Package for Community Ecology and Suitability Analysis

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Documentation for package ‘BiodiversityR’ version 2.17-2

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A B C D E F I L M N O P R S T V W

BiodiversityR-package GUI for biodiversity, suitability and community ecology analysis

-- A --

accumcomp Alternative Species Accumulation Curve Results
accumcomp.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2
accumplot Alternative Species Accumulation Curve Results
accumresult Alternative Species Accumulation Curve Results
add.spec.scores Add Species Scores to Unconstrained Ordination Results
axis.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2

-- B --

balanced.specaccum Balanced Species Accumulation Curves
BCI.env Barro Colorado Island Quadrat Descriptions
BiodiversityR GUI for biodiversity, suitability and community ecology analysis
BiodiversityR.changeLog changeLog file for BiodiversityR
BiodiversityRGUI GUI for Biodiversity, Community Ecology and Ensemble Suitability Analysis

-- C --

CAPdiscrim Canonical Analysis of Principal Coordinates based on Discriminant Analysis
caprescale Rescaling of Capscale Results to Reflect Total Sums of Squares Of Distance Matrix
centroids.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2
check.datasets Synchronize Community and Environmental Datasets
check.ordiscores Synchronize Community and Environmental Datasets
crosstabanalysis Presence-absence Analysis by Cross Tabulation
CucurbitaClim Baseline and Future WorldClim 2.1 Climatic Data for Cucurbita Species

-- D --

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

-- E --

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.bioclim Suitability mapping based on the BIOCLIM algorithm
ensemble.bioclim.graph Graphs of bioclimatic ranges of species and climates
ensemble.bioclim.graph.data Graphs of bioclimatic ranges of species and climates
ensemble.bioclim.object Suitability mapping based on the BIOCLIM algorithm
ensemble.calibrate.models Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.calibrate.models.gbm Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.calibrate.models.nnet Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.calibrate.weights Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.centroids Mapping of environmental zones based on the Mahalanobis distance from centroids in environmental space.
ensemble.chull.apply Area of Occupancy (AOO) and Extent of Occurrence (EOO) via the 'red' library.
ensemble.chull.buffer.distances Area of Occupancy (AOO) and Extent of Occurrence (EOO) via the 'red' library.
ensemble.chull.create Area of Occupancy (AOO) and Extent of Occurrence (EOO) via the 'red' library.
ensemble.chull.MSDM Area of Occupancy (AOO) and Extent of Occurrence (EOO) via the 'red' library.
ensemble.concave.hull Analysis of Niche Overlap in Environmental Space for Changed Climates via Concave Hulls
ensemble.concave.union Analysis of Niche Overlap in Environmental Space for Changed Climates via Concave Hulls
ensemble.concave.venn Analysis of Niche Overlap in Environmental Space for Changed Climates via Concave Hulls
ensemble.drop1 Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.dummy.variables Suitability mapping based on ensembles of modelling algorithms: handling of categorical data
ensemble.ecocrop Suitability mapping via absolute and optimal precipitation and temperature limits as in the ECOCROP model.
ensemble.ecocrop.object Suitability mapping via absolute and optimal precipitation and temperature limits as in the ECOCROP model.
ensemble.envBlock Spatially or environmentally separated folds for cross-validation via blockCV::spatialBlock or blockCV::envBlock
ensemble.envirem.masterstack Calculate bioclimatic variables via the 'envirem' package for data.frames.
ensemble.envirem.run Calculate bioclimatic variables via the 'envirem' package for data.frames.
ensemble.envirem.solradstack Calculate bioclimatic variables via the 'envirem' package for data.frames.
ensemble.environmentalThin Thinning of presence point coordinates in geographical or environmental space
ensemble.environmentalThin.clara Thinning of presence point coordinates in geographical or environmental space
ensemble.evaluate Model evaluation including True Skill Statistic (TSS), AUCdiff and Symmetric Extremal Dependence Index (SEDI).
ensemble.formulae Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
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.outliers Analysis of Niche Overlap in Environmental Space for Changed Climates via Concave Hulls
ensemble.outlierThin Thinning of presence point coordinates in geographical or environmental space
ensemble.pairs 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.PET.seasons Raster calculations of beginnings and lengths of growing seasons from the difference between precipitation (P) and potential evapotranspiration (PET), defining dry months with 2 * P < PET.
ensemble.plot Suitability mapping based on ensembles of modelling algorithms: batch processing
ensemble.prec.season Raster calculations of beginnings and lengths of growing seasons from the difference between precipitation (P) and potential evapotranspiration (PET), defining dry months with 2 * P < PET.
ensemble.raster Suitability mapping based on ensembles of modelling algorithms: consensus mapping
ensemble.red Area of Occupancy (AOO) and Extent of Occurrence (EOO) via the 'red' library.
ensemble.season.suitability Raster calculations of beginnings and lengths of growing seasons from the difference between precipitation (P) and potential evapotranspiration (PET), defining dry months with 2 * P < PET.
ensemble.SEDI Model evaluation including True Skill Statistic (TSS), AUCdiff and Symmetric Extremal Dependence Index (SEDI).
ensemble.simplified.categories Suitability mapping based on ensembles of modelling algorithms: handling of categorical data
ensemble.spatialBlock Spatially or environmentally separated folds for cross-validation via blockCV::spatialBlock or blockCV::envBlock
ensemble.spatialThin Thinning of presence point coordinates in geographical or environmental space
ensemble.spatialThin.quant Thinning of presence point coordinates in geographical or environmental space
ensemble.strategy Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.terra Suitability mapping based on ensembles of modelling algorithms: consensus mapping via the terra package
ensemble.threshold Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.Tjur Model evaluation including True Skill Statistic (TSS), AUCdiff and Symmetric Extremal Dependence Index (SEDI).
ensemble.tmean.season Raster calculations of beginnings and lengths of growing seasons from the difference between precipitation (P) and potential evapotranspiration (PET), defining dry months with 2 * P < PET.
ensemble.VIF Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.VIF.dataframe Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
ensemble.weights Suitability mapping based on ensembles of modelling algorithms: calibration of models and weights
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

