This package provides a GUI (Graphical User Interface, via the R-Commander; BiodiversityRGUI) and some utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website.
Maintainer: Roeland Kindt (World Agroforestry Centre)
We warmly thank all that provided inputs that lead to improvement of the Tree Diversity Analysis manual that describes common methods for biodiversity and community ecology analysis and its accompanying software. We especially appreciate the comments received during training sessions with draft versions of this manual and the accompanying software in Kenya, Uganda and Mali. We are equally grateful to the thoughtful reviews by Dr Simoneta Negrete-Yankelevich (Instituto de Ecologia, Mexico) and Dr Robert Burn (Reading University, UK) of the draft version of this manual, and to Hillary Kipruto for help in editing of this manual. We also want to specifically thank Mikkel Grum, Jane Poole and Paulo van Breugel for helping in testing the packaged version of the software. We also want to give special thanks for all the support that was given by Jan Beniest, Tony Simons and Kris Vanhoutte in realizing the book and software.
We highly appreciate the support of 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) for funding the development for this manual. We also thank VVOB for seconding Roeland Kindt to the World Agroforestry Centre (ICRAF). The tree diversity analysis manual was inspired by research, development and extension activities that were initiated by ICRAF on tree and landscape diversification. We want to acknowledge the various donor agencies that have funded these activities, especially VVOB, DFID, USAID and EU.
We are grateful for the developers of the R Software for providing a free and powerful statistical package that allowed development of BiodiversityR. We also want to give special thanks to Jari Oksanen for developing the vegan package and John Fox for developing the Rcmdr package, which are key packages that are used by BiodiversityR.
Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.
https://www.worldagroforestry.org/output/tree-diversity-analysis
We suggest to use this citation for this software as well (together with citations of all other packages that were used)