** ** ****** ** ** ******** ** ** ***** ** ** ** * ** ** ** *** ** ** ** ** ** * ** ** ** * **** **** ** * ** ** ** ** ** **** ** ** ** ** ** *** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** ** * ** ** ** ** ** ****** ** ** ** ***** ***** ** ** ** ****** ****** ***** ** **** ******** ****** ****** ** ** ** ** * ** ** * ** ** ** ** ****** **** ** ** ** ** **** ****** ** ** ** ** **** ** ** ** ** ** ** ** ** ** ** ** ** * ** ** ** ** ** ** ** ****** ***** ** **** ** ****** ** ** **** KY REGISTER **** KY REGISTER **** KY REGISTER **** KY REGISTER *** MARCH 1989 TABLE OF CONTENTS CCS Spring Seminar Series. . . . . . . . . . . . . . . . . . . . . . 44 UKCC Short Courses . . . . . . . . . . . . . . . . . . . . . . . . . 80 SUPER! . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 Keeping Your Userid Secure . . . . . . . . . . . . . . . . . . . . . 157 BMDP5V: Unbalanced Repeated Measures with Structured Covariance Matrices . . . . . . . . . . . . . . . . . . . . 197 Suggestions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 399 Classifieds . . . . . . . . . . . . . . . . . . . . . . . . . . . . 534 Service Directory . . . . . . . . . . . . . . . . . . . . . . . . . 549 ************************************************************************* CENTER FOR COMPUTATIONAL SCIENCES 1989 SPRING SEMINAR SERIES All of the following seminars are free and open to the public. Unless otherwise noted, all seminars will be held on Wednesdays, 4:00 p.m. in 137 Chemistry-Physics Building. Refreshments at 3:30 p.m. March 1 Opportunities in Computational Chemistry & Materials Science Thomas Weber, NSF and Bell Labs March 8 The Use of Computers in Archaeological Research Christopher Peebles, Indiana University March 20 (Monday) Supercomputers & Conformation of Biological Molecules Harold Scheraga, Cornell University March 29 Phase Transitions in Particle & Condensed Matter Physics Gyan Bhanot, Florida State University April 5 Imaging the Earth's Interior by Supercomputer Larry Brown, Cornell University April 12 Computational Fluid Dynamics Philip M. Gresho, Lawrence Livermore Laboratory April 19 Seismic Modeling of the Earth's Interior Freeman Gilbert, University of California, San Diego ************************************************************************* UKCC SHORT COURSES The following short courses are free to all UK faculty, staff, and students, but preregistration is required. If you register for a course and then find that you will be unable to attend, please cancel your registration by calling 257-UKCC. Failure to do so may jeopardize your right to register for future UKCC short courses. There are several ways you can register, depending on the class: * You can register online. Enter PUBLIC, and then type SHORTCOUrse, or enter VIEW UKCC SHORTCOURSE. Some classes require online registration. * You can register by calling 257-UKCC (this is Voice Mail Exchange, your registration will be confirmed by phone within five days). Many of these classes don't require any knowledge or experience with any computer system. If there are prerequisites for a particular class, they'll be listed in the class description. If you have questions about class content or bypassing prerequisites, call the instructor for that class. INTRODUCTION TO VM/CMS AND XEDIT Monday, March 27 and Tuesday, March 28 6:00 to 8:00 p.m. 103 McVey Hall A basic introduction to interactive use of the IBM mainframe systems, this class presumes no previous knowledge of the IBM systems or any other computer system. You'll learn how to access the computer, how to create and manage files on your account, and how to use online tools such as CALENDAR and VIEW. You'll also learn how to use the CMS text editor, XEDIT, to create and modify individual files. This course will be taught in two two-hour sessions. Both sessions will provide hands-on practice of the commands that are covered. You will be given a class computer account which will remain active for the duration of the course. This course will be offered three times during the Spring semester. Your instructor will be Pat Murphy (257-2244). ADVANCED GRAPHICS PROGRAMMING TOOLS Monday, Wednesday, and Friday March 20, 22, and 24 1:30 p.m. to 3:30 p.m. 326 McVey Hall (CCS) This course will concentrate on more advanced features and capabilities of DI3000 and other mainframe Precision Visuals software modules. Topics will include the use of "metafiles" and the PVI Metafile Translator, fundamental modeling and animation techniques, retained segments and segment storage data structures, and contour and 3-D mesh surface mapping on the IBM systems. Newer additions to the PVI software family will be introduced and demonstrated. Participants in this workshop should be familiar with CMS, VS FORTRAN, and basic DI3000 programming. Bob Williamson will be your instructor (257-2227). Online registration is required for this course. ************************************************************************* SUPER! This year's annual meeting of SUPER! (Supercomputing by University People for Education and Research) will be hosted by the University of Kentucky, April 23 to 26, in Lexington. The theme of the meeting will be "Supercomputing in the 90s." University people actively engaged in IBM-based high-performance computing, including researchers and teachers, computing center staff and management, and user support staff are encouraged to become involved in SUPER! For more information, contact Sandy Leachman at 257-8737; SANDY@UKCC.BITNET; or FAX 606/257-4000; or write Center for Computational Sciences 325 McVey Hall Lexington, KY 40506-0045 ************************************************************************* KEEPING YOUR CMS USERID SECURE Your CMS userid and your files are safe from tampering as long as your password is secure. Here are a few tips: * For maximum security, turn off and then turn on public terminals before you log on (but please leave public terminals on when you leave). If you encounter a terminal with a strange logo or that seems to be running some kind of a program, turning it off and back on will force off whatever might have been running. * Give your password only to those who need it. It's best to not give it out at all. * Never write down your password or enter it on the same line as your userid when logging on. * Change your password frequently (use the PASSWORD command). Avoid passwords that might easily be guessed by someone trying to tamper with your userid (like your name or userid, for example). Use the full eight characters for your password and include some non-alphabetic characters (like digits or punctuation). * Never leave your userid logged on unattended in a public area. When you logoff be sure that your userid is completely logged off before you leave. * If you ever encounter peculiar messages while logging on, if your password isn't accepted, or if you can't log on because your userid is logged on already, contact the UKCC immediately. Although these suggestions are for CMS users, similar measures can be used with most timesharing systems. -- Dave Elbon ************************************************************************* BMDP5V: UNBALANCED REPEATED MEASURES WITH STRUCTURED COVARIANCE MATRICES The latest release of the MVS/370 BMDP statistical subprogram library includes BMDP5V, an interesting new program that will perform analysis of variance of repeated measures or other correlated responses. BMDP5V is useful in solving two frequent difficulties that arise when analyzing such data: modeling the covariance structure of the residual errors and dealing with missing repeated measures. Statistical programs such as SAS, SPSSx, and BMDP include facilities for either the univariate approach assuming sphericity, adjusted F-statistics, or the multivariate approach for unstructured covariances. BMDP5V, on the other hand, enables you to easily analyze data assuming virtually any identifiable covariance structure. It also incorporates analysis adjusting for missing response measures. Repeated Measures Analysis of Variance The usual assumption in analysis of variance is that the random error terms are uncorrelated across measures. When more than one measurement is taken on a subject you have "repeated measures," and this assumption is likely to be false. The usual split-plot or mixed model analysis is still valid if sphericity is assumed in the random errors of the repeated measures. Sphericity holds when orthogonal contrasts of the repeated measures are uncorrelated. In practice, assuming the errors are equally correlated with equal variances (compound symmetry) is sufficient for sphericity and is probably the most natural way for sphericity to occur. This sphericity assumption is very important. If it doesn't hold, the usual split plot tests will be anti-conservative, possibly