Tree diversity

analysis
A manual and software for common statistical
methods for ecological and biodiversity studies

Roeland Kindt and Richard Coe

World Agroforestry Centre, Nairobi, Kenya
Suggested citation: Kindt R and Coe R. 2005. Tree diversity analysis. A manual and software for
common statistical methods for ecological and biodiversity studies. Nairobi: World Agroforestry
Centre (ICRAF).

Published by the World Agroforestry Centre

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Internet:www.worldagroforestry.org

© World Agroforestry Centre 2005

ISBN: 92 9059 179 X

Design and Layout: K. Vanhoutte

Printed in Kenya

This publication may be quoted or reproduced without charge, provided the source is
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Proceeds of the sale will be used for printing the next edition of this book.
Contents
Contents
Acknowledgements iv

Introduction v

Overview of methods described in this manual vi

Chapter 1 Sampling 1

Chapter 2 Data preparation 19

Chapter 3 Doing biodiversity analysis with Biodiversity.R 31

Chapter 4 Analysis of species richness 39

Chapter 5 Analysis of diversity 55

Chapter 6 Analysis of counts of trees 71

Chapter 7 Analysis of presence or absence of species 103

Chapter 8 Analysis of differences in species composition 123

Chapter 9 Analysis of ecological distance by clustering 139

Chapter 10 Analysis of ecological distance by ordination 153

 Acknowledgements

We warmly thank all that provided inputs that the development for this manual. We also thank
lead to improvement of this manual. We especially VVOB for seconding Roeland Kindt to the World
appreciate the comments received during training Agroforestry Centre (ICRAF).
sessions with draft versions of this manual and the This tree diversity analysis manual was inspired
accompanying software in Kenya, Uganda and by research, development and extension activities
Mali. We are equally grateful to the thoughtful that were initiated by ICRAF on tree and landscape
reviews by Dr Simoneta Negrete-Yankelevich diversification. We want to acknowledge the
(Instituto de Ecología, Mexico) and Dr Robert various donor agencies that have funded these
Burn (Reading University, UK) of the draft version activities, especially VVOB, DFID, USAID and
of this manual, and to Hillary Kipruto for help in EU.
editing of this manual. We are grateful for the developers of the R
We highly appreciate the support of the Software for providing a free and powerful
Programme for Cooperation with International statistical package that allowed development
Institutes (SII), Education and Development of Biodiversity.R. We also want to give special
Division of the Netherlands’ Ministry of Foreign thanks to Jari Oksanen for developing the vegan
Affairs, and VVOB (The Flemish Association package and John Fox for developing the Rcmdr
for Development Assistance and Technical package, which are key packages that are used by
Cooperation, Flanders, Belgium) for funding Biodiversity.R.

iv
 Introduction

This manual was prepared during training events It is never possible to produce a guide to all
held in East- and West-Africa on the analysis of tree the methods that will be needed for analysis of
diversity data. These training events targeted data biodiversity data. Data analysis questions are
analysis of tree diversity data that were collected by continually advancing, requiring ever changing
scientists of the World Agroforestry Centre (ICRAF) data collection and analysis methods. This
and collaborating institutions. Typically, data were manual focuses on the analysis of species survey
collected on the tree species composition of quadrats data. We describe a number of methods that can
or farms. At the same time, explanatory variables be used to analyse hypotheses that are frequently
such as land use and household characteristics were important in biodiversity research. These are not
collected. Various hypotheses on the influence the only methods that can be used to analyse these
of explanatory variables on tree diversity can be hypotheses, and other methods will be needed
tested with such datasets. Although the manual when the focus of the biodiversity research is
was developed during research on tree diversity different.
on farms in Africa, the statistical methods can be Effective data analysis requires imagination and
used for a wider range of organisms, for different creativity. However, it also requires familiarity
hierarchical levels of biodiversity, and for a wider with basic concepts, and an ability to use a set
range of environments. of standard tools. This manual aims to provide
These materials were compiled as a second- that. It also points the user to other resources that
generation development of the Biodiversity Analysis develop ideas further.
Package, a CD-ROM compiled by Roeland Kindt Effective data analysis also requires a sound and
with resources and guidelines for the analysis of up to date understanding of the science behind
ecological and biodiversity information. Whereas the investigation. Data analysis requires clear
the Biodiversity Analysis Package provided a range objectives and hypotheses to investigate. These
of tools for different types of analysis, this manual have to be based on, and push forward, current
is accompanied by a new tool (Biodiversity.R) understanding. We have not attempted to link the
that offers a single software environment for all methods described here to the rapidly changing
the analyses that are described in this manual. science of biodiversity and community ecology.
This does not mean that Biodiversity.R is the Data analysis does not end with production
only recommended package for a particular type of statistical results. Those results have to be
of analysis, but it offers the advantage for training interpreted in the light of other information about
purposes that users only need to be introduced to the problem. We can not, therefore, discuss fully
one software package for statistically sound analysis the interpretation of the statistical results, or the
of biodiversity data. further statistical analyses they may lead to.

v
 Overview of methods described in
this manual

On the following page, a general diagram is variables on biodiversity. The analysis methods
provided that describes the data analysis questions can reveal how much of the pattern in species
that you can ask when analysing biodiversity diversity can be explained by the influence of the
based on the methodologies that are provided in environmental variables. Knowing how much of
this manual. Each question is discussed in further a pattern is explained will especially be useful if
detail in the respective chapter. The arrows the research was conducted to arrive at options
indicate the types of information that are used for better management of biodiversity. Note
in each method. All information is derived from that in this context, ‘environmental variables’
either the species data or the environmental data can include characteristics of the social and
of the sites. Chapter 2 describes the species and economic environment, not only the biophysical
environmental data matrices in greater detail. environment.
Some methods only use information on species. You may have noticed that Chapter 3 did
These methods are depicted on the left-hand side not feature in the diagram. The reason is that
of the diagram. They are based on biodiversity this chapter describes how the Biodiversity.R
statistics that can be used to compare the levels software can be installed and used to conduct
of biodiversity between sites, or to analyse how all the analyses described in the manual, whereas
similar sites are in species composition. you may choose to conduct the analysis with
The other methods use information on both different software. For this reason, the commands
species and the environmental variables of the and menu options for doing the analysis in
sites. These methods are shown on the right- Biodiversity.R are separated from the descriptions
hand side of the diagram. These methods provide of the methods, and placed at the end of each
insight into the influence of environmental chapter.

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