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Published by Pelagic Publishing
www.pelagicpublishing.com
PO Box 725, Exeter, EX1 9QU
Community Ecology
Analytical Methods Using R and Excel®
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.
Windows, Excel and Word and are trademarks of the Microsoft Corporation. For more information visit www. microsoft.com. OpenOffice.org
is a trademark of Oracle. For more information visit www.openoffice.org. LibreOffice is a trademark of The Document Foundation. For more
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Cover image: Over under water picture, showing Fairy Basslets (Pseudanthias tuka) amongst Cabbage Coral (Turbinaria reniformis) and
tropical island in the background. Indo Pacific. © David Fleetham/OceanwideImages.com
3
About the author
Mark Gardener (www.gardenersown.co.uk) is an ecologist, lecturer and writer working in the UK. His
primary area of research was in pollination ecology and he has worked in the UK and around the world
(principally Australia and the United States). Since his doctorate he has worked in many areas of ecology,
often as a teacher and supervisor. He believes that ecological data, especially community data, are the most
complicated and ill-behaved and are consequently the most fun to work with. He was introduced to R by a
like-minded pedant whilst working in Australia during his doctorate. Learning R was not only fun but opened
up a new avenue, making the study of community ecology a whole lot easier. He is currently self-employed
and runs courses in ecology, data analysis and R for a variety of organisations. Mark lives in rural Devon with
his wife Christine, a biochemist who consequently has little need of statistics.
Acknowledgements
There are so many people to thank that it is hard to know where to begin. I am sure that I will leave some
people out, so I apologise in advance. Thanks to Richard Rowe (James Cook University) for inspiring me to
use R. Data were contributed from various sources, especially from MSc students doing Biological
Recording; thanks especially to Robin Cure, Jessie MacKay, Mark Latham, John Handley and Hing Kin Lee
for your hard-won data. The MSc programme helped me to see the potential of ‘proper’ biological records and
I thank Sarah Whild for giving me the opportunity to undertake some teaching on the course. Thanks also to
the Field Studies Council in general: many data examples have arisen from field courses I’ve been involved
with.
Software used
Several versions of Microsoft’s Excel® spreadsheet were used in the preparation of this book. Most of the
examples presented show version 2007 for Microsoft Windows® although other versions may also be
illustrated.
The main version of the R program used was 2.12.1 for Macintosh: The R Foundation for Statistical
Computing, Vienna, Austria, ISBN 3-900051-07-0, http://www.R-project.org/. Other versions were used in
testing code.
Support material
Free support material is available on the Community Ecology companion website, which can be accessed via
the book’s resources page: http://www.pelagicpublishing.com/community-ecology-resources.html
Reader feedback
We welcome feedback from readers – please email us at [email protected] and tell us what you
thought about this book. Please include the book title in the subject line of your email.
4
5
Contents
Introduction
6
7. Diversity: species richness
7.1 Comparing species richness
7.2 Correlating species richness over time or against an environmental variable
7.3 Species richness and sampling effort
7.4 Summary
7.5 Exercises
8. Diversity: indices
8.1 Simpson’s index
8.2 Shannon index
8.3 Other diversity indices
8.4 Summary
8.5 Exercises
9. Diversity: comparing
9.1 Graphical comparison of diversity profiles
9.2 A test for differences in diversity based on the t-test
9.3 Graphical summary of the t-test for Shannon and Simpson indices
9.4 Bootstrap comparisons for unreplicated samples
9.5 Comparisons using replicated samples
9.6 Summary
9.7 Exercises
7
13.2 Transect approach to identifying communities
13.3 Using alternative dissimilarity measures for identifying communities
13.4 Indicator species
13.5 Summary
13.6 Exercises
14. Ordination
14.1 Methods of ordination
14.2 Indirect gradient analysis
14.3 Direct gradient analysis
14.4 Using ordination results
14.5 Summary
14.6 Exercises
Appendices
Bibliography
Index
8
Introduction
Interactions between species are of fundamental importance to all living systems and the framework we have
for studying these interactions is community ecology. This is important to our understanding of the planet’s
biological diversity and how species interactions relate to the functioning of ecosystems at all scales. Species
do not live in isolation and the study of community ecology is of practical application in a wide range of
conservation issues.
