R: Multivariate Analysis Using Biplots in R

# Multivariate Analysis Using Biplots in R

## Documentation for package ‘MultBiplotR’ version 25.11.15

- DESCRIPTION file

## Help Pages

A B C D E F G H I K L M N O P R S T U V W Z

MultBiplotR-package | Multivariate Analysis using Biplots

## -- A --

AddBinVars2Biplot | Add suplementary binary variables to a biplot
AddCluster2Biplot | Add clusters to a biplot object
AddContVars2Biplot | Adds supplementary continuous variables to a biplot object
AddOrdVars2Biplot | Adds supplementary ordinal variables to an existing biplot objects.
AddSupVars2Biplot | Adds supplementary variables to a biplot object
anova.RidgeBinaryLogistic | Compares two binary logistic models

## -- B --

Bartlett.Tests | Bartlett tests
BasicDescription | Basic descriptive sataistics
BinaryDistances | Binary Distances
BinaryLogBiplotEM | Binary logistic biplot with the EM algorithm.
BinaryLogBiplotGD | Binary Logistic Biplot with Gradient Descent Estimation
BinaryLogBiplotGDRecursive | Binary Logistic Biplot with Recursive Gradient Descent Estimation
BinaryLogBiplotJoint | Binary logistic biplot with a gradient descent algorithm.
BinaryLogBiplotMirt | Binary logistic biplot with Item Response Theory.
BinaryLogisticBiplot | Binary Logistic Biplot
BinaryPLSFit | Binary PLS Regression.
BinaryPLSR | Partial Least Squares Regression with Binary Data
BinaryProximities | Proximity Measures for Binary Data
Biplot.BinaryPLSR | Biplot for a PLSR model with binary data
Biplot.PLSR | Partial Least Squares Biplot
Biplot.PLSR1BIN | Biplot for a PLSR model with a binary response
Biplot.PLSRBIN | Biplot for a PLSR model with binary responses
BiplotFPCA | External Biplot for functional data from a functional PCA object.
BootstrapDistance | Bootstrap on the distance matrices used for Principal Coordinates Analysis (PCoA)
BootstrapScalar | Bootstrap on the scalar product matrices used for Principal Coordinates Analysis (PCoA)
BootstrapSmacof | Bootstrap on the distance matrices used for MDS with Smacof
BoxPlotPanel | Panel of box plots

## -- C --

CA | Correspondence Analysis
Canonical.Variate.Analysis | Biplot representation of a Canonical Variate Analysis or a Manova (Canonical-Biplot or MANOVA-Biplot)
CanonicalBiplot | Biplot representation of a Canonical Variate Analysis or a Manova (Canonical-Biplot or MANOVA-Biplot)
CanonicalDistanceAnalysis | MANOVA and Canonical Analysis of Distances
CanonicalStatisBiplot | CANONICAL STATIS-ACT for multiple tables with common rows and its associated Biplot
CategoricalDistances | Distances among individuals using nominal variables.
CategoricalProximities | Proximities among individuals using nominal variables.
CCA | Canonical Correspondence Analysis
CheckBinaryMatrix | Checks if a data matrix is binary
CheckBinaryVector | Checks if a vector is binary
Chemical | Chemical data
Circle | Draws a circle
Coinertia | Coinertia Analysis.
ColContributionPlot | Plots the contributios of a biplot
ConcEllipse | Concentration ellipse for a se of two-dimensional points
ConfidenceInterval | Confidence Interval for the mean
ConstrainedLogisticBiplot | Constrained Binary Logistic Biplot
ConstrainedOrdinalLogisticBiplot | Constrained Ordinal Logistic Biplot
ContinuousDistances | Distances for Continuous Data
ContinuousProximities | Proximities for Continuous Data
ContributionPlot | Contribution plots for several Biplots
Convert2ThreeWay | Three way array from a two way matrix
Convert3wArray2List | Converts a three way array into a list
ConvertFactors2Integers | Convert a factor to integer numbers
ConvertList23wArray | Converts a list of matrices into a three way array
CorrelationCircle | Circle of correlations
CrissCross | Alternated Least Squares Biplot
CumSum | Cummulative sums

## -- D --

Dataframe2BinaryMatrix | Converts a Data Frame into a Binary Data Matrix
DataFrame2Matrix4Regression | Prepares a matrix for regression from a data frame
DensityBiplot | Adds Non-parametric densities to a biplot. Separated densities are calculated for different clusters
Dhats | Calculation of Disparities
diagonal | Diagonal matrix from a vector
DimensionLabels | Labels for the selected dimensions in a biplot
dlines | Connects two sets of points by lines
Doctors | Data set extracted from the Careers of doctorate holders survey carried out by Spanish Statistical Office in 2008.
DoctorsNUM | Data set extracted from the Careers of doctorate holders survey carried out by Spanish Statistical Office in 2008, numerical data.

