- ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences
- testdim.multiblock: Selection of the number of dimension by two-fold...
Selection of the number of dimension by two-fold cross-validation for multiblock methods
Function to perform a two-fold cross-validation to select the optimal number of dimensions of multiblock methods, i.e., multiblock principal component analysis with instrumental Variables or multiblock partial least squares
an object of class multiblock created by
integer indicating the number of repetitions
a vector indicating the lower and upper quantiles to compute
other arguments to be passed to methods
An object of class
Stone M. (1974) Cross-validatory choice and assessment of statistical predictions. Journal of the Royal Statistical Society, 36, 111-147
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data(chickenk) Mortality <- chickenk[] dudiY.chick <- dudi.pca(Mortality, center = TRUE, scale = TRUE, scannf = FALSE) ktabX.chick <- ktab.list.df(chickenk[2:5]) resmbpcaiv.chick <- mbpcaiv(dudiY.chick, ktabX.chick, scale = TRUE, option = "uniform", scannf = FALSE) ## nrepet should be higher for a real analysis test <- testdim(resmbpcaiv.chick, nrepet = 10) test if(adegraphicsLoaded()) plot(test)
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- abouheif.eg: Phylogenies and quantitative traits from Abouheif
- acacia: Spatial pattern analysis in plant communities
- add.scatter: Add graphics to an existing plot
- ade4-deprecated: Deprecated functions in ade4
- ade4-internal: Internal ade4 functions
- ade4.package: The ade4 package
- ade4toR: Format Change Utility
- adegraphicsLoaded: Utility function to test if the package adegraphics is loaded
- aminoacyl: Codon usage
- amova: Analysis of molecular variance
- apis108: Allelic frequencies in ten honeybees populations at eight...
- apqe: Apportionment of Quadratic Entropy
- aravo: Distribution of Alpine plants in Aravo (Valloire, France)
- ardeche: Fauna Table with double (row and column) partitioning
- area.plot: Graphical Display of Areas
- arrival: Arrivals at an intensive care unit
- as.taxo: Taxonomy
- atlas: Small Ecological Dataset
- atya: Genetic variability of Cacadors
- avijons: Bird species distribution
- avimedi: Fauna Table for Constrained Ordinations
- aviurba: Ecological Tables Triplet
- bacteria: Genomes of 43 Bacteria
- banque: Table of Factors
- baran95: African Estuary Fishes
- bca.rlq: Between-Class RLQ analysis
- between: Between-Class Analysis
- betweencoinertia: Between-class coinertia analysis
- bf88: Cubic Ecological Data
- bicenter.wt: Double Weighted Centring
- bordeaux: Wine Tasting
- bsetal97: Ecological and Biological Traits
- buech: Buech basin
- butterfly: Genetics-Ecology-Environment Triple
- bwca.dpcoa: Between- and within-class double principal coordinate...
- cailliez: Transformation to make Euclidean a distance matrix
- capitales: Road Distances
- carni19: Phylogeny and quantative trait of carnivora
- carni70: Phylogeny and quantitative traits of carnivora
- carniherbi49: Taxonomy, phylogenies and quantitative traits of carnivora...
- casitas: Enzymatic polymorphism in Mus musculus
- cca: Canonical Correspondence Analysis
- chatcat: Qualitative Weighted Variables
- chats: Pair of Variables
- chazeb: Charolais-Zebus
- chevaine: Enzymatic polymorphism in Leuciscus cephalus
- chickenk: Veterinary epidemiological study to assess the risk factors...
- clementines: Fruit Production
- cnc2003: Frequenting movie theaters in France in 2003
- coinertia: Coinertia Analysis
- coleo: Table of Fuzzy Biological Traits
- combine.4thcorner: Functions to combine and adjust the outputs 3-table methods
- corkdist: Tests of randomization between distances applied to 'kdist'...
- corvus: Corvus morphology
- costatis: STATIS and Co-Inertia : Analysis of a series of paired...
- costatis.randtest: Monte-Carlo test on a Costatis analysis (in C).
- deug: Exam marks for some students
- disc: Rao's dissimilarity coefficient
- discrimin: Linear Discriminant Analysis (descriptive statistic)
- discrimin.coa: Discriminant Correspondence Analysis
- dist.binary: Computation of Distance Matrices for Binary Data
- dist.dudi: Computation of the Distance Matrix from a Statistical Triplet
- dist.genet: Genetic distances from gene frequencies
- dist.ktab: Mixed-variables coefficient of distance
- dist.neig: Computation of the Distance Matrix associated to a...