The study of ecological community data involves many methods of analysis. In this book you will learn
many of the mainstays of community analysis including: diversity, similarity and cluster analysis, ordination
and multivariate analyses. This book is for undergraduate and postgraduate students and researchers seeking a
step-by-step methodology for analysing plant and animal communities using R and Excel.
Microsoft’s Excel spreadsheet is virtually ubiquitous and familiar to most computer users. It is a robust
program that makes an excellent storage and manipulation system for many kinds of data, including
community data. The R program is a powerful and flexible analytical system able to conduct a huge variety of
analytical methods, which means that the user only has to learn one program to address many research
questions. Its other advantage is that it is open source and therefore free. Novel analytical methods are being
added constantly to the already comprehensive suite of tools available in R.
• Diversity – the study of diversity is split into several chapters covering species richness, diversity
indices, beta diversity and dominance–diversity models.
• Similarity and clustering – this is contained in one chapter covering similarity, hierarchical clustering
and clustering by partitioning.
• Association analysis – this shows how you can identify which species belong to which community by
studying the associations between species. The study of associations leads into the identification of
indicator species.
• Ordination – there is a wide range of methods of ordination and they all have similar aims; to represent
complicated species community data in a more simplified form.
The reporting element is not covered explicitly; however the presentation of results is shown throughout the
book. A more dedicated coverage of statistical and scientific reporting can be found in my previous work,
Statistics for Ecologists Using R and Excel.
Throughout the book you will see example exercises that are intended for you to try out. In fact they are
expressly aimed at helping you on a practical level – reading how to do something is fine but you need to do it
9
for yourself to learn it properly. The Have a Go exercises are hard to miss.
Most of the Have a Go exercises utilise data that is available on the companion website. The material on the
website includes various spreadsheets, some containing data and some allowing analytical processes. The
CERE.RData file is the most helpful – this is an R file, which contains data and custom R commands. You
can use the data for the exercises (and for practice) and the custom commands to help you carry out a variety
of analytical processes. The custom commands are mentioned throughout the book and the website contains a
complete directory.
You will also see tips and notes, which will stand out from the main text. These are ‘useful’ items of detail
pertaining to the text but which I felt were important to highlight.
At the end of each chapter there is a summary table to help give you an overview of the material in that
chapter. There are also some self-assessment exercises for you to try out. The answers are in Appendix 1.
Support files
The companion website (see resources page: http://www.pelagicpublishing.com/community-ecology-
resources.html) contains support material that includes spreadsheet calculations and data in Excel and CSV
(comma separated values) format. There is also an R data file, which contains custom R commands and
datasets. Instructions on how to load the R data into your copy of R are on the website. In brief you need to
use the load() command, for Windows or Mac you can type the following:
load(file.choose())
This will open a browser window and you can select the CERE.RData file. On Linux machines you’ll need to
replace the file.choose() part with the exact filename in quotes, see the website for more details.
I hope that you will find this book helpful, useful and interesting. Above all, I hope that it helps you to
discover that analysis of community ecology is not the ‘boring maths’ at the end of your fieldwork but an
enjoyable and enlightening experience.
Mark Gardener, Devon 2013
10
1. Starting to look at communities
The study of community ecology is complicated and challenging, which makes it all the more fun, of course.
Ecology is a science and like all science subjects there is an approach to study that helps to facilitate progress.
In this way, ideas are continually refined and our knowledge of the natural world is expanded. You can split
the scientific process into four parts (more or less): planning, recording, analysing and reporting.
• Planning: This is the stage where you work out what you are going to do. Formulate your idea(s),
undertake background research, decide what your hypothesis will be and determine a method of
collecting the appropriate data and a means by which the hypothesis may be tested.
• Recording: The means of data collection is determined at the planning stage although you may
undertake a small pilot study to see if it works out. After the pilot stage you may return to the planning
stage and refine the methodology. Data are finally collected and arranged in a manner that allows you to
begin the analysis.
