the enhanced, registered version that accompanies this MVSP Ver. 2 -- Users Manual Page 6 manual and may not be copied, except as specified below. This version is only available to people who have made a voluntary monetary contribution to the programming effort of UKL40 or US$75 - (dollar price may change due to exchange rate fluctuations). Neither MVSP Plus nor MVSP Shareware may be modified or dis- assembled in any way and for any reason. Distribution of modified versions are also forbidden. INSTALLATION The program files for MVSP Shareware are distributed in compressed form on one floppy disk. An installation program is provided to automatically decompress the files and place them in the appropriate place on your hard or floppy disk. If you wish, you may also decompress them manually (see below). AUTOMATIC INSTALLATION: Place the disk marked "MVSP Shareware disk" in the appropriate floppy drive, log onto that drive (by typing "A:" if it is the A drive, "B:" for B, etc.), and type "INSTALL". You will see an opening screen, and then will be asked a few questions before the program is installed. You must first specify where the original disk will be during installation, with the current drive being suggested as the default answer. You would normally just press the carriage return to accept this default. Next you will be asked where the program files are to be copied to. If there is a hard disk in your computer a default answer of the directory "C:\MVSP" will be suggested, otherwise it will be a second floppy disk drive. You may edit the default answer with the arrow keys and the backspace; the ESC key will clear the line allowing you to start from scratch. If you are installing the program on a hard disk, the install program will create the directory you specify if it does not already exist. If the directory exists and there is an old version of MVSP in that directory you will be asked if you wish to delete the old files; if you want to keep the old version you will have to specify a new directory, otherwise the install program will automatically replace the old files. The install program will next check to see if there is enough room on the disk for MVSP. This is particularly important for installation on floppy disks as the main files almost completely fill a 5 ¼" double density disk. If there is not enough room you will be prompted to try another disk. The program requires two 5 ¼" double density disks whereas it will fit on a single disk if you are using 5 ¼" high density or any type of 3 ½" disk. Once the preliminaries are finished the program will start decompressing the files and copying them to the appropriate place. It will also attempt to determine the type of video adapter present in your computer so that the appropriate graphics driver file (which provides the interface between MVSP and your graphics hardware) can be copied. You will be asked if the installation program's guess is correct or whether to try another MVSP Ver. 2 -- Users Manual Page 7 type. Generally this guess is accurate and should be accepted. The exceptions are when you have an AT&T 6300 or Compaq Portable III or 386 with 640x400 line resolution, which the install program cannot detect, or if you are installing the program on a disk that will be used on another computer. Once the program has been installed you may run it as described below (under "Starting the program"). When you are at the main menu choose the "Program defaults" option to customize the program and save any changed defaults. In particular you may wish to change the screen colors and the location of the data files. These and other options may be changed at any time. MANUAL INSTALLATION: MVSP is distributed in two self-decompressing files created using software distributed by PKWARE, Inc. These are archive files that each contain a number of separate files in compressed form. The files are executable (with an .EXE extension) and automatically decompress the archived files when they are run. For instance, if the self-decompressing file is called MVSP1.EXE, typing "MVSP1" at the DOS prompt will cause all the files in that archive to be extracted and placed in the current directory. To install the program manually you will first need to create a directory on your hard disk or insert a blank floppy disk in your second disk drive and log on to that drive\directory. Next, place the MVSP Shareware distribution disk in the first floppy drive and run the self-decompressing programs on that disk. Here is a list of the files contained in each self-decompressing file: MVSP-S.EXE mvspshar.exe - main program file for shareware version mvsp.hlp - file of help screens mvsp.doc - documentation for shareware version *.bgi - a variety of video graphics drivers MVSPUTIL.EXE reformat.exe - utility to convert data files between MVSP and Cornell Ecology Program formats sortdata.exe - utility to sort the original data matrix according to the order of the dendrograms from two cluster analyses, then output the matrix in graphic form. *.mvs - example data files plot14.exe - dendrogram plotting program, from Chris Meachem & Joe Felsenstein. plot14.doc - documentation for PLOT14 font? - various font files used by PLOT14 plot.bat - run PLOT14 using PLOTPRM parameter file dot.bat - run PLOT14 using DOTPRM parameter file plotprm - parameters for drawing dendrograms on screen dotprm - parameters for drawing dendrograms on dot matrix printer COMPATIBILITY WITH OLD VERSIONS OF MVSP: The new version of MVSP is used in a similar way to the old version so that there should be few adjustments to be made in your working patterns, except that MVSP ver. 2 will make analyses even easier. There are two points to keep in mind if you have MVSP Ver. 2 -- Users Manual Page 8 installed the new version over the old one. First, the default data file extension is now .MVS instead of .DAT, in order to avoid confusion with the numerous other programs that use the .DAT extension. You may either rename all your existing data files (using the DOS command "REN *.DAT *.MVS") or use the "Program Defaults" option to reset the default extension to .DAT. Also note that the configuration file format for the new version of MVSP is compatible with the old one, so that if you are installing the new version in the old directory your saved defaults will be retained (including the default data file extension). GENERAL USE OF THE PROGRAM STARTING THE PROGRAM: This program is simple to use and menu-driven, presenting you with the possible options at each step. It is initiated by first logging into the disk and directory containing the program (using the DOS commands CD, A:, C:, etc.) and typing the name of the program, MVSPSHAR. For instance, if you have installed MVSP on you hard disk in the directory C:\MVSP, type: C: CD C:\MVSP MVSPSHAR The program file MVSPSHAR.EXE must be in the default directory (the one specified in the CD command above) for the program to work properly. If you wish to use the help facility, the file MVSP.HLP must also be in this directory. If you have changed any of the program defaults, the configuration file named MVSP.CNF (which is created when you save your changes) must also be on the default drive for the new options to be reinstated. You may also specify the location of the MVSP files using DOS environment variables and the commands SET and PATH. For instance, if the MVSP files are in the directory C:\MVSP, you may place the two following commands in your AUTOEXEC.BAT file: PATH C:\;C:\MVSP (this line may also contain other directories) SET MVSP=C:\MVSP After rebooting, you may start the program by typing MVSPSHAR, regardless of the current directory. You may edit your AUTOEXEC file with any word processor or text editor that produces plain text (ASCII) files. Many will have a special non-document mode for this. Refer to your word processor manual for details. As a last resort, DOS' EDLIN program may be used. MENUS: When the program is loaded, you will see an introductory screen giving the name and address of the author, then after pressing any key you will be presented with a menu of available procedures. The first option on the menu will be highlighted by a rectangular cursor. This cursor can be moved through the list of options by using the up and down arrow keys. A choice is made by pressing the carriage return when the correct one is MVSP Ver. 2 -- Users Manual Page 9 highlighted, or alternatively by typing the letter preceding the desired option. Usually, choosing an option will bring up a second menu, from which you can often call up a third, and so on. The number preceding the title on each menu indicates the level you are at in the hierarchy; If you get lost, remember that pressing 'Q' or ESC will bring you back to the previous menu. MVSP now has an extensive help facility that provides information about every menu option. To get help, just place the cursor on the desired option and press the F1 key. After reading the text, pressing any key will bring you back to the menu. ENTERING AND EDITING TEXT: You will often be asked to type in a string of text, such as the name of a data files. In some cases you are provided with a default choice, which you can accept or modify. MVSP has a number of editing commands to help in this modification. You can use the cursor keys to move the cursor back and forth, the DEL and Backspace keys for deleting text, and the letter keys for adding text. When you first begin editing a text string, the program is in insert mode, so that any text you type will be inserted and the remaining text will be pushed the right. Pressing the INS key toggles insert mode on or off (indicated by the thickness of the cursor); with it off old text is overwritten by the new. Pressing ESC will clear the input line to allow you to start from scratch. If you press the Enter key after clearing the line you will exit that procedure. When you are entering the name of the input data file, pressing F3 will recall the last valid filename you entered during that session. You may then use that file again or modify it if you want to use a similarly named file. MENU