# Package for Community Ecology and Suitability Analysis

## Documentation for package ‘BiodiversityR’ version 2.18-1

- DESCRIPTION file
- Package README

## Help Pages

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's cv_spatial() or cv_cluster() functions
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's cv_spatial() or cv_cluster() functions
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.from.Access | Synchronize Community and Environmental Datasets
import.from.Access2007 | Synchronize Community and Environmental Datasets
import.from.Excel | Synchronize Community and Environmental Datasets
import.from.Excel2007 | Synchronize Community and Environmental Datasets
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
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