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>.