Gardener - Statistics for ecologists using R and Excel : data collection, exploration, analysis and presentation

Statistics for Ecologists
Using R and Excel

Data collection, exploration,
analysis and presentation

Mark Gardener

DATA IN THE WILD SERIES

Pelagic Publishing | www.pelagicpublishing.com

Published by Pelagic Publishing
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PO Box 725, Exeter, EX1 9QU

Statistics for Ecologists Using R and Excel
Data collection, exploration, analysis and presentation

ISBN 978-1-907807-12-1 (Pbk)
ISBN 978-1-907807-13-8 (Hbk)

Copyright 2012 Mark Gardener

All rights reserved. No part of this document may be produced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording or otherwise without prior permission from the publisher.

While every effort has been made in the preparation of this book to ensure the accuracy of the information presented, the information contained in this book is sold without warranty, either express or implied. Neither the author, nor Pelagic Publishing, its agents and distributors will be held liable for any damage or loss caused or alleged to be caused directly or indirectly by this book.

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British Library Cataloguing in Publication Data
A catalogue record for this book is available from the British Library.

Cover image istockphoto.com/dulezidar

About the author

Mark began his career as an optician but returned to science and trained as an ecologist. His research is in the area of pollination ecology. He has worked extensively in the UK as well as Australia and the United States. Currently he works as an associate lecturer for the Open University and also runs courses in data analysis for ecology and environmental science.

Acknowledgements

I am especially grateful to Nigel Massen at Pelagic Publishing for his help and perseverance throughout the production of this book.

Thanks go to Anne Goodenough for patiently and thoroughly reviewing the manuscript, your comments and views were most helpful.

With a book of this nature data examples are always useful. Some of the data illustrated here were collected by students and I gratefully acknowledge their efforts and send thanks for allowing me to use these data as examples.

Finally my heartfelt thanks go to Christine, for putting up with me throughout the entire process.

Software used

Various versions of Microsofts Excel spreadsheet were used in the preparation of this manuscript. Most of the examples presented show version 2007 for Microsoft Windows although other versions may also be illustrated (including Excel X for Apple Macintosh).

Several versions of the R program were used and illustrated including 2.8.1. for Windows and 2.11.1 for Macintosh: R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.

Downloading free code examples

Free code examples and further information from the author on using R and Excel for statistics can be found at:

http://www.pelagicpublishing.com/statistics-for-ecologists-resources.html

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Contents

This is not just a statistics textbook! Although there are plenty of statistical analyses here, this book is about the processes involved in looking at data. These processes involve planning what you want to do, writing down what you found and writing up what your analyses showed. The statistics part is also in there of course but this is not a course in sta tistics. By the end I hope that you will have learnt some statistics but in a practical way, i.e. what statistics can do for you . In order to learn about the methods of analysis, well use two main tools: a Microsoft Excel spreadsheet (although Open Office will work just as well) and a computer program called R. The spreadsheet will allow you to collect your data in a sensible layout and also do some basic analyses (as well as a few less basic ones). The R program will do much of the detailed statistical work (although we will also use Excel quite a bit). Both programs will be used to produce graphs. This book is not a course in computer programming; well learn just enough about the programs to get the job done .

It is important to recognise that there is a process involved. This is the scientific process and may be summarised by four main headings:

• Planning
• Data recording
• Data exploration
• Reporting results

The book is arranged into these four broad categories. The sections are rather uneven in size and tend to focus on the analysis. The section on reporting also covers presentation of analyses (e.g. graphs).

Although the emphasis is on ecological work and many of the data examples are of that sort, I hope that other scientists and students of other disciplines will see relevance to what they do.

Mark Gardener 2011

Science is a way of looking at the natural world. In short, the process goes along the following lines:

• You have an idea about something.
• You come up with a hypothesis.
• You work out a way of testing this hypothesis/idea.
• You collect appropriate data in order to apply a test.
• You test the hypothesis and decide if the original idea is supported or rejected.
• If the hypothesis is rejected, then the original idea is modified to take the new findings into account.
• The process then repeats.

In this way, ideas are continually refined and our knowledge of the natural world is expanded. We can split the scientific process into four parts (more or less): planning, recording, analysing and reporting.

Table 1. Stages in the scientific method