ade41.7-22 package

Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

STATIS and Co-Inertia : Analysis of a series of paired ecological tabl...

Dagnelie multinormality test

Rao's dissimilarity coefficient

Discriminant Correspondence Analysis

Add graphics to an existing plot

Deprecated functions in ade4

Internal ade4 functions

The ade4 package

Utility function to test if the package adegraphics is loaded

Analysis of molecular variance

Apportionment of Quadratic Entropy

Graphical Display of Areas

Taxonomy

Between-class coinertia analysis

Between-Class Analysis

Between-Class RLQ analysis

Double Weighted Centring

Between- and within-class double principal coordinate analysis

Transformation to make Euclidean a distance matrix

Coinertia Analysis

Functions to combine and adjust the outputs 3-table methods

Tests of randomization between distances applied to 'kdist' objetcs

Monte-Carlo test on a Costatis analysis (in C).

Linear Discriminant Analysis (descriptive statistic)

Computation of Distance Matrices for Binary Data

Computation of the Distance Matrix from a Statistical Triplet

Mixed-variables coefficient of distance

Computation of the Distance Matrix associated to a Neighbouring Graph

Computation of Distance Matrices of Percentage Data

Computation of Distance Matrices on Quantitative Variables

Rao's diversity coefficient also called quadratic entropy

Maximal value of Rao's diversity coefficient also called quadratic ent...

Representation of many quantitative variables in front of a phylogenet...

Representation of n values on a circle

Double principal coordinate analysis

Multiple Correspondence Analysis

Correspondence Analysis

Decentred Correspondence Analysis

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Ordination of Tables mixing quantitative variables and factors

Ordination of Tables mixing quantitative variables and factors

Non symmetric correspondence analysis

Principal Component Analysis

Principal Coordinates Analysis

Duality Diagram

K-tables Correspondence Analysis with the same rows and the same colum...

Functions to compute the fourth-corner statistic

Moran's I and Geary'c randomization tests for spatial and phylogenetic...

Complete regular grid analysis

Decomposition of inertia (i.e. contributions) in multivariate methods

Is a Distance Matrix Euclidean?

the class of objects 'kdist' (K distance matrices)

Transformation of K distance matrices (object 'kdist') into K Euclidea...

a way to obtain Euclidean distance matrices

Multiple Graphs for the Foucart's Correspondence Analysis

Multiple Graphs for a Multiple Co-inertia Analysis

Multiple Graphs for a Multiple Factorial Analysis

Multiple Graphs for a Partial Triadic Analysis

Generic Function for Multiple Graphs in a K-tables Analysis

Multiple Graphs for Separated Analyses in a K-tables

Multiple Graphs of a STATIS Analysis

Class of the Permutation Tests (in C).

Creation of K-tables from a data frame

Creating a K-tables from a list of data frames.

Creation of a K-tables from a list of duality diagrams

STATIS and Co-Inertia : Analysis of a series of paired ecological tabl...

the class of objects 'ktab' (K-tables)

Process to go from a Within Analysis to a K-tables

Transformation of a Distance Matrix for becoming Euclidean

Leave-one-out cross-validation for a `bca`

Leave-one-out cross-validation for a `discrimin`

analysis

Leave-one-out cross-validation for a `dudi`

Mantel test (correlation between two distance matrices (in C).)

Mantel test (correlation between two distance matrices (in R).)

Multiblock principal component analysis with instrumental variables

Multiblock partial least squares

Multiple CO-inertia Analysis

Multiple Double Principal Coordinate Analysis

Multiple Factorial Analysis

Multi Level Decomposition of unidimensional data

Minimal Spanning Tree

Display and summarize multiblock objects

Multivariate spatial autocorrelation test (in C)

Multivariate spatial analysis

Multivariate spatial autocorrelation test

Neighbourhood Graphs

Create phylogeny

Method to Analyse a pair of tables : Environmental and Faunistic Data

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Originality of a species

Orthonormal basis for orthonormal transform

Principal component analysis with respect to instrumental variables

Principal Component Analysis with respect to orthogonal instrumental v...

