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BiodiversityR (version 1.4.2)

GUI for biodiversity and community ecology analysis

Description

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.

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Version

Install

install.packages('BiodiversityR')

Monthly Downloads

3,609

Version

1.4.2

License

GPL-2

Maintainer

Roeland Kindt

Last Published

November 30th, 2009

Functions in BiodiversityR (1.4.2)

dist.eval

Distance Matrix Evaluation
faramea

Faramea occidentalis abundance in Panama
NMSrandom

Calculate the NMS Result with the Smallest Stress from Various Random Starts
add.spec.scores

Add Species Scores to Unconstrained Ordination Results
deviancepercentage

Calculate Percentage and Significance of Deviance Explained by a GLM
BCI.env

Barro Colorado Island Quadrat Descriptions
disttransform

Community Matrix Transformation
caprescale

Rescaling of Capscale Results to Reflect Total Sums of Squares Of Distance Matrix
loaded.citations

Give Citation Information for all Loaded Packages
nnetrandom

Calculate the NNET Result with the Smallest Value from Various Random Starts
balanced.specaccum

Balanced Species Accumulation Curves
renyiresult

Alternative Renyi Diversity Results
residualssurface

Show and Interpolate Two Dimensional Distribution of Residuals
transfspecies

Hypothetical Example of Turover of Species Composition
distdisplayed

Compare Distance Displayed in Ordination Diagram with Distances of Distance Matrix
CAPdiscrim

Canonical Analysis of Principal Coordinates based on Discriminant Analysis
PCAsignificance

PCA Significance
diversityresult

Alternative Diversity Results
dist.zeroes

Distance Matrix Transformation
makecommunitydataset

Make a Community Dataset from a Stacked Dataset
radfitresult

Alternative Rank Abundance Fitting Results
accumresult

Alternative Species Accumulation Curve Results
rankabundance

Rank Abundance Curves
import.from.Excel

Import Community or Environmental Data from Excel or Access
spatialsample

Spatial Sampling within a Polygon
crosstabanalysis

Presence-absence Analysis by Cross Tabulation
multiconstrained

Pairwise Comparisons for All Levels of a Categorical Variable by RDA, CCA or Capscale
BiodiversityR-package

GUI for biodiversity and community ecology analysis
ordicoeno

Coenoclines for an Ordination Axis
removeNAcomm

Synchronize Community and Environmental Datasets
BiodiversityRGUI

GUI for Biodiversity Analysis and Ordination
warcom

Warburgia ugandensis AFLP Scores
nested.anova.dbrda

Nested Analysis of Variance via Distance-based Redundancy Analysis or Non-parametric Multivariate Analysis of Variance
warenv

Warburgia ugandensis Population Structure
ordisymbol

Add Other Graphical Items to Ordination Diagrams
transfgradient

Gradient for Hypothetical Example of Turover of Species Composition