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MultBiplotR (version 23.11.0)

Multivariate Analysis Using Biplots in R

Description

Several multivariate techniques from a biplot perspective. It is the translation (with many improvements) into R of the previous package developed in 'Matlab'. The package contains some of the main developments of my team during the last 30 years together with some more standard techniques. Package includes: Classical Biplots, HJ-Biplot, Canonical Biplots, MANOVA Biplots, Correspondence Analysis, Canonical Correspondence Analysis, Canonical STATIS-ACT, Logistic Biplots for binary and ordinal data, Multidimensional Unfolding, External Biplots for Principal Coordinates Analysis or Multidimensional Scaling, among many others. References can be found in the help of each procedure.

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Version

Install

install.packages('MultBiplotR')

Monthly Downloads

296

Version

23.11.0

License

GPL (>= 2)

Maintainer

Jose Vicente-Villardon

Last Published

November 21st, 2023

Functions in MultBiplotR (23.11.0)

BinaryLogBiplotEM

Binary logistic biplot with the EM algorithm.
AddOrdVars2Biplot

Adds supplementary ordinal variables to an existing biplot objects.
AddContVars2Biplot

Adds supplementary continuous variables to a biplot object
BinaryLogBiplotGD

Binary Logistic Biplot with Gradient Descent Estimation
BinaryDistances

Binary Distances
Bartlett.Tests

Bartlett tests
AddCluster2Biplot

Add clusters to a biplot object
BasicDescription

Basic descriptive sataistics
AddBinVars2Biplot

Add suplementary binary variables to a biplot
AddSupVars2Biplot

Adds supplementary variables to a biplot object
BinaryPLSFit

Binary PLS Regression.
BinaryPLSR

Partial Least Squares Regression with Binary Data
Biplot.PLSR

Partial Least Squares Biplot
Biplot.PLSR1BIN

Biplot for a PLSR model with a binary response
Biplot.BinaryPLSR

Biplot for a PLSR model with binary data
BinaryLogBiplotGDRecursive

Binary Logistic Biplot with Recursive Gradient Descent Estimation
BinaryLogBiplotMirt

Binary logistic biplot with Item Response Theory.
BinaryProximities

Proximity Measures for Binary Data
BinaryLogBiplotJoint

Binary logistic biplot with a gradient descent algorithm.
BinaryLogisticBiplot

Binary Logistic Biplot
BootstrapSmacof

Bootstrap on the distance matrices used for MDS with Smacof
BootstrapDistance

Bootstrap on the distance matrices used for Principal Coordinates Analysis (PCoA)
Biplot.PLSRBIN

Biplot for a PLSR model with binary responses
BiplotFPCA

External Biplot for functional data from a functional PCA object.
BoxPlotPanel

Panel of box plots
CA

Correspondence Analysis
CheckBinaryMatrix

Checks if a data matrix is binary
CCA

Canonical Correspondence Analysis
CheckBinaryVector

Checks if a vector is binary
Coinertia

Coinertia Analysis.
ConstrainedLogisticBiplot

Constrained Binary Logistic Biplot
ColContributionPlot

Plots the contributios of a biplot
ConstrainedOrdinalLogisticBiplot

Constrained Ordinal Logistic Biplot
ContinuousProximities

Proximities for Continuous Data
ContinuousDistances

Distances for Continuous Data
CanonicalStatisBiplot

CANONICAL STATIS-ACT for multiple tables with common rows and its associated Biplot
ConvertFactors2Integers

Convert a factor to integer numbers
ConvertList23wArray

Converts a list of matrices into a three way array
CanonicalDistanceAnalysis

MANOVA and Canonical Analysis of Distances
BootstrapScalar

Bootstrap on the scalar product matrices used for Principal Coordinates Analysis (PCoA)
Chemical

Chemical data
Dhats

Calculation of Disparities
Circle

Draws a circle
DimensionLabels

Labels for the selected dimensions in a biplot
Doctors

Data set extracted from the Careers of doctorate holders survey carried out by Spanish Statistical Office in 2008.
GeneralizedProcrustes

Generalized Procrustes Analysis
InitialTransform

Initial transformation of data
GowerSimilarities

Gower Dissimilarities for mixed types of data
EuclideanDistance

Classical Euclidean Distance (Pythagorean Distance)
Games_Howell

Games-Howell post-hoc tests for Welch's one-way analysis
ErrorBarPlotPanel

Plots a panel of error bars
ExpandTable

Expands a compressed table of patterns and frequencies
GowerProximities

Gower Dissimilarities for mixed types of data
Integer2Binary

Transforms an Integer Variable into a Binary Variable
CategoricalProximities

Proximities among individuals using nominal variables.
CategoricalDistances

Distances among individuals using nominal variables.
CanonicalBiplot

Biplot representation of a Canonical Variate Analysis or a Manova (Canonical-Biplot or MANOVA-Biplot)
ConcEllipse

