# Step-by-Step (2016)

## Purpose

a) a required supplement to the PC‑ORD workshops;

b) a stand-alone guide for self-taught beginning multivariate analysis.

This companion book is available from MjM Software at www.pcord.com

## Format

The book introduces techniques and procedures in the order in which you would use them if you were to follow this 10-step analysis process:

- get yourself ready--brush up on basic statistical concepts
- get your data ready--enter and screen the data for errors
- get your data structured--structure the matrices for your question of interest
- explore and prepare your data--get to know the properties of your data
- select the tools--select tools appropriate to your data and question
- modify the data--adjust the data as needed to use those tools
- apply the selected tools--run your chosen analysis tools
- confirm the patterns--run some other tools and see what you find
- interpret your results--use graphing tools to infer relationships
- present your 'story'--customize figures to convey your story

## Contents

Step 1. Getting yourself ready

1. Embracing statistics

2. Articulating goals

Step 2. Getting your data ready

3. Meeting matrices

4. Starting in PC-ORD

5. Inputting and screening your data

Step 3. Structuring your data

6. Sampling sufficiently

7. Structuring your matrices

Step 4. Exploring and preparing your data

8. What have you actually measured?

9. How variable are your data?

Step 5. Selecting the tools

10. Distance measures

11. Model form

12. Analysis tools

13. What is ordination?

Step 6. Modifying your data

14. Meeting parametric assumptions

15. Reweighting responses

Step 7a: Guiding pattern (guided ordination)

16. WA: Weighted averaging

17. Polar (Bray-Curtis) ordination

18. CCA: Canonical correspondence analysis

19. RDA: Redundancy analysis

20. FSO: Fuzzy set ordination

21. Interpreting guided ordinations

Step 7b: Seeking pattern (free ordination)

22. PCA: Principal components analysis

23. NMS: Nonmetric multidimensional scaling

Step 7c: Looking for groups (classification)

25. Cluster analysis

26. TWINSPAN

Step 7d: Testing among groups

27. MRPP: Multi-response permutation procedure

28. PerMANOVA: Distance-based MANOVA

29. SumF

30. ISA: Indicator species analysis

Step 7e: Assessing associations

31. Mantel test

32. FCA: Fourth corner analysis

Step 8: Confirming your results

Step 9: Using interpretive tools

33. Finding your story

Step 10: Presenting your story

34. Communicating your message

Appendix A: Other PC-ORD Tools

Appendix B: Matrix Algebra Unplugged

Appendix C: How to Report

Appendix D: Further Reading

Appendix E: Available Supplements

Appendix F: Acronyms & Symbols

## What you'll learn

For each tool, there are sections on:

- what you can do with it
- when you might use it
- what it does
- what it means
- what you need
- what you get
- what else you need to know
- how to run it (in
*PC-ORD*v. 7) - how to interpret it

## Supplements

Supplement A: Check-list Template

Supplement B: Example Analysis Pathways

Supplement C: Examples from the Literature

Supplements D & E are available by request (see Appendix E in Second Edition)

Supplement F: Distance measures calculation spreadsheet

Supplement G: Book figures are available by request (for instruction only)