• Analysing: The method of analysis should have been determined at the planning stage. Analytical
methods (often involving statistics) are used to test the null hypothesis. If the null hypothesis is rejected
then this supports the original idea/hypothesis.
• Reporting: Disseminating your work is vitally important. Your results need to be delivered in an
appropriate manner so they can be understood by your peers (and often by the public). Part of the
reporting process is to determine what the future direction needs to be.
In community ecology the scientific process operates in the same way as in any other branch of science.
Generally you are dealing with complicated situations with many species and samples – methods of analysis
in community ecology are specialised because of this complexity.
1.2.1 Diversity
Diversity is concerned with how many different species there are in a given area. Strictly speaking there are
two main strands of diversity – in the first you simply count the number of different species in an area. In the
second case you take into account the abundance of the species – this leads to the notion of the diversity index.
The term diversity (or biodiversity) is a much used term both in science and in general use. Its meaning in
science is not necessarily the same as that understood by the general public. You can think of diversity as
11
being expressed in two forms:
The first form, number of species in an area, is called species richness (see Chapter 7). This is an easy
measure to understand and you can calculate it from simple species lists. The second form, involving relative
abundance of species, is more complicated because of course you have an extra dimension, abundance
information (see Chapter 8).
Whichever measure of diversity is under question, the scale of measurement is particularly important.
Diversity is usually expressed at three scales (see Chapter 10):
• Alpha diversity – this is diversity measured in a single habitat or sampling unit (e.g. a quadrat); it is the
smallest unit of measurement.
• Beta diversity – this is the diversity between habitats.
• Gamma diversity – this is the diversity of a larger sampling unit, such as a landscape that is composed
of many habitats.
In some measures of diversity however, the relationship can be additive rather than multiplicative (see
Chapter 10).
The species richness measure of diversity can be used when you do not have abundance information –
which can be useful. Species richness can also be used as the response variable in analyses in certain
circumstances (see Section 7.1).
When you have abundance information you are able to carry out different analyses, for example:
• Diversity indices.
• Species abundance curves.
A diversity index is a way to take into account the evenness of a community – if a single species dominates a
community the index is smaller, if the species are all more even in abundance the index is larger (see Chapter
8).
Species abundance curves are another way to look at the evenness of a community – the abundance of each
species is plotted on a graph, with the most abundant being plotted first (see Chapter 11).
• Hierarchical clustering – in this approach the data are repeatedly split into smaller units until you end
up with a kind of ‘family tree’, which shows the relationship between items (see Section 12.2.1).
• Clustering by partitioning – in this approach you take the data and build clusters based on how similar
they are; the data are clumped around so-called medoids, which are the centres of the various groups
(see Section 12.2.2).
You can explore similarity and create clusters of samples even if you do not have species abundance
information – simple presence-absence data can be used.
12
• By area – in this approach you sample in a geographical area and identify the various associations
(which can be positive or negative) and so identify the communities in that area (see Section 13.1).
• By transect – in this approach you sample along a transect, usually because of some underlying
environmental gradient. Often this will lead to a succession of communities and your association
analysis will help you to identify them (see Section 13.2).
The association analysis gives you values for the ‘strength’ of the various associations – this can be thought of
as akin to the similarity and clustering kind of analyses (Chapter 12). A spin-off from association analysis is
the idea of indicator species (see Section 13.4). Here you look to see if certain species can be regarded as
indicative of a particular community. An ideal indicator species would be one that shows great specificity for
a single community.
1.2.4 Ordination
The term ordination covers a range of methods that look to simplify a complicated situation and present it in a
simpler fashion (see Chapter 14). This sounds appealing! In practice you are looking at communities of
species across a range of sites or habitats and the methods of ordination look to present your results in a kind
of scatter plot. Things that appear close are more similar to one another than things that are far apart. Think of
it as being an extension to the similarity and clustering idea.
