Package for Community Ecology and Suitability Analysis


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Documentation for package ‘BiodiversityR’ version 2.7-2

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BiodiversityR-package GUI for biodiversity, suitability and community ecology analysis
accumcomp Alternative Species Accumulation Curve Results
accumplot Alternative Species Accumulation Curve Results
accumresult Alternative Species Accumulation Curve Results
add.spec.scores Add Species Scores to Unconstrained Ordination Results
balanced.specaccum Balanced Species Accumulation Curves
BCI.env Barro Colorado Island Quadrat Descriptions
BiodiversityR GUI for biodiversity, suitability and community ecology analysis
BiodiversityRGUI GUI for Biodiversity Analysis and Ordination
CAPdiscrim Canonical Analysis of Principal Coordinates based on Discriminant Analysis
caprescale Rescaling of Capscale Results to Reflect Total Sums of Squares Of Distance Matrix
check.datasets Synchronize Community and Environmental Datasets
check.ordiscores Synchronize Community and Environmental Datasets
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
diversitycomp Alternative Diversity Results
diversityresult Alternative Diversity Results
diversityvariables Alternative Diversity Results
ensemble.accepted.categories Suitability mapping based on ensembles of modelling algorithms: handling of categorical data
ensemble.analogue Climate analogues from climatic distance raster layers.
ensemble.analogue.object Climate analogues from climatic distance raster layers.
ensemble.area Suitability mapping based on ensembles of modelling algorithms: consensus mapping
ensemble.batch Suitability mapping based on ensembles of modelling algorithms: batch processing
ensemble.centroids Mapping of environmental zones based on the Mahalanobis distance from centroids in environmental space.
ensemble.drop1 Suitability mapping based on ensembles of modelling algorithms: comparison of different algorithms and calibration
ensemble.dummy.variables Suitability mapping based on ensembles of modelling algorithms: handling of categorical data
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.ecocrop.object Mapping of novel environmental conditions (areas where some of the environmental conditions are outside the range of environmental conditions of a reference area).
ensemble.formulae Suitability mapping based on ensembles of modelling algorithms: comparison of different algorithms and calibration
ensemble.habitat.change Suitability mapping based on ensembles of modelling algorithms: consensus mapping
ensemble.mean Suitability mapping based on ensembles of modelling algorithms: batch processing
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.novel.object Mapping of novel environmental conditions (areas where some of the environmental conditions are outside the range of environmental conditions of a reference area).
ensemble.plot Suitability mapping based on ensembles of modelling algorithms: batch processing
ensemble.raster Suitability mapping based on ensembles of modelling algorithms: consensus mapping
ensemble.simplified.categories Suitability mapping based on ensembles of modelling algorithms: handling of categorical data
ensemble.strategy Suitability mapping based on ensembles of modelling algorithms: comparison of different algorithms and calibration
ensemble.test Suitability mapping based on ensembles of modelling algorithms: comparison of different algorithms and calibration
ensemble.test.gbm Suitability mapping based on ensembles of modelling algorithms: comparison of different algorithms and calibration
ensemble.test.nnet Suitability mapping based on ensembles of modelling algorithms: comparison of different algorithms and calibration
ensemble.test.splits Suitability mapping based on ensembles of modelling algorithms: comparison of different algorithms and calibration
ensemble.threshold Suitability mapping based on ensembles of modelling algorithms: comparison of different algorithms and calibration
ensemble.weights 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.
evaluation.strip.data Evaluation strips for ensemble suitability mapping
evaluation.strip.plot Evaluation strips for ensemble suitability mapping
faramea Faramea occidentalis abundance in Panama
ifri Example data from the International Forestry Resources and Institutions (IFRI) research network
importancevalue Importance Value
importancevalue.comp Importance Value
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
nested.npmanova Nested Analysis of Variance via Distance-based Redundancy Analysis or Non-parametric Multivariate Analysis of Variance
NMSrandom Calculate the NMS Result with the Smallest Stress from Various Random Starts
nnetrandom Calculate the NNET Result with the Smallest Value from Various Random Starts
ordibubble Add Other Graphical Items to Ordination Diagrams
ordicluster2 Add Other Graphical Items to Ordination Diagrams
ordicoeno Coenoclines for an Ordination Axis
ordiequilibriumcircle PCA Significance
ordinearest Add Other Graphical Items to Ordination Diagrams
ordisymbol Add Other Graphical Items to Ordination Diagrams
ordivector Add Other Graphical Items to Ordination Diagrams
PCAsignificance PCA Significance
prepare.bioenv Distance Matrix Evaluation
radfitresult Alternative Rank Abundance Fitting Results
rankabuncomp Rank Abundance Curves
rankabundance Rank Abundance Curves
rankabunplot Rank Abundance Curves
removeNAcomm Synchronize Community and Environmental Datasets
removeNAenv Synchronize Community and Environmental Datasets
removezerospecies Synchronize Community and Environmental Datasets
renyiaccumresult Alternative Renyi Diversity Results
renyicomp Alternative Renyi Diversity Results
renyiplot Alternative Renyi Diversity Results
renyiresult Alternative Renyi Diversity Results
replaceNAcomm Synchronize Community and Environmental Datasets
residualssurface Show and Interpolate Two Dimensional Distribution of Residuals
same.sites Synchronize Community and Environmental Datasets
spatialsample Spatial Sampling within a Polygon
subsetcomm Synchronize Community and Environmental Datasets
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