Each Link is to Acrobat PDF file containing a chapter or appendix of the Users' Guide (Chapter 2 is in two files).
Preface (manpref.pdf) i 1. Introduction (manchp01.pdf) 1.1 What is MacAnova? 1-1 1.2 Comments on Version 4.07 1-2 1.3 Conventions in this manual 1-4 1.4 Disclaimer 1-4 1.5 Acknowledgments 1-4 1.6 How to contact the authors 1-6 2. The Basics (manchp2a.pdf) 2.1 Getting Started 2-1 2.2 Quitting 2-1 2.3 Functions and macros 2-2 2.4 Variables 2-3 2.5 Data types REAL, LOGICAL and CHARACTER 2-3 2.6 Shapes of variables scalars, vectors, matrices, arrays 2-4 2.7 Missing values 2-5 2.8 Introduction to MacAnova syntax 2-5 2.8.1 Spaces and comments 2-6 2.8.2 Keywords 2-6 2.8.3 Arithmetic expressions 2-6 2.8.4 Comparison operators and logical operators 2-7 2.8.5 Bit-wise operations on integers 2-8 2.8.6 Mathematical functions and transformations 2-10 2.8.7 Assignment of values to variables 2-12 2.8.8 Arithmetic assignment operators 2-13 2.8.9 print(), write(), list(), listbrief() and delete() 2-13 2.8.10 Vectors vector(), enter and enterchars 2-15 2.8.11 Using subscripts with vectors 2-16 2.8.12 rep() and run() 2-18 2.8.13 Matrices and matrix() 2-19 2.8.14 Using subscripts with matrices 2-20 2.8.15 Arrays array() 2-21 2.8.16 Structures structure() 2-23 2.8.17 Matrix subscripts 2-25 2.9 Getting help help() and usage() 2-26 2.9.1 Using the help() wild card characters "*" and "?" 2-27 2.9.2 Using help() index keys 2-27 2.9.3 Getting help on macros macrousage() 2-28 2.10 Operations with vectors, matrices, and arrays 2-28 2.10.1 Transformations 2-28 2.10.2 Arithmetic with vectors, matrices and arrays 2-29 2.10.3 Matrix transposition 2-30 2.10.4 Matrix multiplication 2-31 2.10.5 Matrix inversion and linear equation solving 2-32 2.10.6 Other matrix functions det(), trace(), hconcat(), vconcat(), diag(), dmat(), nrows(), ncols(), select(), reverse() 2-33 2.11 Reading data from a file 2-35 2.11.1 vecread() 2-36 2.11.2 (manchp2b.pdf) readcols 2-38 2.11.3 matread() and read() 2-39 2.11.4 getdata 2-41 2.11.5 inforead() 2-41 2.11.6 HOME, DATAPATHS and adddatapath 2-42 2.12 Simple statistics 2-43 2.12.1 describe() 2-43 2.12.2 boxplot(), vboxplot, stemleaf() and hist 2-46 2.12.3 sort(), rank(), rankits(), halfnorm(), and grade() 2-51 2.12.4 sum(), prod(), max(), min() 2-54 2.12.5 Computing correlations cor() 2-55 2.12.6 Student's t related functions tval(), t2val(), tint(), t2int() and twotailt 2-56 2.12.7 P-values and cumulative distributions functions cumxxx() functions 2-58 2.12.8 Probability points and inverse cumulatives invxxx() functions 2-62 2.12.9 Grouping data in class intervals bin() 2-63 2.13 Random numbers runi(), rnorm(), rbin() and rpoi() 2-65 2.13.1 Random number "seeding" setseeds() and getseeds() 2-66 2.13.2 Generating other random variables 2-66 2.14 More on rep() and run() 2-67 2.15 Making graphs 2-68 2.15.1 plot() 2-69 2.15.2 lineplot() 2-70 2.15.3 chplot() 2-71 2.15.4 Equally spaced x values 2-73 2.15.5 Graphics keywords 2-73 2.15.6 colplot and rowplot 2-73 2.15.7 Low resolution plots 2-74 2.16 Using spool() to save output 2-74 2.17 Using save() and restore() to preserve work between sessions 2-76 3. Linear Models (manchp03.pdf) 3.1 Introduction to GLM commands 3-1 3.2 Response and independent variables in linear models 3-2 3.3 Variates and factors factor() and makefactor 3-3 3.4 Specifying a model 3-4 3.4.1 Transforming "on-the-fly" 3-6 3.4.2 Model shortcuts: *, ^, /, and * 3-7 3.4.3 Shortcuts for polynomial and periodic regressions 3-8 3.5 Error terms 3-8 3.6 Side effect variables 3-9 3.7 GLM keywords 3-9 3.8 anova() and regress() output 3-11 3.9 Balanced and unbalanced data 3-15 3.10 Parametrization and degrees of freedom 3-16 3.11 Marginal (Type III) sums of squares 3-18 3.12 Cell by cell statistics using tabs() and cellstats() 3-19 3.13 Estimated ANOVA effects and their standard errors coefs() and secoefs() 3-20 3.13.1 Estimated regression coefficients and their standard errors regcoefs 3-22 3.14 Leaving out lower order terms 3-23 3.15 Empty cells 3-24 3.16 Estimating contrasts contrast() 3-27 3.16.1 Contrasts for each level of a factor 3-31 3.17 Residuals resid, resvsyhat, resvsrankits, resvsindex 3-32 3.18 Predicted values regpred(), yhat, predtable(), glmpred() and glmtable() 3-35 3.19 Faster ANOVA calculation fastanova() 3-38 3.20 Selection of a subset of X-variables screen() 3-39 3.21 Power and sample size power(), power2() and samplesize() 3-42 3.22 Multivariate linear models manova() 3-45 3.23 Weighted analyses keyword weights and side effect variable WTDRESIDUALS 3-48 3.24 Retrieving information about a GLM analysis 3-49 3.24.1 modelvars() and varnames() 3-49 3.24.2 xvariables() 3-50 3.24.3 xrows() 3-51 3.24.4 modelinfo() 3-52 3.24.5 Decoding modelinfo(bitmodel:T) 3-55 4. Generalized linear models and robustness (manchp04.pdf) 4.1 Alternatives to Least Squares 4-1 4.2 Generalized Linear Model Commands 4-1 4.2.1 Analysis of Deviance Table 4-2 4.2.2 Side effect variables 4-3 4.2.3 Keywords 4-4 4.2.4 logistic() and probit() 4-5 4.2.5 poisson() and ipf() 4-7 4.2.6 glmfit() 4-7 4.3 Robust regression robust() 4-8 5. Time Series related functions (manchp05.pdf) 5.1 Introduction 5-1 5.2 Functions useful in frequency domain time series analysis 5-1 5.2.1 The DFT (Discrete Fourier Transform) 5-1 5.2.2 Continuous Fourier transform of a finite series 5-3 5.2.3 Representation of Real, Hermitian, and Complex Series 5-3 5.2.4 Functions for manipulating Complex and Hermitian series hconj(), cconj(), hreal(), creal(), himag(), cimag(), cpolar(), hpolar(), crect(), hrect(), htoc(), ctoh(), cmplx() 5-5 5.2.5 padto() and rotate() 5-9 5.2.6 Elementwise products of Complex and Hermitian series hprdh(), hprdhj(), cprdc(), cprdcj() 5-10 5.2.7 Discrete Fourier Transforms rft(), hft() and cft() 5-10 5.2.8 Convolving series using the DFT and function convolve() 5-12 5.3 Functions related to time domain time series analysis 5-14 5.3.1 Moving average and autoregressive operators 5-14 5.3.2 movavg() 5-16 5.3.3 autoreg() 5-17 5.3.4 yulewalker() and partacf() 5-18 5.3.5 toeplitz() 5-19 5.3.6 Finding zeros of polynomials polyroot() 5-20 5.4 Macros useful in time series analysis 5-21 5.4.1 Plotting against time tsplot 5-22 5.4.2 Plotting against frequency ffplot 5-23 5.4.3 Computing auto-covariances autocov 5-26 5.4.4 Removing a polynomial trend detrend 5-27 5.4.5 Using tapers (data windows) costaper and compza 5-27 5.4.6 Smoothing periodograms compfa and spectrum 5-30 5.4.7 Smoothing cross-periodograms compfa and crsspectrum 5-34 5.4.8 Multi-taper spectrum estimation multitaper 5-36 5.4.9 Autoregressive spectrum estimation arspectrum and burg 5-37 6. Other functions (manchp06.pdf) 6.1 Linear model computations using swp() 6-1 6.1.2 Computing a more accurate