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BiodiversityR (version 1.5)

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

3,483

Version

1.5

License

GPL-2

Maintainer

Roeland Kindt

Last Published

January 17th, 2011

Functions in BiodiversityR (1.5)

warcom

Warburgia ugandensis AFLP Scores
ordisymbol

Add Other Graphical Items to Ordination Diagrams
caprescale

Rescaling of Capscale Results to Reflect Total Sums of Squares Of Distance Matrix
nnetrandom

Calculate the NNET Result with the Smallest Value from Various Random Starts
disttransform

Community Matrix Transformation
residualssurface

Show and Interpolate Two Dimensional Distribution of Residuals
crosstabanalysis

Presence-absence Analysis by Cross Tabulation
CAPdiscrim

Canonical Analysis of Principal Coordinates based on Discriminant Analysis
add.spec.scores

Add Species Scores to Unconstrained Ordination Results
makecommunitydataset

Make a Community Dataset from a Stacked Dataset
accumresult

Alternative Species Accumulation Curve Results
NMSrandom

Calculate the NMS Result with the Smallest Stress from Various Random Starts
diversityresult

Alternative Diversity Results
multiconstrained

Pairwise Comparisons for All Levels of a Categorical Variable by RDA, CCA or Capscale
radfitresult

Alternative Rank Abundance Fitting Results
distdisplayed

Compare Distance Displayed in Ordination Diagram with Distances of Distance Matrix
BCI.env

Barro Colorado Island Quadrat Descriptions
warenv

Warburgia ugandensis Population Structure
BiodiversityR-package

GUI for biodiversity and community ecology analysis
transfspecies

Hypothetical Example of Turover of Species Composition
removeNAcomm

Synchronize Community and Environmental Datasets
balanced.specaccum

Balanced Species Accumulation Curves
rankabundance

Rank Abundance Curves
nested.anova.dbrda

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

Spatial Sampling within a Polygon
transfgradient

Gradient for Hypothetical Example of Turover of Species Composition
faramea

Faramea occidentalis abundance in Panama
PCAsignificance

PCA Significance
ordicoeno

Coenoclines for an Ordination Axis
dist.zeroes

Distance Matrix Transformation
loaded.citations

Give Citation Information for all Loaded Packages
deviancepercentage

Calculate Percentage and Significance of Deviance Explained by a GLM
BiodiversityRGUI

GUI for Biodiversity Analysis and Ordination
import.from.Excel

Import Community or Environmental Data from Excel or Access
renyiresult

Alternative Renyi Diversity Results
dist.eval

Distance Matrix Evaluation