There are several methods of ordination (see Chapter 14) but you can split the general idea of ordination
into two broad themes:
• Indirect gradient analysis – in this approach you analyse the species composition and the patterns you
observe allow you to infer environmental gradients that the species may be responding to (see Section
14.2).
• Direct gradient analysis – in this approach you already have environmental data which you use to help
reorder the samples and species data into meaningful patterns (see Section 14.3). A spin-off from this
approach is that you can test hypotheses about the effects of the environmental variable(s) that you
measured.
Ordination is a very commonly used analytical approach in community ecology because the main aim of the
various methods is to distil the complicated community data into a simpler and more readily understood form.
13
hypothesis should relate to a single testable item.
In reality you cannot usually ‘prove’ your hypothesis – it is like a court of law when you do not have to
prove your innocence, you are assumed innocent until proven otherwise. In statistics, the equivalent is the null
hypothesis. This is often written as H0 (or H0) and you aim to reject your null hypothesis and therefore, by
implication, accept the alternative (usually written as H1 or H1).
The H0 is not simply the opposite of what you thought (called the alternative hypothesis, H1) but is written
as such to imply that no difference, no pattern, exists (I like to think of it as the dull hypothesis).
Getting your hypotheses correct (and also the null hypotheses) is an important step in the planning process
as it allows you to decide what data you will need to collect in order to reject the H0. You will examine
hypotheses again later (Section 5.2).
Allied to your hypothesis is the analytical method you will use later to help test and support (or otherwise)
your hypothesis. Even at this early stage you should have some idea of the statistical test or analytical
approach you are going to apply. Certain statistical tests are suitable for certain kinds of data and you can
therefore make some early decisions. You may alter your approach, change the method of analysis and even
modify your hypothesis as part of your planning process.
Some kinds of analysis do not lend themselves to a hypothesis test – this is particularly so in community
ecology. When you have several species and several habitats your analysis may be concerned with looking for
patterns in the data to highlight relationships that were not evident from the raw data. These analytical
methods are important but you cannot always perform a hypothesis test. However, you still need to plan your
approach and decide what method of analysis is best to help you make sense of the ecological situation (see
Chapter 5) – if the best approach is to carry out an analysis that does not test a null hypothesis then that is
what you go with.
1.5 Summary
14
• Area analysis – you sample in a geographical area.
• Transect analysis – you sample along a transect (usually along an environmental gradient).
Association analysis is akin to clustering and similarity and you can use the approach for that
purpose.
A spin-off is that you can identify indicator species, those that are ‘indicative’ of a particular
community and tend to be found there and nowhere else.
Ordination Ordination is the name given to a variety of analytical methods that seek to reorder samples and
species in a meaningful way. The general aim is to represent the complicated community (and
sometimes environmental) data in a more easily interpretable form; usually a 2D plot.
There are two main approaches to ordination:
Indirect With indirect gradient analysis you carry out the analysis using species and sample data. Any
gradient environmental information is inferred at the end from the patterns you observe.
analysis
Direct With direct gradient analysis you utilise environmental data right at the outset and use it to help
gradient form the order of the samples and species.
analysis
Data It is important to get your data into a sensible order. A spreadsheet is an invaluable tool and
recording allows you to keep your data in order as well as giving you the chance to carry out a range of
analyses.
Aims and A hypothesis is a testable statement that you can back-up with a statistical test. The null
hypotheses hypothesis is actually what you test. In community ecology it is not always possible to carry out a
statistical test but you should still have clear aims to provide a framework for your work.
1.6 Exercises
1.1 What are the main topics in community ecology, as set out in this book?
1.2 Diversity can be measured at various scales, from simple samples to whole landscapes. What are the
‘units’ of diversity and how are they related?
1.3 What are the main reasons for carrying out association analysis?
1.4 With indirect gradient analysis you can test hypotheses about the relationship between species
composition and environment – TRUE or FALSE?
1.5 If you had an idea regarding the number of species and an environmental variable your hypothesis
might run along these lines ‘there is a positive correlation between species richness and soil
moisture’. What would an appropriate null hypothesis be?
