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chickens", "topics": [ "chickenk" ] }, { "page": "clementines", "title": "Fruit Production", "topics": [ "clementines" ] }, { "page": "cnc2003", "title": "Frequenting movie theaters in France in 2003", "topics": [ "cnc2003" ] }, { "page": "coinertia", "title": "Coinertia Analysis", "topics": [ "coinertia", "plot.coinertia", "print.coinertia", "summary.coinertia" ] }, { "page": "coleo", "title": "Table of Fuzzy Biological Traits", "topics": [ "coleo" ] }, { "page": "combine.4thcorner", "title": "Functions to combine and adjust the outputs 3-table methods", "topics": [ "combine.4thcorner", "combine.randtest.rlq", "p.adjust.4thcorner" ] }, { "page": "corkdist", "title": "Tests of randomization between distances applied to 'kdist' objetcs", "topics": [ "corkdist", "mantelkdist", "plot.corkdist", "print.corkdist", "RVkdist", "summary.corkdist" ] }, { "page": "corvus", "title": "Corvus morphology", "topics": [ "corvus" ] }, { "page": "costatis", "title": "STATIS and Co-Inertia : Analysis of a series of paired ecological tables", "topics": [ "costatis" ] }, { "page": "costatis.randtest", "title": "Monte-Carlo test on a Costatis analysis (in C).", "topics": [ "costatis.randtest" ] }, { "page": "dagnelie.test", "title": "Dagnelie multinormality test", "topics": [ "dagnelie.test" ] }, { "page": "ade4-deprecated", "title": "Deprecated functions in ade4", "topics": [ "ade4-deprecated" ] }, { "page": "deug", "title": "Exam marks for some students", "topics": [ "deug" ] }, { "page": "disc", "title": "Rao's dissimilarity coefficient", "topics": [ "disc" ] }, { "page": "discrimin", "title": "Linear Discriminant Analysis (descriptive statistic)", "topics": [ "discrimin", "plot.discrimin", "print.discrimin" ] }, { "page": "discrimin.coa", "title": "Discriminant Correspondence Analysis", "topics": [ "discrimin.coa" ] }, { "page": "dist.binary", "title": "Computation of Distance Matrices for Binary Data", "topics": [ "dist.binary" ] }, { "page": "dist.dudi", "title": "Computation of the Distance Matrix from a Statistical Triplet", "topics": [ "dist.dudi" ] }, { "page": "dist.ktab", "title": "Mixed-variables coefficient of distance", "topics": [ "dist.ktab", "kdist.cor", "ldist.ktab", "prep.binary", "prep.circular", "prep.fuzzy" ] }, { "page": "dist.neig", "title": "Computation of the Distance Matrix associated to a Neighbouring Graph", "topics": [ "dist.neig" ] }, { "page": "dist.prop", "title": "Computation of Distance Matrices of Percentage Data", "topics": [ "dist.prop" ] }, { "page": "dist.quant", "title": "Computation of Distance Matrices on Quantitative Variables", "topics": [ "dist.quant" ] }, { "page": "divc", "title": "Rao's diversity coefficient also called quadratic entropy", "topics": [ "divc" ] }, { "page": "divcmax", "title": "Maximal value of Rao's diversity coefficient also called quadratic entropy", "topics": [ "divcmax" ] }, { "page": "dotchart.phylog", "title": "Representation of many quantitative variables in front of a phylogenetic tree", "topics": [ "dotchart.phylog" ] }, { "page": "dotcircle", "title": "Representation of n values on a circle", "topics": [ "dotcircle" ] }, { "page": "doubs", "title": "Pair of Ecological Tables", "topics": [ "doubs" ] }, { "page": "dpcaiv", "title": "Double principal component analysis with respect to instrumental variables", "topics": [ "dpcaiv", "dvaripart", "plot.dpcaiv", "print.dpcaiv", "print.dvaripart", "randtest.dpcaiv", "summary.dpcaiv" ] }, { "page": "dpcoa", "title": "Double