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BiodiversityR (version 2.7-2)

Package for Community Ecology and Suitability Analysis

Description

Graphical User Interface (via the R-Commander) and 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. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.

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Version

Install

install.packages('BiodiversityR')

Monthly Downloads

3,609

Version

2.7-2

License

GPL-2

Maintainer

Roeland Kindt

Last Published

August 29th, 2016

Functions in BiodiversityR (2.7-2)

accumresult

Alternative Species Accumulation Curve Results
deviancepercentage

Calculate Percentage and Significance of Deviance Explained by a GLM
add.spec.scores

Add Species Scores to Unconstrained Ordination Results
caprescale

Rescaling of Capscale Results to Reflect Total Sums of Squares Of Distance Matrix
BiodiversityR-package

GUI for biodiversity, suitability and community ecology analysis
CAPdiscrim

Canonical Analysis of Principal Coordinates based on Discriminant Analysis
crosstabanalysis

Presence-absence Analysis by Cross Tabulation
BCI.env

Barro Colorado Island Quadrat Descriptions
balanced.specaccum

Balanced Species Accumulation Curves
BiodiversityRGUI

GUI for Biodiversity Analysis and Ordination
ensemble.analogue

Climate analogues from climatic distance raster layers.
ensemble.ecocrop

Mapping of novel environmental conditions (areas where some of the environmental conditions are outside the range of environmental conditions of a reference area).
dist.zeroes

Distance Matrix Transformation
dist.eval

Distance Matrix Evaluation
distdisplayed

Compare Distance Displayed in Ordination Diagram with Distances of Distance Matrix
ensemble.batch

Suitability mapping based on ensembles of modelling algorithms: batch processing
disttransform

Community Matrix Transformation
ensemble.dummy.variables

Suitability mapping based on ensembles of modelling algorithms: handling of categorical data
diversityresult

Alternative Diversity Results
ensemble.test

Suitability mapping based on ensembles of modelling algorithms: comparison of different algorithms and calibration
ensemble.zones

Mapping of environmental zones based on the Mahalanobis distance from centroids in environmental space.
faramea

Faramea occidentalis abundance in Panama
importancevalue

Importance Value
makecommunitydataset

Make a Community Dataset from a Stacked Dataset
evaluation.strip.data

Evaluation strips for ensemble suitability mapping
ensemble.raster

Suitability mapping based on ensembles of modelling algorithms: consensus mapping
loaded.citations

Give Citation Information for all Loaded Packages
ensemble.novel

Mapping of novel environmental conditions (areas where some of the environmental conditions are outside the range of environmental conditions of a reference area).
ifri

Example data from the International Forestry Resources and Institutions (IFRI) research network
multiconstrained

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

Alternative Rank Abundance Fitting Results
NMSrandom

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

Coenoclines for an Ordination Axis
removeNAcomm

Synchronize Community and Environmental Datasets
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
ordisymbol

Add Other Graphical Items to Ordination Diagrams
renyiresult

Alternative Renyi Diversity Results
rankabundance

Rank Abundance Curves
PCAsignificance

PCA Significance
warenv

Warburgia ugandensis Population Structure
transfgradient

Gradient for Hypothetical Example of Turover of Species Composition
residualssurface

Show and Interpolate Two Dimensional Distribution of Residuals
warcom

Warburgia ugandensis AFLP Scores
transfspecies

Hypothetical Example of Turover of Species Composition
spatialsample

Spatial Sampling within a Polygon