15
2. Software tools for community ecology
Learning to use your spreadsheet is time well spent. It is important that you can manipulate data and produce
summaries, including graphs. You will see later how the spreadsheet is used for a variety of aspects of data
manipulation as well as for the production of graphs. Many statistical tests can be performed using a
spreadsheet but there comes a point when it is better to use a dedicated computer program for the job. The
more complicated the data analyses are the more cumbersome it is to use a spreadsheet and the more sensible
it is to use a dedicated analytical program. There are many on the market, some are cheap (or even free) and
others are expensive. Some programs will interface with your spreadsheet and others are totally separate.
Some programs are specific to certain types of analysis and others are more general.
In this book you will focus on two programs:
• Microsoft Excel: this spreadsheet is common and widely available. There are alternatives and indeed the
Open Office spreadsheet uses the same set of formulae and can be regarded as equivalent. The Libre
Office spreadsheet is a derivative of Open Office and similarly equivalent to Excel.
• R: the R project for statistical computing is a huge open-source undertaking that is fast becoming the de
facto standard for analysis in many fields of science, engineering and business, to name just a few. It is
a powerful and flexible system.
Excel is particularly useful as a data management system, and throughout this book you will see it used
mainly in that fashion although it is capable of undertaking some statistical analyses and producing various
graphs. The R program is very powerful and flexible, and you will see this used for the majority of the
analyses. Once you learn how to use R it is almost as easy to create a complicated community analysis as it is
to carry out a simple t-test.
2.1 Excel
A spreadsheet in an invaluable tool. The most common is Microsoft Excel and it has many uses:
Generally the more complicated the analysis you are going to undertake, the less likely it is that you will use a
spreadsheet to do the analysis. However, when you have more complicated data it is really important to
manage the data carefully and this is a strength of the spreadsheet. It can act like a database. Part of your
planning process should be to determine how you are going to arrange your data – getting the layout correct
from the start can save an immense amount of time later on.
16
2.1.2 Installing the Analysis Toolpak
The Analysis ToolPak is an add-in for Excel that allows various statistical analyses to be carried out without
the need to use complicated formulae. The add-in is not installed as standard and you will need to set up the
tool before you can use it. The add-ins are generally ready for installation once Excel is installed and you
usually do not require the original disk.
The statistical methods available via the Analysis ToolPak are not very relevant to most community studies
and are more likely to be of use for examining hypotheses relating to individual species. However, you may
be looking at the number of species in a given area (a measure called species richness) and some basic
statistical routines could be helpful. You will see more about species richness in Chapter 7.
In order to install the Analysis ToolPak (or any other add-in) you need to click the Office button (at the top
left of the screen) and select Excel Options.
In Figure 2.1 you can see that there are several add-ins already active and some not yet ready. To activate
(i.e. install) the add-in, you click the Go button at the bottom of the screen. You then select which add-ins you
wish to activate (Figure 2.2).
Once you have selected the add-ins to activate, you click the OK button to proceed. The add-ins are usually
available to use immediately after this process.
To use the Analysis ToolPak you use the Data button on the Ribbon and select the Data Analysis button
(Figure 2.3).
Once you have selected this, you are presented with various analysis tools (Figure 2.4). Each tool requires
the data to be set out in a particular manner; help is available using the Help button.
Other spreadsheets generally use the same functions as Excel, so it is possible to use another program to
17
produce the same result. Graphics will almost certainly be produced in a different manner and you will see
graphics demonstrated with Excel 2007 for Windows throughout this book.
Figure 2.3 The Analysis ToolPak is available from the Data Analysis button on the Excel Data Ribbon.
R is an open-source (GPL) statistical environment modeled after S and S-Plus. The S language was
developed in the late 1980s at AT&T labs. The R project was started by Robert Gentleman and Ross
Ihaka (hence the name R) of the Statistics Department of the University of Auckland in 1995. It has
quickly gained a widespread audience. It is currently maintained by the R core-development team, a
hard-working, international team of volunteer developers. The R project web page is the main site for
information on R. At this site are directions for obtaining the software, accompanying packages and
other sources of documentation.