principal coordinate analysis", "topics": [ "dpcoa", "plot.dpcoa", "print.dpcoa", "summary.dpcoa" ] }, { "page": "dudi", "title": "Duality Diagram", "topics": [ "as.dudi", "dudi", "is.dudi", "print.dudi", "redo.dudi", "summary.dudi", "t.dudi", "[.dudi" ] }, { "page": "dudi.acm", "title": "Multiple Correspondence Analysis", "topics": [ "acm.burt", "acm.disjonctif", "boxplot.acm", "dudi.acm" ] }, { "page": "dudi.coa", "title": "Correspondence Analysis", "topics": [ "dudi.coa" ] }, { "page": "dudi.dec", "title": "Decentred Correspondence Analysis", "topics": [ "dudi.dec" ] }, { "page": "dudi.fca", "title": "Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis", "topics": [ "dudi.fca", "dudi.fpca", "prep.fuzzy.var" ] }, { "page": "dudi.hillsmith", "title": "Ordination of Tables mixing quantitative variables and factors", "topics": [ "dudi.hillsmith" ] }, { "page": "dudi.mix", "title": "Ordination of Tables mixing quantitative variables and factors", "topics": [ "dudi.mix" ] }, { "page": "dudi.nsc", "title": "Non symmetric correspondence analysis", "topics": [ "dudi.nsc" ] }, { "page": "dudi.pca", "title": "Principal Component Analysis", "topics": [ "dudi.pca" ] }, { "page": "dudi.pco", "title": "Principal Coordinates Analysis", "topics": [ "dudi.pco", "scatter.pco" ] }, { "page": "dunedata", "title": "Dune Meadow Data", "topics": [ "dunedata" ] }, { "page": "ecg", "title": "Electrocardiogram data", "topics": [ "ecg" ] }, { "page": "ecomor", "title": "Ecomorphological Convergence", "topics": [ "ecomor" ] }, { "page": "elec88", "title": "Electoral Data", "topics": [ "elec88" ] }, { "page": "escopage", "title": "K-tables of wine-tasting", "topics": [ "escopage" ] }, { "page": "euro123", "title": "Triangular Data", "topics": [ "euro123" ] }, { "page": "fission", "title": "Fission pattern and heritable morphological traits", "topics": [ "fission" ] }, { "page": "foucart", "title": "K-tables Correspondence Analysis with the same rows and the same columns", "topics": [ "foucart", "plot.foucart", "print.foucart" ] }, { "page": "fourthcorner", "title": "Functions to compute the fourth-corner statistic", "topics": [ "fourthcorner", "fourthcorner.rlq", "fourthcorner2", "plot.4thcorner", "print.4thcorner", "summary.4thcorner" ] }, { "page": "friday87", "title": "Faunistic K-tables", "topics": [ "friday87" ] }, { "page": "fruits", "title": "Pair of Tables", "topics": [ "fruits" ] }, { "page": "gearymoran", "title": "Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation", "topics": [ "gearymoran" ] }, { "page": "ggtortoises", "title": "Microsatellites of Galapagos tortoises populations", "topics": [ "ggtortoises" ] }, { "page": "granulo", "title": "Granulometric Curves", "topics": [ "granulo" ] }, { "page": "gridrowcol", "title": "Complete regular grid analysis", "topics": [ "gridrowcol" ] }, { "page": "hdpg", "title": "Genetic Variation In Human Populations", "topics": [ "hdpg" ] }, { "page": "houmousr", "title": "Morphometric data set", "topics": [ "houmousr" ] }, { "page": "housetasks", "title": "Contingency Table", "topics": [ "housetasks" ] }, { "page": "humDNAm", "title": "human mitochondrial DNA restriction data", "topics": [ "humDNAm" ] }, { "page": "ichtyo", "title": "Point sampling of fish community", "topics": [ "ichtyo" ] }, { "page": "inertia.dudi", "title": "Decomposition of inertia (i.e. contributions) in multivariate methods", "topics": [ "inertia", "inertia.dudi", "print.inertia", "summary.inertia" ] }, { "page": "irishdata", "title": "Geary's