| 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)