BiodiversityR-package {BiodiversityR} | R Documentation |
This package provides a GUI (Graphical User Interface, via the R-Commander) 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.
Package: | BiodiversityR |
Type: | Package |
Version: | 1.2 |
Date: | 2008-5-09 |
License: | GPL v2 |
Depends: | R (>= 2.7.0), vegan (>= 1.8-6) |
Suggests: | MASS, mgcv, cluster, Rcmdr (>= 1.3-14), car, RODBC, rpart, effects, multcomp, ellipse, maptree, sp, splancs, spatial, akima, nnet |
Packaged: | Sat May 9 15:09:28 2008; RKINDT |
Built: | R 2.7.0 ; 2008-05-09 15:09:29; windows |
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.
Index:
BCI.env Barro Colorado Island Quadrat Descriptions BiodiversityR-package GUI for biodiversity and community ecology analysis BiodiversityRGUI GUI for Biodiversity Analysis and Ordination CAPdiscrim Canonical Analysis of Principal Coordinates based on Discriminant Analysis NMSrandom Calculate the NMS Result with the Smallest Stress from Various Random Starts PCAsignificance PCA Significance accumresult Alternative Species Accumulation Curve Results add.spec.scores Add Species Scores to Unconstrained Ordination Results balanced.specaccum Balanced Species Accumulation Curves caprescale Rescale capcale scores crosstabanalysis Presence-absence Analysis by Cross Tabulation deviancepercentage Calculate Percentage and Significance of Deviance Explained by a GLM dist.eval Distance Matrix Evaluation dist.zeroes Distance Matrix Transformation distdisplayed Compare Distance Displayed in Ordination Diagram with Distances of Distance Matrix disttransform Community Matrix Transformation diversityresult Alternative Diversity Results faramea Faramea occidentalis abundance in Panama import.from.Excel Import Community or Environmental Data from Excel or Access loaded.citations Give Citation Information for all Loaded Packages makecommunitydataset Make a Community Dataset from a Stacked Dataset multiconstrained Pairwise Comparisons for All Levels of a Categorical Variable by RDA, CCA or Capscale nested.anova.dbrda Nested Analysis of Variance via Distance-based Redundancy Analysis or Non-parametric Multivariate Analysis of Variance nnetrandom Calculate the NNET Result with the Smallest Value from Various Random Starts ordicoeno Coenoclines for an Ordination Axis ordisymbol Add Other Graphical Items to Ordination Diagrams radfitresult Alternative Rank Abundance Fitting Results rankabundance Rank Abundance Curves removeNAcomm Synchronize Community and Environmental Datasets renyiresult Alternative Renyi Diversity Results residualssurface Show and Interpolate Two Dimensional Distribution of Residuals spatialsample Spatial Sampling within a Polygon transfgradient Gradient for Hypothetical Example of Turover of Species Composition transfspecies Hypothetical Example of Turover of Species Composition warcom Warburgia ugandensis AFLP Scores warenv Warburgia ugandensis Population Structure
Roeland Kindt
Maintainer: Roeland Kindt (World Agroforestry Centre [ICRAF]) <R.Kindt@CGIAR.org>
Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.
http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp
We suggest to use this citation for this software as well (together with citations of all other packages that were used)