OPTIONS The main menu lists the six available numerical procedures as well as a few other options. OPTIONS A-F: These options are the basic numerical procedures; principal components analysis, principal coordinates analysis, correspondence analysis (reciprocal averaging), similarities and distances, cluster analysis, and diversity indices. When one of the numerical procedure options (A-F on the main menu) are chosen, you will be asked for the name of the input data file. You may then enter the name of the data file. The program will automatically add your specified default extension if no extension is specified. So, if your datafile is named "STUDY1.MVS" and your default extension is .MVS, you need only type "STUDY1". If you specify another extension, or have a filename with no extension, the program will recognize those as long as the full name is specified. A blank carriage return here will return you to the main menu. You may obtain a directory of the default data disk and path by typing a "?". You may then specify a certain file mask, such as MVSP Ver. 2 -- Users Manual Page 10 "*.MVS" for all files with a .MVS extension or "*.*" for all files. You will then be presented with a list of all files matching that specification. You can now move the cursor around with the cursor keys until you find the one you want, then press "Enter" to select that file. Pressing ESC will take you back to the filename prompt. After an input file has been selected, you will be presented with an "Analytical Defaults" menu. This allows you to set a number of options concerning the analysis about to be performed, such as the destination and types of output, accuracy of solution, data transformation or transposition, and different forms of analysis. The help screens (press F1) describe each of these options. OPTION M: The MANIPULATE DATA option provides facilities for data entry, editing, and transformation. A simple spreadsheet-like data editor is provided for initial entry and subsequent modification of the data. Procedures are also provided for transposing and transforming the data, converting to other scales, and deleting rows and columns. Transforming data by logs or square roots brings the data closer to being normally distributed and can help in increasing the interpretability of the results (Kovach, 1989). The logratio transformation is particularly valuable with percentage or proportional data (Aitchison, 1986). As in Options A-F, you will first be prompted for an input file name. OPTION S: This option, CHANGE DRIVE OR SUBDIRECTORY, allows you to specify the default location of the input and output data files. If you enter a path name without a drive specification, the default drive is assumed. If you enter just a drive specification (e.g. "A" or "A:") the default path will be the current directory of that drive. A "?" lists the sub-directories of the current directory. A carriage return with no other input exits this option with no changes. OPTION Q: QUIT MVSP will exit the MVSP program and return to the DOS prompt. OPTION P: The CHANGE PROGRAM DEFAULTS option allows you to change many of the default settings for the program. These specifications can be saved to the file MVSP.CNF, which will be reloaded each time the program is run, reinstating these defaults. When you choose this option you will be presented with a menu asking which type of default should be changed. The descriptions of these default options are not given in this abbreviated manual. However, the help screens for each option provide brief descriptions. MVSP Ver. 2 -- Users Manual Page 11 DATA EDITOR Data files may be constructed using the MVSP data editor. This editor is similar to a spreadsheet program. Data are entered and presented in a tabular format, with the rows being the variables and the columns being the individual cases or objects. To use the data editor, first choose the "Manipulate Data" option from the main menu and specify a filename. If that file exists, it will be loaded into the editor for modification; if not, you will be asked if you want to create a new file. You will now be presented with the Data Manipulation menu. Choose "Enter/Edit Data". If you are creating a new file, you will have the option of reading in data from another file for modification and saving under the new name. You will next be asked to enter the maximum number of rows and columns needed for the data matrix. MVSP must set aside a certain amount of memory for working with the data matrix. If you are editing an existing data matrix and don't plan to add new rows or columns, then just accept the default values for rows and columns. If you are adding rows or columns to either a new or old matrix, then enter the maximum number needed. If you aren't sure of the exact number, over-estimate. This will only cause MVSP to set aside some extra memory while you are editing; it will not have any lasting effect. You will also be asked to enter or modify a title for the file. This title identifies the data, and will be printed out along with the results