very anti-conservative. Examples exist showing how an F-statistic for a null interaction that would be significant at a 0.05 level under sphericity actually has a 0.6+ level! So whether or not you have any effects, if sphericity does not hold and you assume it is true, depending upon the covariance structure, you're likely to get "significant" F-statistics. By assuming sphericity, you are assuming a very specific structure to the covariances of the repeated measures. If sphericity is not reasonable, the usual univariate analysis is probably not appropriate. An alternative to the sphericity assumption is to assume that the covariances of the repeated measures are unstructured. This suggests a multivariate analysis. Suppose Y1, Y2, and Y3 are responses to a repeated measure. The multivariate test that Y1-Y2 and Y2-Y3 are simultaneously zero is actually testing the "main effect" of the repeated measure. For such contrasts in the response, the usual multivariate tests of "between subject" factors will correspond to tests of interactions of the repeated measure and between subject factors. However, these tests will often lose power to detect differences relative to the univariate tests. Another approach is to adjust the statistics in the univariate analysis for lack of sphericity, usually using the Box correction factor, epsilon, as an estimate of the amount of sphericity. If sphericity does not hold, an approximate test can be generated by comparing the usual F-ratio with the significance point derived from an F-distribution where both the numerator and denominator degrees of freedom have been multiplied by epsilon. This leads to the Box-Greenhouse-Geisser-Imhof or the Huhyn-Feldt F corrections printed by SAS, SPSSx, BMDP2V, and BMDP4V. Both of these approaches assume either a rather restrictive covariance structure, sphericity, or no structure at all. However, there are times you may wish to assume other covariance structures among the repeated measures. Econometricians have used AR(1) autoregressive error structures, where, for example, the errors one time unit apart have correlation p, while those two units apart have correlation p**2, three apart p**3, etc. Thus errors closer in time will be more highly correlated. In other analyses you may wish to use more general autoregressive covariance structures, a factor analytic structure, a random coefficients model, or some general linear structure. Contrasts for repeated measures assuming these structures will generally not be spherical, and, presumably, multivariate modeling with an unstructured covariance matrix will lose power. Again, BMDP5V allows virtually any identifiable covariance structure. The second major limitation to the usual repeated measures analyses is dealing with missing repeated measures. First, the multivariate approach requires complete data. Incomplete response vectors must be deleted. To access the special features for repeated measures in the standard packages, the data have to be entered in this multivariate mode. Even if you want a univariate analysis, all measures for a subject are deleted if any of the repeated measures are missing, when using the specific repeated measures features. You could reformulate the data and explicitly enter a subject effect, but that has other limitations. For example, between subject factors are usually completely parameterized; that is, one between subjects parameter is introduced for each subject. Such designs often exceed computing capacity when you add interaction error terms. By comparison, BMDP5V does not require complete data on all measures. It requires the assumption that the probability a response is missing is independent of the "true" value of the response, so-called "missing at random." If sphericity holds, the between subject factors are fully parameterized, and the data are missing at random, the usual tests for repeated measures factors against within subject error are exact, but the usual tests (using subject means) for between subject factors aren't. Apparently, unless there are absolutely no repeated measures/sub-plot effects, these tests are not even asymptotically valid. BMDP5V provides asymptotically valid, maximum likelihood estimates and associated tests for such missing data situations. BMDP5V is not appropriate for all analyses. However, when you have a repeated measures or a split-plot analysis with an unusual covariance