Contents

Chapter 1: Introduction 6

1.1 Main features 6

1.2 Major changes compared to ver. 5.1 6

1.3 History 6

1.4 Selected references on SYN-TAX versions 7

1.5 Further reading 7

1.6 Acknowledgements 8

1.7 Correspondence 8

Chapter 2: Quick start 9

2.1 The Main Window 9

2.2 Data grid 10

2.3 The File menu 10

2.4 Your first session in SYN-TAX 2000 11

Chapter 3: Input specifications, file conversions 14

3.1 Raw data files 14

3.1.1 Ungrouped raw data 14

3.1.2 Data with two groups of variables 15

3.1.3 Data with several groups of objects 15

3.2 Distance/dissimilarity matrices in input files 16

3.3 Group membership array (vector) defining a partition 16

3.4 Partition cluster seeds 17

3.5 Labels 17

3.6 Converting file formats: distances 18

3.7 Transposing data 18

3.8 Excel files 18

Chapter 4: Graphics 20

4.1 General features of SYN-TAX 2000 graphics 20

4.1.1 Graphics files 20

4.1.2 Graphics formats, metafiles 20

4.1.3 Pop-up menus 20

4.1.4 Graphics settings 21

4.2 Types of graphics 21

4.2.1 Additive trees 21

4.2.2 Biplots 22

4.2.3 Canonical correlation analysis ordinations 23

4.2.4 Canonical variates analysis ordinations 23

4.2.5 Dendrograms 24

4.2.6 Joint plots 25

4.2 7 Minimum spanning trees 25

4.2.8 Rotating plots: 3D scattergrams 26

4.2.9 Scree plots 27

4.2.10 Shepard diagrams 28

4.2.11 Simple scattergram 28

4.2.12 Superimposed convex polygons 28

4.2.13 Superimposed minimum spanning trees 28

4.2.14 Ternary plots 28

4.2.15 Triplots 29

4.3 Graphics commands 29

4.3.1 Axis caption font 29

4.3.2 Axis color 29

4.3.3 Background color/Panel color 29

4.3.4 Copy 30

4.3.5 Dendrogram shape 30

4.3.6 Dragging diagrams 30

4.3.7 Labels/Labeling objects/Labeling variables 30

4.3.8 Label font/Object label font/Variable label font 31

4.3.9 Line width/Printer scaling 31

4.3.10 New axes 31

4.3.11 Print 31

4.3.12 Resizing graphics 31

4.3.13 Save 31

4.3.14 Scaling axes 32

4.3.15 Symbol definitions 32

4.3.16 Title font 33

4.3.17 Tree color 33

4.3.18 Triangle color 33

4.3.19 Unrooted tree shape 33

4.3.20 Zoom 33

Chapter 5: Theory in brief 35

5.1 Data transformation and standardization 35

5.2 Distance and dissimilarity 36

5.2.1 Coefficients for binary (presence/absence) data 36

5.2.2 Coefficients for ordinal data 37

5.2.3 Coefficients for ratio scale data 38

5.2.4 Coefficients for mixed data 39

5.2.5 A coefficient for nominal data 41

5.3 Non-hierarchical clustering 41

5.3.1 K-means clustering 41

5.3.2 Multiple partitioning 42

5.3.3 Quick clustering 42

5.3.4 Global optimization 42

5.3.5 Fuzzy clustering 43

5.3.6 Ordinal clustering 43

5.4 Hierarchical clustering 43

5.4.1 Agglomerative methods 44

5.4.2 Divisive methods 44

5.4.3 Minimum spanning trees 44

5.4.4 Additive trees 45

5.4.5 Ordinal clustering 45

5.5 Ordination 45

5.5.1 Metric methods 46

5.5.2 Constrained ordination 47

5.5.3 Non-metric methods 47

Chapter 6: Utilities and related features 48

6.1 Text Editor 48

6.2 Randomizing raw data 48

6.3 Partition from a dendrogram 49

6.4 General options 49

6.5 Summary 49

Appendix A: Filename extensions 50

Appendix B: Troubleshooting 51