cross product matrix bcprd() 6-4 6.2 Computation of eigenvalues and eigenvectors 6-5 6.2.1 Ordinary eigenvalues and eigenvectors eigenvals() and eigenvectors() 6-5 6.2.2 Eigenvalues and eigenvectors of a tridiagonal matrix trideigen() 6-7 6.2.3 Relative eigenvectors and eigenvalues of a symmetric matrix releigenvals() and releigen() 6-8 6.3 Singular value decomposition svd() 6-10 6.4 QR decomposition qr() 6-11 6.5 Cholesky decomposition cholesky() 6-13 6.6 Working with triangular matrices triupper(), trilower() and triunpack() 6-13 6.7 Cluster analysis 6-15 6.7.1 Hierarchical analysis cluster() 6-15 6.7.2 K-means analysis kmeans() 6-19 6.8 Factor rotation rotation() 6-22 7. Files (manchp07.pdf) 7.1 Format of data readable by matread() and read() 7-1 7.1.1 REAL and LOGICAL data 7-5 7.1.2 CHARACTER data 7-6 7.1.3 Structures 7-6 7.1.4 Labels and notes 7-7 7.1.5 matread() and read() keywords 7-8 7.2 Reading CHARACTER data from files 7-8 7.3 "Reading" from CHARACTER variables 7-11 7.3.1 "Decoding" a CHARACTER variable 7-12 7.3.2 Finding ASCII codes for a CHARACTER variable getascii() 7-12 7.4 Writing data to the screen and to files 7-14 7.4.1 print() and write() 7-15 7.4.2 matprint() and matwrite() 7-17 7.4.3 putascii() 7-20 7.5 Macro files 7-21 7.5.1 macroread() and the format of macro files 7-21 7.5.2 macrowrite() 7-23 7.5.3 getmacros 7-24 7.5.4 addmacrofile 7-25 7.6 Executing commands in a file batch() 7-25 7.7 Additional options on save( and restore() 7-27 7.8 Customizing MacAnova 7-29 7.8.1 Using a start up file 7-29 7.8.2 Environmental variable MACANOVA 7-30 8. Advanced Features (manchp08.pdf) 8.1 MacAnova options 8-1 8.1.1 getoptions() 8-1 8.1.2 setoptions() 8-2 8.1.3 List of available options 8-3 8.2 Treatment of errors 8-7 8.3 Creating CHARACTER variables 8-8 8.3.1 Building custom CHARACTER variables paste() 8-9 8.3.2 Formatting paste() output 8-9 8.3.3 Creating CHARACTER vectors using paste() 8-11 8.3.4 Creating CHARACTER variables using putascii() 8-11 8.4 Coordinate labels 8-12 8.4.1 Adding labels to a variable setlabels() 8-12 8.4.2 Retrieving labels from a variable getlabels() and haslabels 8-16 8.4.3 Transforming labels 8-17 8.4.4 Propagation of labels 8-18 8.5 More on plotting 8-20 8.5.1 Keywords affecting appearance and bounds 8-20 8.5.2 Other graphics keywords 8-21 8.5.3 Replotting graphs and GRAPH variables 8-23 8.5.4 Writing graphs to a file 8-25 8.6 More on help() and usage() 8-26 8.6.1 Using more than one help file 8-26 8.6.2 Finding what's new 8-27 8.7 Running other programs from within MacAnova 8-28 8.7.1 shell() 8-28 8.7.2 shell() keyword phrases interact:T and keep:T 8-29 8.7.3 Lines starting with "!" 8-29 8.8 Recalling previous commands 8-30 8.8.1 Macros redo and REDO 8-30 8.8.2 Keyboard and menu recall 8-30 8.8.3 gethistory() and sethistory() 8-31 8.9 "Notes" attached to variables 8-32 8.9.1 attachnotes(), appendnotes(), getnotes() and hasnotes 8-33 9. Programming MacAnova (manchp09.pdf) 9.1 Working with structures 9-1 9.1.1 Creating structures structure(), strconcat() and split() 9-1 9.1.2 Getting information about a structure ncomps() and compnames() 9-5 9.1.3 Changing a structure changestr() 9-5 9.2 Compound commands, conditional commands, and looping commands 9-6 9.2.1 Compound commands 9-6 9.2.2 Conditional commands if, elseif and else 9-7 9.2.3 Looping for and while 9-9 9.2.4 Escaping from