structure, or have missing data in your repeated measures or sub-plots, you may wish to use this program for your analysis. Some Specific BMDP5V Commands /DESIGN DPName = varname Names dependent variable for MODEL paragraph. DPVar = var list Specifies list of (repeated) variables for each subject. GROUP = var list Specifies between subject factors. REPEATED = namelist Names the repeated measures factors. LEVEL = # list Lists number of levels for each variable named in the REPEATED statement. CVNAME = covariate Lists covariates associated with dependent variables. name list. (time-varying covariates) cov name 1 = var list 1. cov name 2 = var list 2. etc. CONTRAST(var) = c list. Specifies partition of effects into c1 = #1, #2, #3, ..., #n. contrasts. c2 = #1, #2, #3, ..., #n. etc. /MODEL dependent var = 'list of terms to include in model'. INTERCEPT or NO INTERcept. for example: Y='A + B + A.B'. /STRUCTURE TYPE (one only) CS Compound symmetry. UNSTRUC Unstructured. AR1 Autoregressive of order 1. BANDED Toeplitz (general autoregressive). FACTOR Factor analytic. RANDOM Random effects. LINEAR Linear in a set of specified basis matrices. USER Other user specified structure. (The last four structures require additional parameters to define the covariance structure.) /COMPUTE ALGorithm (one only) NR Maximum Likelihood using Newton Raphson FS Maximum Likelihood using Fisher Scoring GEM Maximum Likelihood using Generalized EM REML Restricted Maximum Likelihood using Generalized EM REML Restricted Maximum Likelihood using Quasi-scoring MAXIT=#. Specifies maximum number of iterations. /PRINT COVR. Prints estimated covariance matrix of regression coefficients. COVC. Prints estimated covariance matrix of covariance parameters. (Not available when ALG = REML or QSR) RES. Prints response, residuals, etc. An Example Suppose you've measured a response, y, to one of three levels of some treatment. You took measurements the same time each day for two days, once in the morning and once in the evening. Overall, you have four repeated measures. You decide it is appropriate to analyze this as two repeated measures factors, specifically, day and ampm, for time of day. Finally, you suppose an AR(1) error structure seems appropriate. A possible BMDP5V program for this would be: /PROBLEM TITLE IS 'ONE-GROUPING, TWO TRIAL FACTORS'. /INPUT VARIABLES ARE 5. FORMAT IS FREE. /VARIABLE NAMES ARE TREAT,YAM1,YPM1,YAM2,YPM2. /GROUPING CODE(TREAT)=1,2,3. /DESIGN GROUPING=TREAT. LEVEL=2,2. REPEATED=DAY,AMPM. DPNAME=Y. DPVAR=YAM1,YPM1,YAM2,YPM2. /MODEL Y='TREAT + DAY + DAY.TREAT + AMPM + AMPM.TREAT + DAY.AMPM + DAY.AMPM.TREAT'. /STRUCTURE TYPE=AR1. /PRINT COVR. COVC. /END 1 10 * 11 12 data 3 13 14 15 15 BMDP5V is described in the BMDP technical report #86, "BMDP 5V - Unbalanced Repeated Measures Models with Structured Covariance Matrices." A reference copy is available in the Consulting Room, 110 McVey Hall. A more detailed description of the algorithms appears in Jennrich and Schluchter's paper in "Biometrics," 1986, pp. 805-820. For more information or help with BMDP5V, contact Steve Thomson, STEVE@UKCC, 120 McVey Hall, 257-2259. -- Steve Thomson ************************************************************************* SUGGESTIONS 1. Does anybody know how to unerase files for the Macintosh? Many thanks in advance. >>>It's sometimes possible to recover erased files, and there are a number of commercially available utilities for this. The MacZap package is one. 2. I'm using a hard-wired IBM PS2 model 30 and Kermit to call the library hookup LS/2000. I want to read the library holdings into a text file so that I can manipulate it with WordPerfect to make bibliographies. Is this possible via UKnet? Will Kermit work, or do I have to use a communications package like PC Modem? If I can use my UKCC account, please give directions for making an XEDIT textfile out of the library information which I can then download. Thanks. >>>Try using Kermit's session logging. This copies characters that appear on the screen during connect into a specified file on your PC. Kermit-MS->log session filename.ext Kermit-MS->connect Logon to the library system and call up what you want recorded. When you've captured everything you need, escape back to kermit ms Kermit-MS->close session You can then bring the file into WordPerfect and modify as needed. 