of each analysis. You may enter up to 79 characters, so be as descriptive as you can. Note, however, that the "Distances and Similarities" procedure pirates the last few characters of the title to place a label on the output symmetric matrix file identifying the coefficient used. If you use most or all of the 79 available characters, make sure no vital information is at the end of the title, or it will be overwritten by the identifier. ENTERING DATA LABELS: When creating a new file, you are first presented with a blank spreadsheet with the cursor in the upper left corner. You must first enter some labels for the rows and columns. You will notice that the cursor will only move about in rows and columns that have labels or in the next blank row or column. This is to avoid having spurious values placed in areas that aren't meant for data. By entering a row or column label, you are telling the program that this is another variable or case to include in the matrix. When you enter a new label, that row or column will then be filled with zeros to indicate that it is now considered part of the data matrix. To enter labels, all you need to do is to start typing the label while the cursor is in the desired row or column. When you start typing, the bottom line will display the word "INPUT>" and the characters you type will appear on this line. You may edit the text using the backspace, cursor, insert, and delete keys, as described in the section "Entering and editing text" above. Once you are finished typing the label, you then place the label in MVSP Ver. 2 -- Users Manual Page 12 the matrix by typing one of the cursor keys (not the Enter key). This tells the editor whether the label is for a row or column. Typing the up or down arrow cursor keys declare that label to be for a row, while a left or right arrow key indicates a column label. The cursor will also move in the appropriate direction so that you are ready to enter another label. The labels themselves can be up to eight characters long and may consist of any printable character, except spaces. The following are all valid labels: ROW1 COLUMN_2 1st-Loc. #3-Site This label is NOT valid: SITE 1 It will be read as two labels, "SITE" and "1". If you are using labels that begin with a number (such as 1st-Loc.), you must precede the label with a single or double quote (' or ") so that the program will know that you are not attempting to enter numeric data. ENTERING DATA: Once you have a few labels entered, you may start entering the data themselves. This is done in a similar way to the labels; just start typing a number when the cursor is in the appropriate place. Input of each number is finished by pressing one of the cursor keys or the "Enter" key. If you enter any characters that cannot be converted to numeric form, an error message will be displayed and you may edit the input to correct the mistake. The only valid characters for numeric data are '0'-'9', '-', '+', '.', and 'E'. The 'E' is used for entering numbers in scientific notation, so that 0.00001 (1.0 x 10-5) may also be entered as as "1.0E-05". EDITING LABELS AND DATA: Editing of data and labels can be done in two ways. In either case, the cursor must first be placed in the appropriate row and column. Then you may either type the value anew, as you would for entering data, or you may use one of the editing function keys. The function of each of these keys is listed at the bottom of the screen. Pressing F2 will bring the datum to the bottom line of the screen, where it can be edited. F3 will allow you to edit the row label and F4 the column label. These can be edited and entered into the matrix as described above. SAVING DATA MATRIX: Pressing the F9 key will save the data matrix to a file along with all the changes you have made so far. I would suggest doing this frequently to avoid losing any changes you have made due to malfunction or mistakes in editing. The F10 key will save the changes and exit back to the main menu. If you decide to abandon the current editing session, press the ESC key. You will first be asked to confirm that you want to exit, then you will be MVSP Ver. 2 -- Users Manual Page 13 returned to the main menu. All changes made since your last save will be lost. UTILITIES REFORMAT: The program REFORMAT.EXE is a utility I've written to convert data files between the MVSP format and the compressed format used by the Cornell Ecology Program series (CEP; DECORANA, TWINSPAN) and other related programs such as Cajo T. F. ter BraakÆs CANOCO program (ter Braak, 1986). The Cornell programs were developed by M.O. Hill (see Hill & Gauch, 1980). These programs use a compressed data file format in which only non-zero abundances are included. The data are presented in couplets, with the first number indicating the taxon, and the second being the actual abundance. The couplets for each sample are grouped on one or more lines, with the sample number being specified at the beginning of each. This reformatting utility is run by typing the following command at the DOS prompt: REFORMAT