Concentration ellipse for a se of two-dimensional points
Convert3wArray2List

Converts a three way array into a list
Canonical.Variate.Analysis

Biplot representation of a Canonical Variate Analysis or a Manova (Canonical-Biplot or MANOVA-Biplot)
Convert2ThreeWay

Three way array from a two way matrix
DataFrame2Matrix4Regression

Prepares a matrix for regression from a data frame
CumSum

Cummulative sums
MGC

Mixture Gaussian Clustering
CorrelationCircle

Circle of correlations
MultiTableStatistics

Statistics for multiple tables
Matrix2Proximities

Matrix to Proximities
DensityBiplot

Adds Non-parametric densities to a biplot. Separated densities are calculated for different clusters
Dataframe2BinaryMatrix

Converts a Data Frame into a Binary Data Matrix
Fraction

Selection of a fraction of the data
ConfidenceInterval

Confidence Interval for the mean
Hermquad

Gauss-Hermite quadrature
MDS

Multidimensional Scaling
HJ.Biplot

HJ Biplot with added features.
GD.Biplot

Biplot for continuous data based on gradient descent methods
LogFrequencyBiplot

Weighted Biplot for a table of frequencies
OrdVarBiplot

Plots an ordinal variable on the biplot
Fact2Bin

Converts a Factor into its indicator matrix
FA.Biplot

Biplot for Factor Analysis.
InBox

Checks if a point is inside a box.
NIPALS.Biplot

Biplot using the NIPALS algorithm
GetBiplotScales

Calculates the scales for the variables on a linear biplot
HistogramPanel

Panel of histograms
Multiquad

Multidimensional Gauss-Hermite quadrature
OrdinalLogisticFit

Fits an ordinal logistic regression with ridge penalization
ExtractTable

Extracts unique patterns and its frequencies for a discrete data matrix (numeric)
ExternalBinaryLogisticBiplot

External Logistic Biplot for binary Data
Numeric2Binary

Converts a numeric variable into a binary one
GetCCAScales

Calculates scales for plotting the environmental variables in a Canonical Correspondence Analysis
MultiTableTransform

Initial Transformation of a multi table object
CrissCross

Alternated Least Squares Biplot
NIPALSPCA

NIPALS algorithm for PCA
OrdVarCoordinates

Coordinates of an ordinal variable on the biplot.
PCA.Analysis

Classical PCA Biplot with added features.
MonotoneRegression

Weighted Isotonic Regression (Weighted Monotone Regression)
PCA.Biplot

Classical PCA Biplot with added features.
MultBiplotR-package

Multivariate Analysis using Biplots
NiceNumber

Nice numbers: simple decimal numbers
PCA.Bootstrap

Principal Components Analysis with bootstrap confidence intervals.
PlotOrdinalResponses