3. Many of the terminals in 111 McVey Hall do not work or have bad keys. Teaching students how to use the computer systems is becoming more and more difficult because of this. Would someone please take the time to fix these terminals so that finding one to use isn't as hard as finding a parking place? >>>Thanks for bringing this to our attention. Much of the equipment in 111 McVey is very old, and we're trying to secure funds for upgrades. In the meantime, we're continually trying to keep up with the necessary repairs. Whenever you find a broken terminal, please report it to the Data Center immediately. 4. I heard some time ago there was an Amiga 2000 in the Micro Lab. I recently went there to use that machine and was informed it was out for repairs and that it had been out for repairs a long, long time. What's going on? Amigas would be valuable additions to the Micro Lab since there are so many Amiga owners on campus. >>>We've had a lot of problems with the machine, with the company we purchased it from, with the same company when it came time for repairs, and in getting the money for the repairs. A local company is now repairing the machine, and we hope it will be back with us soon. 5. An online ZIP CODE directory would be very handy. >>>We agree. We're working on getting this information online, and details will be published as soon as they're available. 6. Would it be possible to add an option to the calendar that would let you see one week at a time and allow more information for each day to show up on the screen without going to the detail? >>>We'll add that to our list of possible future enhancements. Thanks for the suggestion. 7. I recently obtained an account on UKCCXA. I used my profile exec to define: SET PF1 RECALL, and it isn't working. I also can't change my password. Is there any way to implement these features which are used in almost all systems? Can make SAS accessible on systems other than UKCC? I'm trying to use SAS Graphics. >>>Use SET PF1 RETRIEVE. XA requires RETRIEVE; the other VM systems accept both RETRIEVE and RECALL. Password changing will be available after VM/XA SP 2 is available and the necessary programs have been converted. We're working on it. We don't have a SAS license for the IBM 3090. 8. It would be helpful if there was a command that could be issued to find one's project numbers. Is this possible? >>>The BALANCE command can give you the account number for CPU time. It doesn't display this directly, but it has a STACK option that will give it to you. To see what this does, use the STK command: STK BALANCE ( STACK This will execute BALANCE with the STACK option and display the stacked data. See HELP BALANCE for more information. There is no way to determine your disk account number at this time, but we'll add it to our list of possible future enhancements. 9. We're connecting a TVI955 to an Apple ImageWriter II. What is the procedure for printing locally using the PRIMEs, IBMs, etc.? Does the print key on the TVI955 do anything? What is the appropriate set-up? >>>Your TeleVideo 955 manual should explain what, if any, local print functions it supports. When logged on to VM and using CMS the APRINT command may be able to print on an attached printer. It has support for a TeleVideo 950 and that may work with a 955 also. See HELP APRINT for more information. 10. The LWSAS procedure doesn't generate PostScript in the suggested style as documented in Appendix C of the "PostScript Language Reference Manual." If someone does LWSAS (file to have the output file saved, then FTP the resulting file over to a Math Sciences machine for output, the "%!" line at the beginning is missing. While it isn't a big deal to add that line, it would be a great help if it were there. As is documented, the Unix printer drivers do PostScript stuff when they see that "%!" line at the beginning. >>>Both LWSAS and LWPLOT now generate files that start off with "%!PS-Adobe-2.0." Use LWSAS (CCxxx VIA *. The PostScript file will go into your reader. You need a valid printer, even though it's not used. Add the KEEP option if you want to keep the SAS metafile. 