infilename [outfilename] where 'infilename' is the name of your input file and 'outfilename' is the name of the new file for the converted matrix. If 'outfilename' is not specified, then the input file name is used, with a new extension, '.RFM'. If REFORMAT finds an MVSP file header (discussed under "Importing Data Files"), then it will convert this file to CEP format. If the MVSP file header is not found, it will assume that the input file is in the proper format for CEP programs, and will convert it to MVSP format. If the file is not in the correct CEP format, the results will be unpredictable (but you will probably get a numeric format error). Note that, due to the lack of built in formatting capabilities in the READ procedure in the Pascal computer language used to write REFORMAT, the format statement in the CEP file is not followed. Instead, the data are read in free format, so the data elements must be separated by spaces. SORTDATA: In many of my analyses I perform clusterings of both the samples and species. I've found it very valuable to present the resulting two diagrams with the original data matrix in between, sorted in the order of the dendrograms. The data can be split into abundance classes, which are represented by different characters, so that the differing abundances can be seen at a glance. In this way the structure revealed by the cluster analyses can be seen directly in the data matrix (see Kovach, 1989 for some examples). SORTDATA is a utility I've written to help produce these diagrams. To produce one of these combination diagrams, you must first run two cluster analyses of the same data matrix, one with the matrix transposed, the other not. Make sure that both the "Tree MVSP Ver. 2 -- Users Manual Page 14 Description" and "Tree Order" options are turned on. This will produce four files, two with descriptions of the dendrograms for PLOTGRAM and two with the order of the objects in the dendrogram for SORTDATA. Next run SORTDATA with the following parameters: SORTDATA datafile.MVS order1.ORD order2.ORD [output.SRT] where "datafile.MVS" is your original data file used for input to the distance and similarity procedure, "order1.ORD" and "order2.ORD" are the tree order files for analyses of the transposed and non-transposed matrices, and "output.SRT" is the file that will contain the sorted data matrix. If "output.SRT" is missing the output will be put into a file named "datafile" with a .SRT extension. When the program is run, it will first read the original data matrix, determine the lowest and highest data values, and then ask you to define the ranges of four data classes. First you must enter the value below which no symbol is plotted; if your data are counts, this value will be 1. Then enter the cutoff points between the four classes. When you are done the program will sort the data and translate them to the abundance classes, placing the results in a file. To assemble the resulting diagram, you must first print out the sorted data matrix. You can use your word processor to print it, perhaps adjusting the character font (pica, elite, or condensed) and the line spacing to fit the diagram on one page. Then measure the width and length of the matrix and use PLOTGRAM to produce the dendrograms, setting the YSIZE parameter to the appropriate length (in cm) so that the dendrogram will be the same size as the sorted data matrix. The whole diagram may then be assembled on a large (A3 or 11"x17") piece of paper. PLOTGRAM: This is a program for producing high quality printouts of dendrograms on a variety of hard copy devices. It was written by Chris Meachem, mainly for use in producing evolutionary trees such as cladograms and phylograms. His version was written to work with plotters, laser printers, and the computer's video screen. Joe Felsenstein modified the program to produce DOTGRAM, which works with dot matrix printers. I've combined the two versions into one program, called PLOT14. Drs Meachem and Felsenstein have kindly given me permission to distribute their program with MVSP, allowing you to produce high quality dendrograms. The Pascal source code for the combined version is available from me upon request (please send a floppy disk). The full documentation for using this program is provided in a file on the utility disk called PLOT14.DOC. This gives general instructions on using both PLOTGRAM and PLOTREE (another program for producing evolutionary ball and stick diagrams that isn't distributed with MVSP) and specific details of PLOTGRAM. This describes all the various options that can be invoked in this very flexible program, including changing the form of the dendrogram, its size, the angle of the labels, etc. MVSP Ver. 2 -- Users Manual Page 15 To use PLOT14 you must first run a cluster analysis with MVSP, making sure that the "Tree Description" option is turned on. This will produce a file with a description of the dendrogram that can be read and interpreted by PLOT14. To run PLOT14, you must first exit from MVSP to the DOS prompt and type the command: PLOT14 