## -- E --

ErrorBarPlotPanel | Plots a panel of error bars
EuclideanDistance | Classical Euclidean Distance (Pythagorean Distance)
ExpandTable | Expands a compressed table of patterns and frequencies
ExternalBinaryLogisticBiplot | External Logistic Biplot for binary Data
ExtractTable | Extracts unique patterns and its frequencies for a discrete data matrix (numeric)

## -- F --

FA.Biplot | Biplot for Factor Analysis.
Factor2Binary | Converts a Factor into its indicator matrix
Fraction | Selection of a fraction of the data

## -- G --

Games_Howell | Games-Howell post-hoc tests for Welch's one-way analysis
GD.Biplot | Biplot for continuous data based on gradient descent methods
GeneralizedProcrustes | Generalized Procrustes Analysis
GetBiplotScales | Calculates the scales for the variables on a linear biplot
GetCCAScales | Calculates scales for plotting the environmental variables in a Canonical Correspondence Analysis
ginv | G inverse
GowerProximities | Gower Dissimilarities for mixed types of data
GowerSimilarities | Gower Dissimilarities for mixed types of data

## -- H --

Hermquad | Gauss-Hermite quadrature
HistogramPanel | Panel of histograms
HJ.Biplot | HJ Biplot with added features.

## -- I --

InBox | Checks if a point is inside a box.
InitialTransform | Initial transformation of data
Integer2Binary | Transforms an Integer Variable into a Binary Variable

## -- K --

Kruskal.Wallis.Tests | Kruskal Wallis Tests

## -- L --

Levene.Tests | Levene Tests
LogFrequencyBiplot | Weighted Biplot for a table of frequencies
logit | Logit function

## -- M --

Matrix2Proximities | Matrix to Proximities
matrixsqrt | Matrix squared root
matrixsqrtinv | Inverse of the Matrix squared root
MDS | Multidimensional Scaling
MGC | Mixture Gaussian Clustering
MonotoneRegression | Weighted Isotonic Regression (Weighted Monotone Regression)
moth | Moth data
MultBiplot | Multivariate Analysis using Biplots
Multiquad | Multidimensional Gauss-Hermite quadrature
MultiTableStatistics | Statistics for multiple tables
MultiTableTransform | Initial Transformation of a multi table object

## -- N --

NiceNumber | Nice numbers: simple decimal numbers
NIPALS.Biplot | Biplot using the NIPALS algorithm
NIPALSPCA | NIPALS algorithm for PCA
NominalDistances | Distances among individuals with nominal variables
NormalityTests | Normality tests
Numeric2Binary | Converts a numeric variable into a binary one

## -- O --

ones | Matrix of ones
OrdinalBiplotExpectedValues | Expected Values for the Ordinal Logistic Biplot.
OrdinalLogBiplotGDRecursive | Ordinal Logistic Biplot with a recursive Gradien Descent Alternating algorithm.
OrdinalLogisticFit | Fits an ordinal logistic regression with ridge penalization
OrdLogBipEM | Alternated EM algorithm for Ordinal Logistic Biplots
OrdVarBiplot | Plots an ordinal variable on the biplot
OrdVarCoordinates | Coordinates of an ordinal variable on the biplot.
OrthogonalizeScores | Orthogonalize a set of Scores calculated by other procedure