11. When I try to access the UKCC FTP server from another campus machine the server allows the connection but doesn't establish a "working directory". I'm unable to list the files on any of my CMS minidisks or to move files back and forth between the machines. Efforts to establish such a "working directory" result in an obscure error message being sent by the UKCC FTP server. How can the working directory on the remote machine be established? Is it not possible to use the UKCC FTP server to move files onto a CMS minidisk (as opposed to getting them from a minidisk)? Thanks. >>>We use AUTOLINK to authorize links to most minidisks instead of the standard VM password scheme. Since there is no password for the minidisk, the FTP server can't link to it, regardless of what you put on the CD command. For now, you can't FTP from a remote host to UKCC when a private minidisk is involved. You can FTP when a public disk is involved, such as PUBLIC 191. You can also log onto UKCC and use FTP to the remote host to transfer files. ************************************************************************* UKCC CLASSIFIEDS Ads are free to UK students, faculty, and staff. If you'd like to place a computing-related ad, contact the Editor at 257-2219, EDITOR@UKCC, 200 McVey Hall for details. FOR SALE: NEC Multispeed Laptop computer, 640K, two 3.5" drives, clock speed 9.54 Mhz or 4.77 Mhz selectable, weight approx. 5 kg. Built-in calendar, detachable LCD screen, full keyboard with ten function keys and number pad. A very nice computer and used only for nine months during a sabbatical. $850.00. Call Newbery at 257-6746 or 252-6944. ************************************************************************* UKCC SERVICE DIRECTORY McVey Service E-Mail Address Phone Hall Vice President, Information Services Eugene R. Williams DPS128@UKCC 257-3609 Director, University Computing Services Dr. Douglas Hurley HURLEY@UKCC 257-2900 128 Director, Communications & Distributed Systems Doyle Friskney DOYLE@UKCC 257-6225 Director, Computational Sciences Dr. John Connolly CONNOLLY@UKCC 257-8737 324 Academic Consulting Services Lavine Thrailkill UKC105@UKCC 257-2257 121 CMS Consulting Bob Crovo CROVO@UKCC 257-2258 109 Complaints Carol Lotz LOTZ@UKCC 257-2213 129 Consultant for Remote Sites Wanda Dixon Spisak WANDA@UKCC 257-2206 115 Consulting Consultant on Duty SUGGEST@UKCC 257-2249 110 Contingency Planning & Security Jack L. Coffman UKA051@UKCC 257-2273 218 Database - IDMS Rick Chlopan DBA003@UKCC 257-2211 230E Data Center 257-2222 61 Data Entry Frank McCormick OPFRANK@UKCC 257-2216 72 Disk Rental Janet Hyatt HYATT@UKCC 257-2212 130 Larry Johnson JOHNSON@UKCC 257-2217 130 Facilities Operations Joe Williams UKA048@UKCC 257-2231 122 Graphics Consultation Bob Williamson ROBERTT@UKCC 257-2227 207 Information Center Judy Kisil UKA041@UKCC 257-2241 222 Information Resources Dr. Jon Hesseldenz UKA045@UKCC 257-3904 230D Instructional Software Wayne Beech WAYNE@UKCC 257-2238 100 Machine Room 257-2222 59 Management Information Systems Forrest Hahn UKA006@UKCC 257-2260 123 Memos and Manuals Consulting Room 257-2249 110 Micro Lab 257-2207 107 Network/Telecommunications UKT101@UKCC 257-2229 New Accounts Janet Hyatt HYATT@UKCC 257-2212 130 Larry Johnson JOHNSON@UKCC 257-2217 130 Numerical Analysis Consulting Anne Leigh ANNE@UKCC 257-2205 109B Optical Scanner - NCS Chris Corman CHRIS@UKCC 257-2243 109 Bob Crovo CROVO@UKCC 257-2258 109 Passwords Janet Hyatt HYATT@UKCC 257-2212 130 Larry Johnson JOHNSON@UKCC 257-2217 130 PRIME Information Peggy Akridge PEGGY@UKCC 257-2237 100 Program Documentation/Libraries Consulting Room 257-2249 110 Publications Office Marguerite Floyd EDITOR@UKCC 257-2219 200 Refunds Consulting Room 257-2249 110 SAS and SPSS Consulting Steve Thomson STEVE@UKCC 257-2259 120 Lorinda Wang UKC333@UKCC 257-2204 109B Statistical Consulting Steve Thomson STEVE@UKCC 257-2259 120 Tapes to Borrow, Tape Storage Data Center 257-2222 61 Tours of UKCC Lavine Thrailkill UKC105@UKCC 257-2257 121 User Account Services Janet Hyatt HYATT@UKCC 257-2212 130 Larry Johnson JOHNSON@UKCC 257-2217 130 Vectorization Consulting Tom Faller TOMFAL@UKCC 257-2236 314 ************************************************************************* UNIVERSITY COMPUTING ADVISORY COMMITTEE Douglas E. Hurley, Central Administration H. Clay Owen, Central Administration A.J. Hauselman, Community Colleges James W. Phillips, Community Colleges Raphael Finkel, Lexington Campus Leonard K. Peters, Lexington Campus N. Clare Detraz, Medical Center David A. Nash, Medical Center T. Earle Bowen, Ex Officio Ben W. Carr, Ex Officio Wimberly C. Royster, Ex Officio Donald E. Sands, Ex Officio Eugene R. Williams, Ex Officio *************************************************************************