treefile.PLG parmfile [output] where 'treefile.PLG' is the tree description produced by MVSP, 'parmfile' is a file containing the various parameters you have chosen for producing the dendrogram, and 'output' is a file to hold the output to the printer or plotter, if it is not sent directly to the device. There are certain parameters that must be placed in the 'parmfile' for the dendrograms from MVSP to be produced properly. These are: PLOTTER S DIAGRAMTYPE Y TIPS Y PLOTTER declares the device to which you wish to send the output; in this case it is 'S', the IBM-PC screen. With this option, the program will detect the type of graphics adapter you have in your computer and will automatically use the highest resolution possible. Other possible options are listed in PLOT14.DOC. If you wish to send output to a dot matrix printer, replace PLOTTER with PRINTER and use the appropriate code, such as 'E' for Epson compatible printers. Note that PLOTTER or PRINTER should be the first option in the parameter file. When this option is encountered all other options are set to their default values for that plotter or printer, therefore any options set before this will be lost. DIAGRAMTYPE specifies which of the three basic types of diagrams to produce. The 'Y' type is called the phylogram in PLOT14.DOC; for this diagram the lengths listed in the 'treefile' are the distances between nodes of the dendrogram. In the default phylogram type the tips of the tree, indicating the individual objects, don't necessarily line up evenly, so 'TIPS Y' must be set to force them to be even along the right side, as is usual for dendrograms. Some other options you may find useful are: FONT 1 *This is a comment YSIZE 20 ROTATION 90.0 The FONT command chooses one of five fonts for producing the lettering. They are as follows: FONT 1 - single-stroke roman, FONT 2 - double-stroke roman, FONT 3 - multi-stroke roman, FONT 4 - double-stroke italic, and FONT 5 - triple-stroke italic. YSIZE indicates the length of the dendrogram in centimeters (XSIZE would change the width). ROTATION allows you to rotate the dendrogram to fit most conveniently on the paper; ROTATION of 0 MVSP Ver. 2 -- Users Manual Page 16 would place the tips of the dendrogram along the top; 90 places them down the right side. Also note that any line beginning with a '*' is not interpreted by the program and acts as a comment line; it can also be used to temporarily disable an option. The use of the 'output' file differs with different devices. For plotting on the screen an output file need not be specified, and will be ignored if it is. The plotters and the Postscript laser printer produce output that is text-based, forming commands to the device to draw lines. These may be placed into an output file for printing later (perhaps being sent to a mainframe computer), or may be directed to the output port to which the device is attached. On the IBM-PC these ports are designated by the names COMx for serial ports or LPTx for parallel ports, where the 'x' indicates the number of the particular port. You will need to know which your plotter is attached to before using PLOT14 (check you hardware manuals). In the original program dot matrix printer output could also be directed to a file, but that sometimes caused problems with the IBM PC, so I've modified it so that the output is always sent directly to the printer. You may override this by setting the option BIOSPRINT to N. I've included two batch files with the program that make PLOT14 easier to use. PLOT.BAT calls PLOT14 using a parameter file that is set up to work with video screens (PLOTPRM) while DOT.BAT uses DOTPRM, with the PRINTER keyword rather than PLOTTER. These parameter files also have the appropriate commands for producing dendrograms correctly from MVSP treefiles. To use these files first make sure the PRINTER and PLOTTER keywords in the parameter files are set correctly for your printer and screen/plotter, then type either PLOT treefile.PLG or DOT treefile.PLG depending on which device you wish to use. If the PLOTTER is set to use the screen, you can first preview the dendrogram on your screen, then send it to the printer without having to edit a parameter file. DISCLAIMER The accuracy of this program has of course been extensively tested against the results of other programs. However, unforeseen errors in computation can and have crept up even in the most sophisticated and widely used statistical packages. You may wish to initially run comparisons with the results of other programs, using your own data set, to ensure that it is working properly with your type of data. Note when running comparisons that there are often many methods of computing the same routine, and results may vary, especially in the more complex eigenanalysis procedures. In principal components analysis, for instance, there are numerous ways of MVSP Ver. 2 -- Users Manual Page 17 transforming the data before eigenanalysis (see Greig-Smith, 1983, pp. 247ff), and the component loadings can be scaled either to unity (as they are here) or to