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BiodiversityR (version 2.12-3)

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

3,390

Version

2.12-3

License

GPL-3

Maintainer

Roeland Kindt

Last Published

December 17th, 2020

Functions in BiodiversityR (2.12-3)

BiodiversityR.changeLog

changeLog file for BiodiversityR
balanced.specaccum

Balanced Species Accumulation Curves
NMSrandom

Calculate the NMS Result with the Smallest Stress from Various Random Starts
BCI.env

Barro Colorado Island Quadrat Descriptions
BiodiversityRGUI

GUI for Biodiversity, Community Ecology and Ensemble Suitability Analysis
add.spec.scores

Add Species Scores to Unconstrained Ordination Results
CAPdiscrim

Canonical Analysis of Principal Coordinates based on Discriminant Analysis
BiodiversityR-package

GUI for biodiversity, suitability and community ecology analysis
PCAsignificance

PCA Significance
accumresult

Alternative Species Accumulation Curve Results
deviancepercentage

Calculate Percentage and Significance of Deviance Explained by a GLM
crosstabanalysis

Presence-absence Analysis by Cross Tabulation
caprescale

Rescaling of Capscale Results to Reflect Total Sums of Squares Of Distance Matrix
dist.eval

Distance Matrix Evaluation
distdisplayed

Compare Distance Displayed in Ordination Diagram with Distances of Distance Matrix
dist.zeroes

Distance Matrix Transformation
disttransform

Community Matrix Transformation
diversityresult

Alternative Diversity Results
ensemble.calibrate.models

Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.PET.season

Calculate the balance between precipitation and potential evapotranspiration for the dry season with the largest balance (maximum climatological water deficit, accumulated aridity).
ensemble.evaluate

Model evaluation including True Skill Statistic (TSS), AUCdiff and Symmetric Extremal Dependence Index (SEDI).
ensemble.dummy.variables

Suitability mapping based on ensembles of modelling algorithms: handling of categorical data
ensemble.bioclim.graph

Graphs of bioclimatic ranges of species and climates
ensemble.raster

Suitability mapping based on ensembles of modelling algorithms: consensus mapping
ensemble.bioclim

Suitability mapping based on the BIOCLIM algorithm
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).
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).
ensemble.red

Area of Occupancy (AOO) and Extent of Occurrence (EOO) via the red library.
ensemble.analogue

Climate analogues from climatic distance raster layers.
ensemble.batch

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

Faramea occidentalis abundance in Panama
ensemble.spatialThin

Thinning of presence point coordinates in geographical or environmental space
evaluation.strip.data

Evaluation strips for ensemble suitability mapping
ifri

Example data from the International Forestry Resources and Institutions (IFRI) research network
loaded.citations

Give Citation Information for all Loaded Packages
multiconstrained

Pairwise Comparisons for All Levels of a Categorical Variable by RDA, CCA or Capscale
ensemble.zones

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

Importance Value
nested.anova.dbrda

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

Make a Community Dataset from a Stacked Dataset
residualssurface

Show and Interpolate Two Dimensional Distribution of Residuals
renyiresult

Alternative Renyi Diversity Results
ordisymbol

Add Other Graphical Items to Ordination Diagrams
spatialsample

Spatial Sampling within a Polygon
radfitresult

Alternative Rank Abundance Fitting Results
nnetrandom

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

Rank Abundance Curves
ordicoeno

Coenoclines for an Ordination Axis
sites.long

Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2
removeNAcomm

Synchronize Community and Environmental Datasets
transfgradient

Gradient for Hypothetical Example of Turover of Species Composition
warenv

Warburgia ugandensis Population Structure
warcom

Warburgia ugandensis AFLP Scores
transfspecies

Hypothetical Example of Turover of Species Composition