Plot the response functions along the directions of best fit.
PoliticalFigures

Political Figures in the USA
PLSRBin

Partial Least Squares Regression with several Binary Responses
PLSRBinFit

PLS binary regression.
PLSRfit

Partial Least Squares Regression (PLSR)
RidgeBinaryLogistic

Ridge Binary Logistic Regression for Binary data
Levene.Tests

Levene Tests
SSI3w

Sustainability Society Index (3w)
OrthogonalizeScores

Orthogonalize a set of Scores calculated by other procedure
Three2TwoWay

Converts a multitable list to a two way matrix
SSI

Sustainability Society Index
PLSR

Partial Least Squares Regression
plot.PCoABootstrap

Plots an object of class PCoABootstrap
PlotBiplotClusters

Plot clusters on a biplot.
Kruskal.Wallis.Tests

Kruskal Wallis Tests
RidgeBinaryLogisticFit

Fits a binary logistic regression with ridge penalization
NormalityTests

Normality tests
PLSR1Bin

Partial Least Squares Regression with Binary Response
SeparateVarTypes

Separation of different types of variables into a list
PrincipalCoordinates

Principal Coordinates Analysis
NominalDistances

Distances among individuals with nominal variables
OrdLogBipEM

Alternated EM algorithm for Ordinal Logistic Biplots
dlines

Connects two sets of points by lines
diagonal

Diagonal matrix from a vector
RemoveRowsWithNaNs

Remove rows that contains NaNs (missing data)
RAPD

Sugar Cane Data
SSIHuman3w

Sustainability Society Index
PolyOrdinalLogBiplot

Factor Analysis Biplot based on polychoric correlations
RidgeOrdinalLogistic

Ordinal logistic regression with ridge penalization
Protein

Protein consumption data.
SpidersEnv

Hunting spiders environmental data.
anova.RidgeBinaryLogistic

Compares two binary logistic models
plot.Binary.Logistic.Biplot

Plots the results of a Binary Logistic Biplot
WeightedPCoA

Weighted Principal Coordinates Analysis
TransformIni

Initial transformation of a data matrix
RidgeMultinomialLogisticRegression

Ridge Multinomial Logistic Regression
RidgeMultinomialLogisticFit

Multinomial logistic regression with ridge penalization
Unfolding

Multidimensional Unfolding
plot.CanonicalDistanceAnalysis

Plots a Canonical Distance Analysis
VarBiplot

Draws a variable on a biplot
ThreeWay2FrontalSlices

Three to two way data
plot.PCA.Analysis

Plots a Principal Component Analysis
matrixsqrt

Matrix squared root
SpidersSp

Hunting Spiders Data
plot.MGC

Plot the results of Model-Based Gaussian Clustering algorithms
matrixsqrtinv

Inverse of the Matrix squared root
plot.CA.sol

Plot the solution of a Coorespondence Analysis
SMACOF

SMACOF
plot.Canonical.Biplot

Plots a Canonical Biplot
SimpleProcrustes

Simple Procrustes Analysis
Sparse.NIPALSPCA

Sparse version of the NIPALS algorithm for PCA.
PrettyTicks

Calculates loose axis ticks and labels using nice numbers
plot.ContinuousBiplot

Plots a biplot for continuous data.
plot.External.Binary.Logistic.Biplot

Plots an External Logistic Biplot for binary data
plot.fraction

Plots a fraction of the data as a cluster
Truncated.NIPALSPCA

Truncated version of the NIPALS algorithm for PCA.
print.MGC

Prints the results of Model-Based Gaussian Clustering algorithms
plot.CCA.sol

Plots the solution of a Canonical Correspondence Analysisis
plot.Principal.Coordinates

Plots an object of class Principal.Coordinates
plot.Procrustes

Plots an object of class "Procrustes"
plot.CVA

Plot of a Canonical Variate Analysis
spiders

Hunting Spiders Data
summary.CCA.sol

Summary of the solution of a CCA
summary.CVA

Summary of a Canonical Variate Analysis
summary.Canonical.Biplot

Summary of the solution of a Canonical Biplot Analysis
StatisBiplot

STATIS-ACT for multiple tables with common rows and its associated Biplot
plot.PCA.Bootstrap

Plots the Bootstrap information for Principal Components Analysis (PCA)
TetraDualStatis

Dual STATIS-ACT for binary data based on Tetrachoric Correlations
SSIEnvir3w

Sustainability Society Index
SSIEcon3w

Sustainability Society Index
textsmart

Labels of a Scatter
moth

Moth data
summary.ContinuousBiplot

Summary of the solution of a Biplot for Continuous Data
wine

Wine data
summary.MGC

Summary of Model-Based Gaussian Clustering results
zeros

Matrix of zeros as in Matlab
wa

Extracts the weighted averages of a CCA solution
plot.ellipse

Plot a concentration ellipse.
summary.Principal.Coordinates

Summary of the results of a Principal Coordinates Analysis
summary.RidgeBinaryLogistic

Summary of a Binary Logistic Regression with Ridge Penalization
plot.Ordinal.Logistic.Biplot

Plots an ordinal Logistic Biplot
plot.Unfolding

Plots an Unfolding Representation
logit

Logit function
plot.TetraDualStatis

Plots an object of class "tetraDualStatis".
ginv

G inverse
print.RidgeBinaryLogistic

prints an object of class RidgeBinaryLogistic
plot.StatisBiplot

Plots a Statis Biplot Object
summary.PCA.Bootstrap

Summary of a PCA.Bootstrap object
riano

Ecological data from Riano (Spain)
summary.PCA.Analysis

Summary of the results of a PCA.
ones

Matrix of ones
wcor

Weighted correlations
weighted.quantile

Weighted quantiles
summary.PLSR

Summary of a PLSR object
smoking

Smoking habits
summary.PLSR1Bin

Summary of PLSR with a Binary Response
scores.CCA.sol

Extract the scores of a CCA solution object
t3pcovr

Tucker 3 Principal Covariates Regression
summary.TetraDualStatis

Summary of the results of TetraDualStatis