the variance of that principal component, or in other manners. Also, the eigenanalysis can rotate the cloud of points in different directions, so that signs of the scores are reversed and the actual values different. The configuration of the points will be the same, however. If you do run into any problems with this program, whether they be in the results or abnormalities in the running of the program, please contact me by post or through electronic mail at the addresses given on the acknowledgements page. Please give full details of the problem and, if possible, the data set which you were running when the bug cropped up. Please note that no warranty is given for this program. The author (Warren L. Kovach) shall not be legally liable for any damages or lost profits arising from use or misuse of this program. FUTURE PLANS MVSP is always changing and growing as I explore new types of multivariate methods and programming techniques. Some of my plans for future versions of MVSP are as follows: I will be adding a detrending option to the correspondence analysis procedure (Hill & Gauch, 1980). This method is commonly used in community ecology in order to smooth out the arch effect often encountered in ordination. It will, however, entail a complete rewrite of the existing correspondence analysis procedure. Cajo ter Braak has developed a further extension of CA, canonical correspondence analysis, that allows two data matrices, one of species data and one of environmental data, to be ordinated together. I am investigating the possibilities of adding this procedure. More distance and similarity measures will be added and I hope to incorporate dendrogram plotting directly into MVSP, so that draft copies of dendrograms are easily produced. I will also be adding a section that will allow data to be imported directly from a number of other common programs, such as Lotus 1-2-3 spreadsheets and dBase databases. I am considering rewriting MVSP to work under the new Microsoft Windows ver. 3.0 graphical operating environment. I believe that this will make the program even easier to use and will allow the results to be transferred to other Windows programs, so that you can incorporate these in a report written with a Windows wordprocessor or graph the results with a Windows graphics package. With computers based on 80286 or 80386 microprocessors, Windows 3.0 allows programs to use all available memory and, with the 386 chip, can even directly use disk space as an extension of memory. The Windows memory management scheme will not impose as much overhead as the current memory management scheme, therefore the actual calculations of MVSP should run faster. Unfortunately, Windows imposes a lot of overhead in writing to MVSP Ver. 2 -- Users Manual Page 18 the screen and doing things like choosing menu options, so although the calculations may run faster, the response of the user interface may seem slow on a slow machine. This is one of the tradeoffs I will have to consider in deciding whether to make this change to Windows. If you have any other comments about the procedures in this program, or about procedures NOT in this program, which you feel would be useful to include, these should be sent to me at the address on the title page of this manual. THANK YOU! 80x87 SUPPORT If you aren't satisfied with the speed of this program, a faster version that uses the 80x87 math coprocessor is distributed with MVSP Plus, which is available to users who have made a voluntary monetary contribution of UKL40 or US$75 (see section on User - Supported Concept above). This coprocessor (which is an optional chip that can be plugged into your computer) greatly speeds up the processing of real number, floating point arithmetic. Often this increase in speed can amount to 10 times! This is particularly noticeable for calculation that use logarithms and trigonometric calculations. The calculation of the Brillouin diversity index, which uses log factorials, for an 84x84 matrix took 9 minutes 14 seconds without a math chip but 2 minutes 41 seconds with one. A PCA, which uses mostly arithmetic operations, of a 45x45 data matrix took one hour with the standard version of the program, but only twenty minutes with the 8087 version. Turbo Pascal, the compiler used in developing MVSP, has an option for creating programs that take advantage of this processor. The programs compiled using this option will only work on machines that have the 80x87 installed. The installation program will detect whether your computer has a math chip and will install the appropriate version. MVSP Ver. 2 -- Users Manual Page 19 REFERENCES Aitchison, J., 1986. The Statistical Analysis of Compositional Data. Chapman and Hall, London. Bayer, U., 1985. Lecture notes in earth sciences. 