## -- P --

PCA.Analysis | Classical PCA Biplot with added features.
PCA.Biplot | Classical PCA Biplot with added features.
PCA.Bootstrap | Principal Components Analysis with bootstrap confidence intervals.
plot.Binary.Logistic.Biplot | Plots the results of a Binary Logistic Biplot
plot.CA.sol | Plot the solution of a Coorespondence Analysis
plot.Canonical.Biplot | Plots a Canonical Biplot
plot.CanonicalDistanceAnalysis | Plots a Canonical Distance Analysis
plot.CCA.sol | Plots the solution of a Canonical Correspondence Analysisis
plot.ContinuousBiplot | Plots a biplot for continuous data.
plot.CVA | Plot of a Canonical Variate Analysis
plot.ellipse | Plot a concentration ellipse.
plot.External.Binary.Logistic.Biplot | Plots an External Logistic Biplot for binary data
plot.fraction | Plots a fraction of the data as a cluster
plot.MGC | Plot the results of Model-Based Gaussian Clustering algorithms
plot.Ordinal.Logistic.Biplot | Plots an ordinal Logistic Biplot
plot.PCA.Analysis | Plots a Principal Component Analysis
plot.PCA.Bootstrap | Plots the Bootstrap information for Principal Components Analysis (PCA)
plot.PCoABootstrap | Plots an object of class PCoABootstrap
plot.Principal.Coordinates | Plots an object of class Principal.Coordinates
plot.Procrustes | Plots an object of class "Procrustes"
plot.StatisBiplot | Plots a Statis Biplot Object
plot.TetraDualStatis | Plots an object of class "tetraDualStatis".
plot.Unfolding | Plots an Unfolding Representation
PlotBiplotClusters | Plot clusters on a biplot.
PlotOrdinalResponses | Plot the response functions along the directions of best fit.
PLSR | Partial Least Squares Regression
PLSR1Bin | Partial Least Squares Regression with Binary Response
PLSRBin | Partial Least Squares Regression with several Binary Responses
PLSRBinFit | PLS binary regression.
PLSRfit | Partial Least Squares Regression (PLSR)
PoliticalFigures | Political Figures in the USA
PolyBiplot | Logistic Biplot for ordinal data based on polychoric correlations
PolychorMatrix | Calculates a matrix of polychoric correlations among a set of ordinal variables
PrettyTicks | Calculates loose axis ticks and labels using nice numbers
PrincipalCoordinates | Principal Coordinates Analysis
print.MGC | Prints the results of Model-Based Gaussian Clustering algorithms
print.RidgeBinaryLogistic | prints an object of class RidgeBinaryLogistic
Protein | Protein consumption data.

## -- R --

RAPD | Sugar Cane Data
RemoveRowsWithNaNs | Remove rows that contains NaNs (missing data)
riano | Ecological data from Riano (Spain)
RidgeBinaryLogistic | Ridge Binary Logistic Regression for Binary data
RidgeBinaryLogisticFit | Fits a binary logistic regression with ridge penalization
RidgeMultinomialLogisticFit | Multinomial logistic regression with ridge penalization
RidgeMultinomialLogisticRegression | Ridge Multinomial Logistic Regression
RidgeOrdinalLogistic | Ordinal logistic regression with ridge penalization

## -- S --

scores.CCA.sol | Extract the scores of a CCA solution object
SeparateVarTypes | Separation of different types of variables into a list
sigmoide | Logistic function
SimpleProcrustes | Simple Procrustes Analysis
SMACOF | SMACOF
smoking | Smoking habits
Sparse.NIPALSPCA | Sparse version of the NIPALS algorithm for PCA.
spiders | Hunting Spiders Data
SpidersEnv | Hunting spiders environmental data.
SpidersSp | Hunting Spiders Data
SSI | Sustainability Society Index
SSI3w | Sustainability Society Index (3w)
SSIEcon3w | Sustainability Society Index
SSIEnvir3w | Sustainability Society Index
SSIHuman3w | Sustainability Society Index
StatisBiplot | STATIS-ACT for multiple tables with common rows and its associated Biplot
summary.Canonical.Biplot | Summary of the solution of a Canonical Biplot Analysis
summary.CCA.sol | Summary of the solution of a CCA
summary.ContinuousBiplot | Summary of the solution of a Biplot for Continuous Data
summary.CVA | Summary of a Canonical Variate Analysis
summary.MGC | Summary of Model-Based Gaussian Clustering results
summary.PCA.Analysis | Summary of the results of a PCA.
summary.PCA.Bootstrap | Summary of a PCA.Bootstrap object
summary.PLSR | Summary of a PLSR object
summary.PLSR1Bin | Summary of PLSR with a Binary Response
summary.Principal.Coordinates | Summary of the results of a Principal Coordinates Analysis
summary.RidgeBinaryLogistic | Summary of a Binary Logistic Regression with Ridge Penalization
summary.TetraDualStatis | Summary of the results of TetraDualStatis

## -- T --

TetraDualStatis | Dual STATIS-ACT for binary data based on Tetrachoric Correlations
textsmart | Labels of a Scatter
Three2TwoWay | Converts a multitable list to a two way matrix
ThreeWay2FrontalSlices | Three to two way data
TransformIni | Initial transformation of a data matrix
Truncated.NIPALSPCA | Truncated version of the NIPALS algorithm for PCA.

## -- U --

Unfolding | Multidimensional Unfolding

## -- V --

VarBiplot | Draws a variable on a biplot

## -- W --

wa | Extracts the weighted averages of a CCA solution
wcor | Weighted correlations
weighted.quantile | Weighted quantiles
WeightedPCoA | Weighted Principal Coordinates Analysis
wine | Wine data

## -- Z --

zeros | Matrix of zeros as in Matlab