loops break and breakall 9-11 9.2.5 Skipping to the end of a loop 9-12 9.3 Macros 9-13 9.3.1 Creating macros 9-14 9.3.2 Argument substitution 9-14 9.3.3 The use of temporary variables and $$ 9-16 9.3.4 Other expanding macro symbols 9-18 9.3.5 In-line and out-of line macros 9-19 9.3.6 Using delete(result,return:T) in a macro 9-20 9.4 Functions useful in macros 9-21 9.4.1 Functions unique() and match() 9-21 9.4.2 Checking the characteristics of variables isxxxx() functions 9-22 9.43 Other miscellaneous functions anymissing(), nameof(), error() and gettime() 9-24 9.4.4 Keywords in macros using $k and $K 9-25 9.4.5 Checking and evaluating keyword phrase arguments keyvalue() 9-27 9.4.6 Checking and evaluating non-keyword arguments argvalue() 9-28 9.4.7 Properties checked by keyvalue() and argvalue() 9-29 9.5 Indirect evaluation of MacAnova commands 9-30 9.5.1 evaluate() 9-30 9.5.2 Indirect references using <<...>> 9-30 9.6 Analysis of macro regs 9-31 9.7 User functions 9-33 9.7.1 loadUser() 9-33 9.7.2 User() 9-33 9.7.3 User function arguments and returned values 9-34 9.7.4 Passing integer arguments aslong() 9-36 10. Examples of Linear Model Analyses (manchp10.pdf) 10.1 Introduction 10-1 10.2 Simple descriptive statistics 10-1 10.3 Simple linear regression 10-3 10.4 Multiple linear regression 10-5 10.5 One way ANOVA 10-6 10.6 Polynomial regression 10-8 10.7 Variance stabilizing transformations 10-9 10.8 Randomized complete block 10-13 10.8.1 Multiple comparisons 10-14 10.8.2 Randomized block with data missing 10-17 10.9 Latin squares 10-18 10.10 Balanced incomplete blocks 10-18 10.11 Analysis of covariance 10-19 10.12 Factorial models 10-22 10.13 Factorial designs with confounding 10-26 10.14 Fractional factorial designs 10-27 10.15 Split plot designs 10-29 10.16 Multivariate analysis of variance 10-30 10.16.1 Multivariate test statistics 10-33 10.16.2 MANOVA canonical variables 10-34 10.17 Repeated measures designs 10-35 10.18 Logistic regression 10-40 10.19 Poisson regression 10-41 10.20 Robust regression 10-42 11. Summary of Usage (manchp11.pdf) 11.1 Commands, functions and macros 11-1 11.2 Operators 11-16 11.2.1 Arithmetic operators 11-16 11.2.2 Comparison operators 11-16 11.2.3 Logical operators 11-17 11.2.4 Matrix operators 11-17 11.2.5 Bitwise operators 11-17 11.2.6 Assignment operators 11-18 11.3 Control syntax elements 11-18 11.3.1 Syntax elements for conditional execution 11-18 11.3.2 Syntax elements for looping 11-18 11.3.3 Syntax elements for leaving a loop 11-19 11.3.4 Syntax element for skipping to the end of a loop 11-19 11.4 Some differences from S-Plus 11-19 References (manrefs.pdf) Ref-1 Appendix A Commands and Macros Grouped by Topic (manapdxa.pdf) A-1 Appendix B MacAnova on a Macintosh (manapdxb.pdf) B.1 Introduction B-1 B.1.1 MacAnova windows B-1 B.1.2 Versions for different types of Macintoshes B-1 B.1.3 File names B-2 B.2 Launching MacAnova B-2 B.3 Menus B-2 B.3.1 The Apple and Help menus B-3 B.3.2 The File menu B-3 B.3.3 The Edit menu B-5 B.3.4 The Windows menu B-7 B.3.5 The Command menu B-9 B.3.6 The Options menu B-11 B.3.7 The Font menu B-14 B.4 Graph windows B-15 B.5 Location of files B-16 B.6 Other features B-16 B.6.1 Interrupting MacAnova B-16 B.6.2 Running other programs while in MacAnova B-16 B.6.3 Editing Macros B-16 B.6.4 Using keys to move around the command/output window B-17 B.6.5 Recalling previous