- dist.prop: Computation of Distance Matrices of Percentage Data
- dist.quant: Computation of Distance Matrices on Quantitative Variables
- divc: Rao's diversity coefficient also called quadratic entropy
- divcmax: Maximal value of Rao's diversity coefficient also called...
- dotchart.phylog: Representation of many quantitative variables in front of a...
- dotcircle: Representation of n values on a circle
- doubs: Pair of Ecological Tables
- dpcoa: Double principal coordinate analysis
- dudi: Duality Diagram
- dudi.acm: Multiple Correspondence Analysis
- dudi.coa: Correspondence Analysis
- dudi.dec: Decentred Correspondence Analysis
- dudi.fca: Fuzzy Correspondence Analysis and Fuzzy Principal Components...
- dudi.hillsmith: Ordination of Tables mixing quantitative variables and...
- dudi.mix: Ordination of Tables mixing quantitative variables and...
- dudi.nsc: Non symmetric correspondence analysis
- dudi.pca: Principal Component Analysis
- dudi.pco: Principal Coordinates Analysis
- dunedata: Dune Meadow Data
- ecg: Electrocardiogram data
- ecomor: Ecomorphological Convergence
- EH: Amount of Evolutionary History
- elec88: Electoral Data
- escopage: K-tables of wine-tasting
- euro123: Triangular Data
- fission: Fission pattern and heritable morphological traits
- foucart: K-tables Correspondence Analysis with the same rows and the...
- fourthcorner: Functions to compute the fourth-corner statistic
- friday87: Faunistic K-tables
- fruits: Pair of Tables
- fuzzygenet: Reading a table of genetic data (diploid individuals)
- gearymoran: Moran's I and Geary'c randomization tests for spatial and...
- genet: A class of data: tables of populations and alleles
- ggtortoises: Microsatellites of Galapagos tortoises populations
- granulo: Granulometric Curves
- gridrowcol: Complete regular grid analysis
- hdpg: Genetic Variation In Human Populations
- housetasks: Contingency Table
- humDNAm: human mitochondrial DNA restriction data
- ichtyo: Point sampling of fish community
- inertia.dudi: Statistics of inertia in a one-table analysis
- irishdata: Geary's Irish Data
- is.euclid: Is a Distance Matrix Euclidean ?
- julliot: Seed dispersal
- jv73: K-tables Multi-Regions
- kcponds: Ponds in a nature reserve
- kdist: the class of objects 'kdist' (K distance matrices)
- kdist2ktab: Transformation of K distance matrices (object 'kdist') into K...
- kdisteuclid: a way to obtain Euclidean distance matrices
- kplot: Generic Function for Multiple Graphs in a K-tables Analysis
- kplot.foucart: Multiple Graphs for the Foucart's Correspondence Analysis
- kplot.mcoa: Multiple Graphs for a Multiple Co-inertia Analysis
- kplot.mfa: Multiple Graphs for a Multiple Factorial Analysis
- kplot.pta: Multiple Graphs for a Partial Triadic Analysis
- kplot.sepan: Multiple Graphs for Separated Analyses in a K-tables
- kplot.statis: Multiple Graphs of a STATIS Analysis
- krandtest: Class of the Permutation Tests (in C).
- ktab: the class of objects 'ktab' (K-tables)
- ktab.data.frame: Creation of K-tables from a data frame
- ktab.list.df: Creating a K-tables from a list of data frames.
- ktab.list.dudi: Creation of a K-tables from a list of duality diagrams
- ktab.match2ktabs: STATIS and Co-Inertia : Analysis of a series of paired...
- ktab.within: Process to go from a Within Analysis to a K-tables
- lascaux: Genetic/Environment and types of variables
- lingoes: Transformation of a Distance Matrix for becoming Euclidean
- lizards: Phylogeny and quantitative traits of lizards
- macaca: Landmarks
- macon: Wine Tasting
- macroloire: Assemblages of Macroinvertebrates in the Loire River (France)
- mafragh: Phyto-Ecological Survey
- mantel.randtest: Mantel test (correlation between two distance matrices (in...
- mantel.rtest: Mantel test (correlation between two distance matrices (in...