R is a powerful statistical program but it is first and foremost a programming language. Many routines
have been written for R by people all over the world and made freely available from the R project
website as ‘packages’. However, the basic installation (for Linux, Windows or Mac) contains a powerful
set of tools for most purposes.
Because R is a programming language it can seem a bit daunting; you have to type in commands to get it to
18
work; however, it does have a graphical user interface (GUI) to make things easier and it is not so different
from typing formulae into Excel. You can also copy and paste text from other applications (e.g. word
processors). So if you have a library of these commands, it is easy to pop in the ones you need for the task at
hand.
R will cope with a huge variety of analyses and someone will have written a routine to perform nearly any
type of calculation. R comes with a powerful set of routines built in at the start but there are some useful extra
‘packages’ available on the website. These include routines for more specialised analyses covering many
aspects of scientific research as well as other fields (e.g. economics).
There are many advantages in using R:
2.3.1 Getting R
Getting R is easy via the Internet. The R Project website is a vast enterprise and has local mirror sites in many
countries. The first step is to visit the main R Project webpage at http://www.r-project.org.
Figure 2.5 Getting R from the R Project website. Click the download link and select the nearest mirror site.
Once you have clicked the download R link (Figure 2.5), you have the chance to select a mirror site. These
mirror sites are hosted in servers across the world and using a local one will generally result in a speedier
download.
Figure 2.6 Getting R from the R Project website. Once you have selected the mirror site for your location you
can choose the file to download.
Once you have selected a mirror site, you can click the link that relates to your operating system (Figure 2.6).
If you use a Mac then you will go to a page where you can select the best option for you (there are versions
for various flavours of OSX). If you use Windows then you will go to a Windows-specific page. (Figure 2.7)
If you are a Linux user then read the documentation; you can often install R through the terminal and link to a
version in a distro-specific repository.
19
Figure 2.7 Getting R from the R Project website. The Windows-specific page allows you to get the version
that is right for your Windows OS.
Assuming you have navigated to the Windows page, you will see something similar to Figure 2.7. Most users
will want to select the base link, which will take you to a page where you can (finally) get the latest version of
the installer file (Figure 2.8).
Figure 2.8 Getting R from the R Project website. The final link will download the latest version (the one
shown was current as of September 2012).
Now the final step is to click the link and download the installer file. This is an EXE file and it will download
in the usual manner according to the setup of your computer.
2.3.2 Installing R
Once you have downloaded the install file, you need to run it to get R onto your computer. The process
depends upon your operating system:
• If you use a Mac you need to double-click the disk image file to mount the virtual disk. Then double-
click the package file to install R.
• If you use Linux you can simply double click the file you downloaded and installation will proceed. If
you install via the terminal then the terminal commands you use will carry out the process of
installation.
• If you use Windows then you need to find the EXE file and run it. If you use Vista or later then it is a
good idea to right-click the file and run as administrator (Figure 2.9).
Figure 2.9 Installing R. If you have Windows Vista or later it is a good idea to right-click the install file and
run as administrator.
The installation process asks a few basic questions, allowing you to select a language other than English for
example. It is usual to accept the default location for the R files (a directory called R). The next screen asks if
you wish to use customised startup options. In most cases for installing programs you are strongly suggested
to say ‘no’ and to accept the defaults – this is no different, accept the defaults.
2.4 Summary
20
Excel spreadsheet Excel is virtually ubiquitous and is a reliable and easy to use program (at least for basic
things).
Excel is most useful as data storage software but you can also use it to help manage and
manipulate your data, and as a simple database.
Excel can carry out a range of statistical analyses and is especially useful as a ‘first look’
and to produce summary graphs and charts.
Other spreadsheets The Open Office and Libre Office software packages are analogous to Microsoft Office.
The spreadsheets use the same formulae/functions and in most senses are equivalent.
Analysis ToolPak The Analysis ToolPak is an add-in for Excel (later version Windows only) that allows you
to run a variety of basic statistical analyses more easily that using regular formulae.
The R program for The R program is a powerful statistical and graphical environment. It is a huge Open
statistical Source project and is free, with versions running on all computer systems (Windows, Mac
computing and Linux).