commands B-18 B.6.6 "Console" input on the Macintosh B-18 B.7 Non-interactive mode B-19 B.8 Miscellaneous information B-20 B.8.1 Compilers B-20 B.8.2 Distribution of MacAnova for Macintosh B-20 Appendix C DOS versions of MacAnova on an IBM Compatible (manapdxc.pdf) C.1 Introduction C-1 C.1.1 Extended memory version (MACANODJ) C-1 C.1.2 Limited memory version C-1 C.2 Launching MacAnova C-2 C.2.1 Launching MacAnova at the DOS prompt C-2 C.2.2 Launching MacAnova in Windows and Windows 95 C-2 C.3 Graphics C-2 C.3.1 Graphics in the extended memory version C-3 C.3.2 Graphics in the limited memory version C-3 C.4 Location of files C-3 C.5 Other features C-3 C.5.1 Interrupting MacAnova C-3 C.5.2 Running other programs while in MacAnova C-4 C.5.3 Editing Macros C-4 C.5.4 Editing the current command line C-4 C.5.5 Recalling and editing previous commands C-4 C.5.6 "Console" input in DOS MacAnova C-4 C.6 Command line arguments C-6 C.6.1 File options C-6 C.6.2 Path options C-7 C.6.3 Other options C-7 C.7 Non-interactive mode C-8 C.8 Miscellaneous information C-8 C.8.1 Compilers C-8 C.8.2 Distribution of DOS versions of MacAnova C-8 Appendix D Windows version of MacAnova on an IBM Compatible (manapdxd.pdf) D.1 Introduction D-1 D.1.1 MacAnova windows D-1 D.1.1 File names D-2 D.2 Launching MacAnova D-2 D.2.1 Launching Windows MacAnova at the DOS prompt D-2 D.3 Menus D-2 D.3.1 The File menu D-2 D.3.2 The Edit menu D-4 D.3.3 The Windows menu D-5 D.3.4 The Help menu D-6 D.4 Graph windows D-6 D.5 Location of files D-7 D.6 Other features D-7 D.6.1 Interrupting MacAnova D-7 D.6.2 Running other programs while in MacAnova D-7 D.6.3 Editing Macros D-8 D.6.4 Using keys to move around the command/output window D-8 D.6.5 Recalling previous commands D-8 D.6.6 "Console" input under Windows D-8 D.7 Command line arguments D-9 D.8 Non-interactive mode D-9 D.9 Miscellaneous information D-9 D.9.1 Compilers D-9 D.9.2 Distribution of Windows version of MacAnova D-9 Appendix E Unix version of MacAnova (non Motif) (manapdxe.pdf) E.1 Introduction E-1 E.2 Launching MacAnova E-1 E.3 Graphics E-1 E.4 Location of files E-2 E.4.1 Changing the default file locations E-3 E.5 Other features E.5.1 Interrupting MacAnova E-3 E.5.2 Running other programs while in MacAnova E-3 E.5.3 Editing Macros E-3 E.5.4 Editing the current command line E-4 E.5.5 Recalling and editing previous commands E-4 E.5.6 "Console" input in Unix MacAnova E-4 E.5.7 Viewing data and macros E-4 E.6 Command line arguments E-4 E.7 Non-interactive mode E-4 E.8 Miscellaneous information E-4 E.8.1 Compilers E-4 E.8.2 Distribution of Unix versions of MacAnova E-4 Appendix F Motif version of MacAnova (manapdxf.pdf) F.1 Introduction F-1 F.2 Launching MacAnova F-1 F.3 Menus F-1 F.3.1 The File menu F-1 F.3.2 The Edit menu F-1 F.3.3 The Windows menu F-2 F.3.4 The Help menu F-2 F.4 Graph windows F-2 F.5 Location of files F-2 F.6 Other features F-2 F.6.1 Interrupting MacAnova F-2 F.6.2 Running other programs while in MacAnova F-2 F.6.3 Editing Macros F-2 F.6.4 Using keys to move around the command/output window F-3 F.6.5 Recalling previous commands F-3 F.6.6 "Console" input under Windows F-3 F.6.7 Viewing data and macros F-3 F.7 Command line arguments F-3 F.8 Non-interactive mode F-3 F.9 Miscellaneous information F-3 F.9.1 Compilers F-3 F.9.2 Distribution of MacAnova F-3
Last Updated Tue Jan 29 08:57:18 CST 2002