2 Pattern recognition problems in geology and palaeontology. Springer- Verlag. Beals, E.W., 1984. Bray-Curtis ordination: An effective strategy for analysis of multivariate ecological data. Advances in Ecological Research, 14:1-55. Birks, H.J.B., 1987. Multivariate analysis in Geology and geochemistry: An introduction. Chemometrics and Intelligent Laboratury Systems, 2:15-28. Birks, H.J.B. & Gordon, A.D., 1985. Numerical Methods in Quaternary Pollen Analysis. Academic Press, London. Cooke, D., Craven, A.H., & Clarke, G.M., 1982. Basic Statistical Computing. Edward Arnold (Publishers) Ltd., London. Davis, J.C., 1986. Statistics and Data Analysis in Geology, 2nd Edition. John Wiley & Sons, New York. Duigan, C. A. & Kovach, W.L., in press. A study of the distribution and ecology of littoral freshwater chydorid (Crustacea, Cladocera) communities in Ireland using multivariate analyses. Journal of Biogeography. Everitt, B., 1980. Cluster Analysis. 2nd Edition. Gower Publishing Co., Hampshire, 136 pp. Felsenstein, J., 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39:783-791. Gauch, H.G. Jr., 1982. Multivariate Analysis in Community Ecology. Cambridge University Press, New York. Gordon, A.D., 1981. Classification. Chapman and Hall, London. Greig-Smith, P., 1983. Quantitative Plant Ecology. University of California Press, Berkely. Hill, M.O., 1973. Reciprocal averaging: An eigenvector method of ordination. Journal of Ecology, 61:237-249. Hill, M.O., & Gauch, H.G. Jr., 1980. Detrended correspondence analysis: An improved ordination technique. Vegetatio, 42:47-58. Jolicoeur, P., & Mosimann, J.E., 1960. Size and shape variation in the Painted Turtle. A principal component analysis. Growth, 24:339-354. Jolliffe, I.T., 1986. Principal Components Analysis. Springer- Verlag, New York. MVSP Ver. 2 -- Users Manual Page 20 Kovach, W. L., 1988. Multivariate methods of analyzing paleoecological data. In: W. A. DiMichele & S. L. Wing (eds.), Methods and applications of plant paleoecology. The Paleontological Society Special Publication, 3:72-104. Kovach, W.L., 1988. Quantitative palaeoecology of megaspores and other dispersed plant remains from the Cenomanian of Kansas, USA. Cretaceous Research, 9:265-283. Kovach, W.L., 1989. Comparisons of multivariate analytical techniques for use in pre-Quaternary plant paleoecology. Review of Palaeobotany and Palynology, 60:255-282. Kovach, W.L. & Batten, D.J., in press. Association of palynomorphs and palynodebris with depositional environments: quantitative approaches. In: Traverse, A. (ed.), Sedimentation of Organic Particles. Cambridge University Press. Lance, G.N. & Williams, W.T., 1966. A generalized sorting strategy for computer classifications. Nature, 212:218. Legendre, L., & Legendre, P., 1983. Numerical Ecology. Elseveir Scientific Publishing Company, New York. Lesperance, P.J., 1990. Cluster analysis of previously described ' communities from the Ludlow of the Welsh Borderland. Palaeontology, 33:209-224. Noy-Meir, I., 1973. Data transformations in ecological ordination. I. Some advantages of non-centering. Journal of Ecology, 61:329-341. Orloci, L., 1978. Multivariate Analysis in Vegetation Research, 2nd edition. W. Junk, Boston. Pielou, E.C., 1969. An Introduction to Mathematical Ecology. Wiley-Interscience, New York. Pielou, E.C., 1984. The Interpretation of Ecological Data. Wiley-Interscience, New York. Prentice, I.C., 1980. Multidimensional scaling as a research tool in Quaternary palynology: A review of theory and methods. Review of Paleobotany & Palynology, 31:71-104. Sneath, D.H., & Sokal, R.R., 1973. Numerical Taxonomy. W.H. Freeman & Co., San Francisco. ter Braak, C.J.F., 1986. Canonical correspondence analysis: A new eigenvector technique for multivariate direct gradient analysis. Ecology, 67:1167-1179. MVSP Ver. 2 -- Users Manual Page 21 REGISTRATION FORM FOR MVSP Plus Please complete this form and return it to the address below, along with a cheque or money order for UKL40 or US$75 to the - address below. Please make cheques payable to "Warren L. Kovach". Note that the US$ price assumes an exchange rate of approximately 1.90 $/L. If the exchange rates are very different - (more than 10 cents either way) please adjust the US$ price accordingly. Dr. Warren L. Kovach Institute of Earth Studies University College of Wales Aberystwyth, Wales SY23 3DB U.K. Name:____________________________________________________________ Address:_________________________________________________________ _________________________________________________________________ City:____________________________ State/Province:________________ Post Code_________________ Country:______________________________ Email (Bitnet, Compuserve, etc.)_________________________________ Please check disk size required: ____ 5 1/4" (360K) ____ 3 1/2" (720K) I would appreciate it if you could answer the following questions: What other types of analyses would you like to see in MVSP? Would you be interested in a version written for Windows 3.0? What type of computer do you use? (please specify brand, CPU type (8088, 80286, 80386, 80486), amount of memory, size of hard disk, whether you have an 80x87 math chip, etc. Where did you get this copy of MVSP Shareware? (if from a BBS or shareware distributer, then the phone number or address would be useful to me for future updates).