-- F --

faramea Faramea occidentalis abundance in Panama

-- I --

ifri Example data from the International Forestry Resources and Institutions (IFRI) research network
import.with.readxl Synchronize Community and Environmental Datasets
importancevalue Importance Value
importancevalue.comp Importance Value

-- L --

loaded.citations Give Citation Information for all Loaded Packages

-- M --

makecommunitydataset Make a Community Dataset from a Stacked Dataset
multiconstrained Pairwise Comparisons for All Levels of a Categorical Variable by RDA, CCA or Capscale

-- N --

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

-- O --

ordibubble Add Other Graphical Items to Ordination Diagrams
ordicluster2 Add Other Graphical Items to Ordination Diagrams
ordicoeno Coenoclines for an Ordination Axis
ordiellipse.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2
ordiequilibriumcircle PCA Significance
ordinearest Add Other Graphical Items to Ordination Diagrams
ordisurfgrid.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2
ordisymbol Add Other Graphical Items to Ordination Diagrams
ordivector Add Other Graphical Items to Ordination Diagrams

-- P --

PCAsignificance PCA Significance
prepare.bioenv Distance Matrix Evaluation
pvclust.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2

-- R --

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
renyi.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2
renyiaccumresult Alternative Renyi Diversity Results
renyicomp Alternative Renyi Diversity Results
renyicomp.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2
renyiplot Alternative Renyi Diversity Results
renyiresult Alternative Renyi Diversity Results
replaceNAcomm Synchronize Community and Environmental Datasets

-- S --

same.sites Synchronize Community and Environmental Datasets
sites.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2
spatialsample Spatial Sampling within a Polygon
species.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2
stackcommunitydataset Make a Community Dataset from a Stacked Dataset
subsetcomm Synchronize Community and Environmental Datasets

-- T --

transfgradient Gradient for Hypothetical Example of Turover of Species Composition
transfspecies Hypothetical Example of Turover of Species Composition
treegoer.filter Calculate climate scores with the Tree Globally Observed Environmental Ranges (TreeGOER) database.
treegoer.map Calculate climate scores with the Tree Globally Observed Environmental Ranges (TreeGOER) database.
treegoer.position Calculate climate scores with the Tree Globally Observed Environmental Ranges (TreeGOER) database.
treegoer.score Calculate climate scores with the Tree Globally Observed Environmental Ranges (TreeGOER) database.
treegoer.widen Calculate climate scores with the Tree Globally Observed Environmental Ranges (TreeGOER) database.

-- V --

vectorfit.long Helper Functions to Prepare Plotting of Accumulation, Diversity Profile and Ordiplot Results via ggplot2

-- W --

warcom Warburgia ugandensis AFLP Scores
warenv Warburgia ugandensis Population Structure