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Tree diversity analysis

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

Effective data analysis requires familiarity with basic concepts and an ability to use a set of standard tools, as well as creativity and imagination. Tree diversity analysis provides a solid practical foundation for training in statistical methods for ecological and biodiversity studies.

This manual arose from training researchers to analyse tree diversity data collected on African farms, yet the statistical methods can be used for a wider range of organisms, for different hierarchical levels of biodiversity and for a variety of environments — making it an invaluable tool for scientists and students alike.

Focusing on the analysis of species survey data, Tree diversity analysis provides a comprehensive review of the methods that are most often used in recent diversity and community ecology literature including:
  • Species accumulation curves for site-based and individual-based species accumulation, including a new technique for exact calculation of site-based species accumulation.
  • Description of appropriate methods for investigating differences in diversity and evenness such as Rényi diversity profiles, including methods of rarefaction to the same sample size for different subsets of the data.
  • Modern regression methods of generalized linear models and generalized additive models that are often appropriate for investigating patterns of species occurrence and species counts.
  • Methods of ordination for investigating community structure and the influence of environmental characteristics, including recent methods such as distance-based redundancy analysis and constrained analysis of principal coordinates.
Acknowledgements, introduction and overview of methods
Chapter 1: Sampling Chapter 6: Analysis of counts of trees
Chapter 2: Data preparation Chapter 7: Analysis of presence or absence of species
Chapter 3: Doing biodiversity analysis with Biodiversity.R Chapter 8: Analysis of differences in species composition
Chapter 4: Analysis of species richness Chapter 9: Analysis of ecological distance by clustering
Chapter 5: Analysis of diversity Chapter 10: Analysis of ecological distance by ordination

The manual also introduces a powerful new software programme, BiodiversityR, that is capable of performing all the statistical analyses described in the book. The software is built using the free R language and environment for statistical computing, and several of its libraries such as the vegan community ecology package and the R-commander graphical user interface.

The original software is provided on the CD-ROM, but the software has recently been developed into a standard package for R (version 2.5). Follow these links to access the updated software: As the R package and its additional packages keep changing, we can not promise that we will be able to keep up to speed with these developments. However, check this space for updates.
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Roeland Kindt is an ecologist with interests in community ecology, conservation, ecoagriculture and training. He is currently leading a World Agroforestry Centre project on enhanced utilization of tree diversity at the landscape level.

Richard Coe is a biometrician and has more than 25 years experience in providing research support to scientists in the fields of ecology, agroforestry and natural resource management. He is leading the Research Support Unit of the World Agroforestry Centre.

Questions & Answers


Funding for the production and publication of this manual was provided by the Programme for Cooperation with International Institutes (SII), Education and Development Division of the Netherlands’ Ministry of Foreign Affairs, and VVOB (The Flemish Association for Development Cooperation and Technical Assistance, Flanders, Belgium).

This manual was inspired by research, development and extension activities initiated by ICRAF on tree and landscape diversification. We are grateful to the various donor agencies that have funded these activities, especially VVOB, DFID, USAID and EU.

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