The R program is very flexible and there are packages available for it that will carry out
all the analyses you can imagine (and many you cannot).
The program uses basic text commands to ‘drive’ it. This permits great flexibility as you
can save commands and reuse them.
The program is available from the Internet at www.r-project.org where you can also
obtain much documentation.
2.5 Exercises
2.1 What are the main uses for Excel (or any spreadsheet) in community ecology?
2.2 If you install the Analysis ToolPak for Excel – to help you carry out a range of statistical operations –
where in Excel can you access the ToolPak?
2.3 The R program for statistical computing is available for a nominal fee from the Internet – TRUE or
FALSE?
2.4 The R program is only useful for complicated statistical procedures – TRUE or FALSE?
21
3. Recording your data
The data you write down are of fundamental importance to your ability to make sense of your research at a
later stage. If you are collecting new data then you are able to work out the recording of the data as part of
your initial planning. If you have past data then you may have to spend some time rearranging before you can
do anything useful.
There are other items that may be added, depending upon your purpose, as you shall see later.
Table 3.1 An example of biological data: bat species abundance at various sites around Milton Keynes (only
part of the data is shown).
• It means that you won’t forget some important aspect of the data.
• It allows someone else to repeat the exercise exactly.
22
In the example above, you can see that someone (M Atherton) is trying to ascertain the abundance of various
species of bat at sites around Milton Keynes in the UK. It would be easy for him to forget the date because it
doesn’t seem to matter that much. But if someone tries to repeat his experiment, they need to know what time
of year he was surveying at. Alternatively, if environmental conditions change, it will be essential to know
what year he did the work.
If you fail to collect complete biological data, or fail to retain and communicate all the details in full, then
your work may be rendered unrepeatable and therefore useless as a contribution to science.
Once your biological data are compiled in this format, you can sort them by the various columns, export the
grid references to mapping programs, and convert the data into tables for further calculations using a
spreadsheet. They can also be imported into databases and other computer programs for statistical analysis.
Supporting information
As part of your planning process (including maybe a pilot study), you should decide what data you are going
to collect. Just because you can collect information on 25 different environmental variables does not mean
that you should. The date, location and the name of the person collecting the data are basic items that you
always need but there may also be additional information that will help you to understand the biological
situation as you process the data later. These things include field sketches and site photographs.
A field sketch can be very helpful because you can record details that may be hard to represent in any other
manner. A sketch can also help you to remember where you placed your quadrats; a grid reference is fine but
meaningless without a map! Photographs may also be helpful and digital photography enables lots of images
to be captured with minimum fuss; however, it is also easy to get carried away and forget what you were there
for in the first place. Any supporting information should be just that – support for the main event: your data.
Table 3.2 Data table layout. Complex data are best set out in separate columns. Here butterfl y abundance is
recorded for four diff erent factors.
23
When you collect biological data, enter each record on a separate line and set out your spreadsheet so that
each column represents a factor. For example, Table 3.2 shows a small part of a complex dataset. Here you
have recorded the abundance of several butterfly species. You could have recorded the species in several
columns, one for each; however, you also have different locations. These locations are themselves further
subdivided by management. If you wrote down the information separately you would end up with several
smaller tables of data and it would be difficult to carry out any actual analyses. By recording the information
in separate columns you can carry out analyses more easily.
The data in Table 3.2 can be split into various subsections using your spreadsheet and the filter command
(Section 4.2.2). You can also use the Pivot Table function to review the data (Section 4.2.7).
Now you have gone through the planning process. Ideally, you would have worked out a hypothesis and
know what data you need to collect to support your hypothesis (or to reject it). You ought to know at this
stage what type of analysis you are going to run on your data (Chapter 5).
3.3 Summary
24
with a digital camera.
3.4 Exercises
3.1 What are the basic elements of a biological record?
3.2 What sort of items should make up the columns of your data?
3.3 It is important to write down the date because you will need to show your supervisor when you were
out recording data – TRUE or FALSE?
25
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XV
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