- maples: Phylogeny and quantitative traits of flowers
- mariages: Correspondence Analysis Table
- mbpcaiv: Multiblock principal component analysis with instrumental...
- mbpls: Multiblock partial least squares
- mcoa: Multiple CO-inertia Analysis
- mdpcoa: Multiple Double Principal Coordinate Analysis
- meau: Ecological Data : sites-variables, sites-species, where and...
- meaudret: Ecological Data : sites-variables, sites-species, where and...
- mfa: Multiple Factorial Analysis
- microsatt: Genetic Relationships between cattle breeds with...
- mjrochet: Phylogeny and quantitative traits of teleos fishes
- mld: Multi Level Decomposition of unidimensional data
- mollusc: Faunistic Communities and Sampling Experiment
- monde84: Global State of the World in 1984
- morphosport: Athletes' Morphology
- mstree: Minimal Spanning Tree
- multiblock: Display and summarize multiblock objects
- multispati: Multivariate spatial analysis
- multispati.randtest: Multivariate spatial autocorrelation test (in C)
- multispati.rtest: Multivariate spatial autocorrelation test
- neig: Neighbourhood Graphs
- newick2phylog: Create phylogeny
- newick.eg: Phylogenetic trees in Newick format
- niche: Method to Analyse a pair of tables : Environmental and...
- nipals: Non-linear Iterative Partial Least Squares (NIPALS) algorithm
- njplot: Phylogeny and trait of bacteria
- olympic: Olympic Decathlon
- optimEH: Nee and May's optimizing process
- oribatid: Oribatid mite
- originality: Originality of a species
- orisaved: Maximal or minimal amount of originality saved under optimal...
- orthobasis: Orthonormal basis for orthonormal transform
- orthogram: Orthonormal decomposition of variance
- ours: A table of Qualitative Variables
- palm: Phylogenetic and quantitative traits of amazonian palm trees
- pap: Taxonomy and quantitative traits of carnivora
- pcaiv: Principal component analysis with respect to instrumental...
- pcaivortho: Principal Component Analysis with respect to orthogonal...
- pcoscaled: Simplified Analysis in Principal Coordinates
- pcw: Distribution of of tropical trees along the Panama canal
- perthi02: Contingency Table with a partition in Molecular Biology
- phylog: Phylogeny
- PI2newick: Import data files from Phylogenetic Independance Package
- piosphere: Plant traits response to grazing
- plot.between: Between-Class Analysis
- plot.phylog: Plot phylogenies
- plot.within: Within-Class Analysis
- presid2002: Results of the French presidential elections of 2002
- procella: Phylogeny and quantitative traits of birds
- procuste: Simple Procruste Rotation between two sets of points
- procuste.randtest: Monte-Carlo Test on the sum of the singular values of a...
- procuste.rtest: Monte-Carlo Test on the sum of the singular values of a...
- pta: Partial Triadic Analysis of a K-tables
- quasieuclid: Transformation of a distance matrice to a Euclidean one
- randboot: Bootstrap simulations
- randboot.multiblock: Bootstraped simulations for multiblock methods
- randEH: Nee and May's random process
- randtest: Class of the Permutation Tests (in C).
- randtest.amova: Permutation tests on an analysis of molecular variance (in...
- randtest.between: Monte-Carlo Test on the between-groups inertia percentage (in...
- randtest.coinertia: Monte-Carlo test on a Co-inertia analysis (in C).
- randtest.discrimin: Monte-Carlo Test on a Discriminant Analysis (in C).
- randtest.pcaiv: Monte-Carlo Test on the percentage of explained (i.e....
- randxval: Two-fold cross-validation
- rankrock: Ordination Table
- reconst: Reconstitution of Data from a Duality Diagram
- rhizobium: Genetic structure of two nitrogen fixing bacteria influenced...
- rhone: Physico-Chemistry Data
- rlq: RLQ analysis
- rpjdl: Avifauna and Vegetation
- rtest: Class of the Permutation Tests (in R).
- rtest.between: Monte-Carlo Test on the between-groups inertia percentage (in...
- rtest.discrimin: Monte-Carlo Test on a Discriminant Analysis (in R).
- RVdist.randtest: Tests of randomization on the correlation between two...
- RV.rtest: Monte-Carlo Test on the sum of eigenvalues of a co-inertia...
