GENSTAT DISCOVERY EDITION FOR EVERYDAY USE Flemish Association for Development Co-Operation and Technical Assistance (VVOB) World Agroforestry Centre (ICRAF) Research Support Unit University of Reading Statistical Services Centre GenStat Discovery Edition for everyday use Wim Buysse, Roger Stern and Ric Coe Correct citation : Wim Buysse, Roger Stern and Ric Coe, 2004. GenStat Discovery Edition for everyday use . ICRAF Nairobi, Kenya. 114 pp. ISBN 92 9059 158 7 Copyright © 2004 World Agroforestry Centre. This publication is the intellectual property of the University of Reading and the World Agroforestry Centre (ICRAF). While use of the information it contains is encouraged, the content should not be republished in any way without the permission of the publishers. The publishers and the authors make no representation, express or implied, with regard to the accuracy of the information contained in this book and cannot accept any legal responsibility or liability for any errors or omissions that may be made. All terms mentioned in this book that are known to be trademarks or service marks have been appropriately capitalized. The publishers and the authors cannot attest to the accuracy of this information. Use of a term in this book should not be regarded as affecting the validity of any trademark or service mark. The University of Reading The World Agroforestry Centre Whiteknights ICRAF PO Box 217 PO Box 30677 Reading 00100 Nairobi Berkshire RG6 6AH United Kingdom Kenya http://www.reading.ac.uk http://www.worldagroforestrycentre.org/rsu Contents 1 GenStat Discovery Edition ............................................................................................1 1.1 What is this guide about?.......................................................................................1 1.2 The origins of the Discovery Edition.....................................................................2 1.3 Configuration.........................................................................................................2 1.4 Acknowledgements................................................................................................2 1.5 Reference for GenStat Discovery Edition .............................................................3 2 GenStat Basics...............................................................................................................5 2.1 Starting GenStat Discovery Edition.......................................................................5 2.2 Data input...............................................................................................................7 2.2.1 Data input using the Spread Menu.................................................................7 2.2.1.1 Naming colums..........................................................................................8 2.2.1.2 Adding extra description............................................................................8 2.2.1.3 Naming spreadsheets...............................................................................10 2.2.2 Data input from Excel worksheets...............................................................10 2.2.3 Advanced data input. ...................................................................................14 2.2.4 Leaving GenStat..........................................................................................14 2.3 Some basic data manipulation. ............................................................................15 2.3.1 Summary statistics.......................................................................................15 2.3.2 Calculating and formatting columns............................................................17 2.3.3 Columns containing factors. ........................................................................21 2.3.4 Saving data from GenStat to Excel..............................................................26 2.3.5 Importing factors from Excel.......................................................................27 2.3.6 Deleting data................................................................................................27 2.4 Understanding how GenStat works. ....................................................................28 2.4.1 Available variables......................................................................................28 2.4.2 A first introduction to the GenStat command language. .............................29 2.4.3 Server sessions.............................................................................................33 3 Simple statistical ideas.................................................................................................35 3.1 First some more data manipulation: appending spreadsheets..............................35 3.2 Visual data exploration........................................................................................38 3.2.1 Boxplots.......................................................................................................38 3.2.2 Median and quartiles....................................................................................39 3.2.3 The use of boxplots......................................................................................42 3.3 Hypothesis testing................................................................................................44 3.3.1 Testing a hypothesis about the population mean.........................................44 3.3.2 Comparison of samples................................................................................45 3.3.3 Paired t-test..................................................................................................48 3.3.4 A non-parametric example...........................................................................51 3.4 A fast and simple regression................................................................................52 4 Review of chapters 2–3................................................................................................55 5 Challenge 1..................................................................................................................57 6 Before starting an Analysis of Variance......................................................................59 6.1 Factors and data organization ..............................................................................59 6.1.1 In a GenStat spreadsheet..............................................................................59 i 6.1.1.1 Melon yields.............................................................................................60 6.1.1.2 Layers and light regimes..........................................................................62 6.1.2 From an Excel spreadsheet. .........................................................................63 6.1.2.1 Survival of Salmonella typhimurium.......................................................63 6.2 Exploratory analysis.............................................................................................66 6.2.1 Melon yields.................................................................................................66 6.2.2 Layers and light regimes..............................................................................68 6.2.3 Survival of Salmonella typhimurium...........................................................69 6.3 A real example. ....................................................................................................73 7 Challenge 2..................................................................................................................81 8 Analysis of variance.....................................................................................................83 8.1 Two simple ANOVA’s ........................................................................................83 8.2 Getting more out of the output.............................................................................85 8.3 Defining the treatment structure ..........................................................................89 8.3.1 Factorial treatment structure........................................................................89 8.3.2 Nested blocking structure.............................................................................96 8.3.3 Checking for outliers..................................................................................100 8.4 Randomising an Experiment..............................................................................103 9 Challenge 3................................................................................................................107 10 Further Reading.....................................................................................................109 10.1 Other free documentation...................................................................................109 10.2 The Help menu...................................................................................................109 10.3 “Hidden” user guides .........................................................................................111 10.4 Non-English speakers........................................................................................113 10.5 The GenStat user community.............................................................................113 ii 1 GenStat Discovery Edition 1.1 What is this guide about? This guide is intended primarily for scientists who wish to use GenStat for the analysis of their