Simplified Analysis in Principal Coordinates

Phylogeny

Import data files from Phylogenetic Independance Package

Between-Class Analysis

Plot phylogenies

Within-Class Analysis

Monte-Carlo Test on the sum of the singular values of a procustean rot...

Simple Procruste Rotation between two sets of points

Monte-Carlo Test on the sum of the singular values of a procustean rot...

Partial Triadic Analysis of a K-tables

Transformation of a distance matrice to a Euclidean one

Bootstraped simulations for multiblock methods

Bootstrap simulations

Permutation tests on an analysis of molecular variance (in C).

Monte-Carlo Test on the between-groups inertia percentage (in C).

Monte-Carlo test on a Co-inertia analysis (in C).

Monte-Carlo Test on a Discriminant Analysis (in C).

Permutation test for double principal coordinate analysis (DPCoA)

Monte-Carlo Test on the percentage of explained (i.e. constrained) ine...

Class of the Permutation Tests (in C).

Two-fold cross-validation

Reconstitution of Data from a Duality Diagram

RLQ analysis

Monte-Carlo Test on the between-groups inertia percentage (in R).

Monte-Carlo Test on a Discriminant Analysis (in R).

Class of the Permutation Tests (in R).

Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (i...

Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (i...

Tests of randomization on the correlation between two distance matrice...

Monte-Carlo Test on the sum of eigenvalues of a within-class co-inerti...

Plot of the factorial maps for the projection of a vector basis

Plot of the factorial maps with polygons of contour by level of a fact...

Plot of factorial maps with representation of point classes

Plot of the factorial maps of a correlation circle

Plot of a frequency distribution

Display of a scatterplot and its two marginal histograms

Graph of a variable using image and contour

Scatter Plot with Kernel Density Estimate

Scatter Plot

Representation of an object in a graph by a picture

Scatterplot of two sets of coordinates and a partionning into classes

Plot of Paired Coordinates

Graph of frequency profiles (useful for instance in genetic)

Trajectory Plot

Representation of a value in a graph

Compute or scale data using (weighted) means, variances and covariance...

Plot of the factorial maps in a Multiple Correspondence Analysis

Plot of the factorial maps for a correspondence analysis

Plot of the Factorial Maps

Plot of the factorial maps for a fuzzy correspondence analysis

Graphical representation of the outputs of a multivariate analysis

Graphical utility functions

Representation of the link between a variable and a set of qualitative...

1D plot of a numeric score and a factor with labels

Representation by mean- standard deviation of a set of weight distribu...

Relationships between one score and qualitative variables

1D plot of a numeric score with labels

1D plot of a pair of numeric scores with labels

Graph to Analyse the Relation between a Score and Quantitative Variabl...

Graphs to study one factor in a Multiple Correspondence Analysis

Reciprocal scaling after a correspondence analysis

Graphs to Analyse a factor in a Mixed Analysis

Graphs to Analyse a factor in PCA

Graphs for One Dimension

Separated Analyses in a K-tables

Monte-Carlo test on a Statico analysis (in C).

STATIS and Co-Inertia : Analysis of a series of paired ecological tabl...

STATIS, a method for analysing K-tables

Projections of Supplementary Columns

Projection of additional items in a PCO analysis

Projections of Supplementary Rows for a Partial Triadic Analysis of K-...

Projections of Supplementary Rows

Representation of a quantitative variable in front of a phylogenetic t...

Plot of Contingency Tables

Graph Display for Distance Matrices

Plot of the arrays by grey levels

Plot arrays in front of a phylogenetic tree

Plot of the Arrays

Selection of the number of dimension by two-fold cross-validation for ...

Function to perform a test of dimensionality

Triangular Representation and Groups of points

Triangular Plotting

Elimination of Duplicated Rows in a Array

The phylogenetic ANOVA

Partition of the variation of a response multivariate table by 2 expla...

Within-class coinertia analysis

Within-Class Analysis

Within-Class RLQ analysis

Normed within principal component analysis

Internal Correspondence Analysis

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

Maintainer: AurĂ©lie Siberchicot License: GPL (>= 2) Last published: 2023-02-06