- santacatalina: Indirect Ordination
- sarcelles: Array of Recapture of Rings
- s.arrow: Plot of the factorial maps for the projection of a vector...
- scalewt: Compute or scale data using (weighted) means, variances and...
- scatter: Graphical representation of the outputs of a multivariate...
- scatter.acm: Plot of the factorial maps in a Multiple Correspondence...
- scatter.coa: Plot of the factorial maps for a correspondence analysis
- scatter.dudi: Plot of the Factorial Maps
- scatter.fca: Plot of the factorial maps for a fuzzy correspondence...
- scatterutil: Graphical utility functions
- s.chull: Plot of the factorial maps with polygons of contour by level...
- s.class: Plot of factorial maps with representation of point classes
- sco.boxplot: Representation of the link between a variable and a set of...
- sco.class: 1D plot of a numeric score and a factor with labels
- sco.distri: Representation by mean- standard deviation of a set of weight...
- sco.gauss: Relationships between one score and qualitative variables
- sco.label: 1D plot of a numeric score with labels
- sco.match: 1D plot of a pair of numeric scores with labels
- sco.quant: Graph to Analyse the Relation between a Score and...
- s.corcircle: Plot of the factorial maps of a correlation circle
- score: Graphs for One Dimension
- score.acm: Graphs to study one factor in a Multiple Correspondence...
- score.coa: Reciprocal scaling after a correspondence analysis
- score.mix: Graphs to Analyse a factor in a Mixed Analysis
- score.pca: Graphs to Analyse a factor in PCA
- s.distri: Plot of a frequency distribution
- seconde: Students and Subjects
- sepan: Separated Analyses in a K-tables
- s.hist: Display of a scatterplot and its two marginal histograms
- s.image: Graph of a variable using image and contour
- s.kde2d: Scatter Plot with Kernel Density Estimate
- skulls: Morphometric Evolution
- s.label: Scatter Plot
- s.logo: Representation of an object in a graph by a picture
- s.match: Plot of Paired Coordinates
- s.match.class: Scatterplot of two sets of coordinates and a partionning into...
- s.multinom: Graph of frequency profiles (useful for instance in genetic)
- statico: STATIS and Co-Inertia : Analysis of a series of paired...
- statico.krandtest: Monte-Carlo test on a Statico analysis (in C).
- statis: STATIS, a method for analysing K-tables
- steppe: Transect in the Vegetation
- s.traject: Trajectory Plot
- supcol: Projections of Supplementary Columns
- suprow: Projections of Supplementary Rows
- s.value: Representation of a value in a graph
- symbols.phylog: Representation of a quantitative variable in front of a...
- syndicats: Two Questions asked on a Sample of 1000 Respondents
- t3012: Average temperatures of 30 French cities
- table.cont: Plot of Contingency Tables
- table.dist: Graph Display for Distance Matrices
- table.paint: Plot of the arrays by grey levels
- table.phylog: Plot arrays in front of a phylogenetic tree
- table.value: Plot of the Arrays
- tarentaise: Mountain Avifauna
- taxo.eg: Examples of taxonomy
- testdim: Function to perform a test of dimensionality
- testdim.multiblock: Selection of the number of dimension by two-fold...
- tintoodiel: Tinto and Odiel estuary geochemistry
- tithonia: Phylogeny and quantitative traits of flowers
- tortues: Morphological Study of the Painted Turtle
- toxicity: Homogeneous Table
- triangle.class: Triangular Representation and Groups of points
- triangle.plot: Triangular Plotting
- trichometeo: Pair of Ecological Data
- ungulates: Phylogeny and quantitative traits of ungulates.
- uniquewt.df: Elimination of Duplicated Rows in a Array
- variance.phylog: The phylogenetic ANOVA
- vegtf: Vegetation in Trois-Fontaines
- veuvage: Example for Centring in PCA
- wca.rlq: Within-Class RLQ analysis
- westafrica: Freshwater fish zoogeography in west Africa
- within: Within-Class Analysis
- withincoinertia: Within-class coinertia analysis
- withinpca: Normed within principal component analysis
- witwit.coa: Internal Correspondence Analysis
- woangers: Plant assemblages in woodlands of the conurbation of Angers...
- worksurv: French Worker Survey (1970)
- yanomama: Distance Matrices
- zealand: Road distances in New-Zealand