Irish Data", "topics": [ "irishdata" ] }, { "page": "is.euclid", "title": "Is a Distance Matrix Euclidean?", "topics": [ "is.euclid", "summary.dist" ] }, { "page": "julliot", "title": "Seed dispersal", "topics": [ "julliot" ] }, { "page": "jv73", "title": "K-tables Multi-Regions", "topics": [ "jv73" ] }, { "page": "kcponds", "title": "Ponds in a nature reserve", "topics": [ "kcponds" ] }, { "page": "kdist", "title": "the class of objects 'kdist' (K distance matrices)", "topics": [ "as.data.frame.kdist", "c.kdist", "kdist", "print.kdist", "[.kdist" ] }, { "page": "kdist2ktab", "title": "Transformation of K distance matrices (object 'kdist') into K Euclidean representations (object 'ktab')", "topics": [ "kdist2ktab" ] }, { "page": "kdisteuclid", "title": "a way to obtain Euclidean distance matrices", "topics": [ "kdisteuclid" ] }, { "page": "kplot", "title": "Generic Function for Multiple Graphs in a K-tables Analysis", "topics": [ "kplot" ] }, { "page": "kplot.foucart", "title": "Multiple Graphs for the Foucart's Correspondence Analysis", "topics": [ "kplot.foucart" ] }, { "page": "kplot.mcoa", "title": "Multiple Graphs for a Multiple Co-inertia Analysis", "topics": [ "kplot.mcoa" ] }, { "page": "kplot.mfa", "title": "Multiple Graphs for a Multiple Factorial Analysis", "topics": [ "kplot.mfa" ] }, { "page": "kplot.pta", "title": "Multiple Graphs for a Partial Triadic Analysis", "topics": [ "kplot.pta" ] }, { "page": "kplot.sepan", "title": "Multiple Graphs for Separated Analyses in a K-tables", "topics": [ "kplot.sepan", "kplotsepan.coa" ] }, { "page": "kplot.statis", "title": "Multiple Graphs of a STATIS Analysis", "topics": [ "kplot.statis" ] }, { "page": "krandtest", "title": "Class of the Permutation Tests (in C).", "topics": [ "as.krandtest", "krandtest", "plot.krandtest", "print.krandtest", "[.krandtest", "[[.krandtest" ] }, { "page": "ktab", "title": "the class of objects 'ktab' (K-tables)", "topics": [ "c.ktab", "col.names", "col.names.ktab", "col.names<-", "col.names<-.ktab", "is.ktab", "ktab", "ktab.util.addfactor", "ktab.util.names", "print.ktab", "row.names.ktab", "row.names<-.ktab", "t.ktab", "tab.names", "tab.names.ktab", "tab.names<-", "tab.names<-.ktab", "[.ktab" ] }, { "page": "ktab.data.frame", "title": "Creation of K-tables from a data frame", "topics": [ "ktab.data.frame" ] }, { "page": "ktab.list.df", "title": "Creating a K-tables from a list of data frames.", "topics": [ "ktab.list.df" ] }, { "page": "ktab.list.dudi", "title": "Creation of a K-tables from a list of duality diagrams", "topics": [ "ktab.list.dudi" ] }, { "page": "ktab.match2ktabs", "title": "STATIS and Co-Inertia : Analysis of a series of paired ecological tables", "topics": [ "ktab.match2ktabs" ] }, { "page": "ktab.within", "title": "Process to go from a Within Analysis to a K-tables", "topics": [ "ktab.within" ] }, { "page": "lascaux", "title": "Genetic/Environment and types of variables", "topics": [ "lascaux" ] }, { "page": "lingoes", "title": "Transformation of a Distance Matrix for becoming Euclidean", "topics": [ "lingoes" ] }, { "page": "lizards", "title": "Phylogeny and quantitative traits of lizards", "topics": [ "lizards" ] }, { "page": "loocv.bca", "title": "Leave-one-out cross-validation for a 'bca'", "topics": [ "loocv.between", "plot.bcaloocv", "print.bcaloocv" ] }, { "page": "loocv.discrimin", "title": "Leave-one-out cross-validation for a 'discrimin' analysis", "topics": [ "loocv.discrimin", "plot.discloocv", "print.discloocv" ] }, { "page": "loocv.dudi", "title": "Leave-one-out cross-validation for a 'dudi'", "topics": [ "loocv", "loocv.dudi" ] }, { "page": "macaca", "title": "Landmarks", "topics": [ "macaca" ] }, { "page": "macon", "title": "Wine Tasting", "topics": [ "macon" ] }, { "page": "macroloire", "title": "Assemblages of Macroinvertebrates in the Loire River (France)", "topics": [ "macroloire" ] }, { "page": "mafragh", "title": "Phyto-Ecological Survey", "topics": [ "mafragh" ] }, { "page": "mantel.randtest", "title": "Mantel test (correlation between two distance matrices (in C).)", "topics": [ "mantel.randtest" ] }, { "page": "mantel.rtest", "title": "Mantel test (correlation between two distance matrices (in R).)", "topics": [ "mantel.rtest" ] }, { "page": "maples", "title": "Phylogeny and quantitative traits of flowers", "topics": [ "maples" ] }, { "page": "mariages", "title": "Correspondence Analysis Table", "topics": [ "mariages" ] }, { "page": "mbpcaiv", "title": "Multiblock principal component analysis with instrumental variables", "topics": [ "mbpcaiv" ] }, { "page": "mbpls", "title": "Multiblock partial least squares", "topics": [ "mbpls" ] }, { "page": "mcoa", "title": "Multiple CO-inertia Analysis", "topics": [ "mcoa", "plot.mcoa", "print.mcoa", "summary.mcoa" ] }, { "page": "mdpcoa", "title": "Multiple Double Principal Coordinate Analysis", "topics": [ "kplotX.mdpcoa", "mdpcoa", "prep.mdpcoa" ] }, { "page": "meau", "title": "Ecological Data : sites-variables, sites-species, where and when", "topics": [ "meau" ] }, { "page": "meaudret", "title": "Ecological Data : sites-variables, sites-species, where and when", "topics": [ "meaudret" ] }, { "page": "mfa", "title": "Multiple Factorial Analysis", "topics": [ "mfa", "plot.mfa", "print.mfa", "summary.mfa" ] }, { "page": "microsatt", "title": "Genetic Relationships between cattle breeds with microsatellites", "topics": [ "microsatt" ] }, { "page": "mjrochet", "title": "Phylogeny and quantitative traits of teleos fishes", "topics": [ "mjrochet" ] }, { "page": "mld", "title": "Multi Level Decomposition of unidimensional data", "topics": [ "haar2level", "mld" ] }, { "page": "mollusc", "title": "Faunistic Communities and Sampling Experiment", "topics": [ "mollusc" ] }, { "page": "monde84", "title": "Global State of the World in 1984", "topics": [ "monde84" ] }, { "page": "morphosport", "title": "Athletes' Morphology", "topics": [ "morphosport" ] }, { "page": "mstree", "title": "Minimal Spanning Tree", "topics": [ "mstree" ] }, { "page": "multiblock", "title": "Display and summarize multiblock objects", "topics": [ "print.multiblock", "summary.multiblock" ] }, { "page": "neig", "title": "Neighbourhood Graphs", "topics": [ "nb2neig", "neig", "neig.util.GtoL", "neig.util.LtoG", "neig2mat", "neig2nb", "print.neig", "scores.neig", "summary.neig" ] }, { "page": "newick.eg", "title": "Phylogenetic trees in Newick format", "topics": [ "newick.eg" ] }, { "page": "newick2phylog", "title": "Create phylogeny", "topics": [ "hclust2phylog", "newick2phylog", "newick2phylog.addtools", "taxo2phylog" ] }, { "page": "niche", "title": "Method to Analyse a pair of tables : Environmental and Faunistic Data", "topics": [ "niche", "niche.param", "plot.niche", "print.niche", "rtest.niche" ] }, { "page": "nipals", "title": "Non-linear Iterative Partial Least Squares (NIPALS) algorithm", "topics": [ "nipals", "print.nipals", "scatter.nipals" ] }, { "page": "njplot", "title": "Phylogeny and trait of bacteria", "topics": [ "njplot" ] }, { "page": "olympic", "title": "Olympic Decathlon", "topics": [ "olympic" ] }, { "page": "oribatid", "title": "Oribatid mite", "topics": [ "oribatid" ] }, { "page": "originality", "title": "Originality of a species", "topics": [ "originality" ] }, { "page": "orthobasis", "title": "Orthonormal basis for orthonormal transform", "topics": [ "is.orthobasis", "orthobasis", "orthobasis.circ", "orthobasis.haar", "orthobasis.line", "orthobasis.mat", "orthobasis.neig", "plot.orthobasis", "print.orthobasis", "summary.orthobasis" ] }, { "page": "ours", "title": "A table of Qualitative Variables", "topics": [ "ours" ] }, { "page": "palm", "title": "Phylogenetic and quantitative traits of amazonian palm trees", "topics": [ "palm" ] }, { "page": "pap", "title": "Taxonomy and quantitative traits of carnivora", "topics": [ "pap" ] }, { "page": "pcaiv", "title": "Principal component analysis with respect to instrumental variables", "topics": [ "pcaiv", "plot.pcaiv", "print.pcaiv", "summary.pcaiv" ] }, { "page": "pcaivortho", "title": "Principal Component Analysis with respect to orthogonal instrumental variables", "topics": [ "pcaivortho", "summary.pcaivortho" ] }, { "page": "pcoscaled", "title": "Simplified Analysis in Principal Coordinates", "topics": [ "pcoscaled" ] }, { "page": "pcw", "title": "Distribution of of tropical trees along the Panama canal", "topics": [ "pcw" ] }, { "page": "perthi02", "title": "Contingency Table with a partition in Molecular Biology", "topics": [ "perthi02" ] }, { "page": "phylog", "title": "Phylogeny", "topics": [ "phylog", "phylog.extract", "phylog.permut", "print.phylog" ] }, { "page": "PI2newick", "title": "Import data files from Phylogenetic Independance Package", "topics": [ "PI2newick" ] }, { "page": "piosphere", "title": "Plant traits response to grazing", "topics": [ "piosphere" ] }, { "page": "plot.phylog", "title": "Plot phylogenies", "topics": [ "enum.phylog", "plot.phylog", "radial.phylog" ] }, { "page": "presid2002", "title": "Results of the French presidential elections of 2002", "topics": [ "presid2002" ] }, { "page": "procella", "title": "Phylogeny and quantitative traits of birds", "topics": [ "procella" ] }, { "page": "procuste", "title": "Simple Procruste Rotation between two sets of points", "topics": [ "plot.procuste", "print.procuste", "procuste", "randtest.procuste" ] }, { "page": "procuste.randtest", "title": "Monte-Carlo Test on the sum of the singular values of a procustean rotation (in C).", "topics": [ "procuste.randtest" ] }, { "page": "procuste.rtest", "title": "Monte-Carlo Test on the sum of the singular values of a procustean rotation (in R).", "topics": [ "procuste.rtest" ] }, { "page": "pta", "title": "Partial Triadic Analysis of a K-tables", "topics": [ "plot.pta", "print.pta", "pta" ] }, { "page": "quasieuclid", "title": "Transformation of a distance matrice to a Euclidean one", "topics": [ "quasieuclid" ] }, { "page": "randboot", "title": "Bootstrap simulations", "topics": [ "as.krandboot", "as.randboot", "print.krandboot", "print.randboot", "randboot" ] }, { "page": "randboot.multiblock", "title": "Bootstraped simulations for multiblock methods", "topics": [ "randboot.multiblock" ] }, { "page": "randtest", "title": "Class of the Permutation Tests (in C).", "topics": [ "as.randtest", "plot.randtest", "print.randtest", "randtest" ] }, { "page": "randtest.amova", "title": "Permutation tests on an analysis of molecular variance (in C).", "topics": [ "randtest.amova" ] }, { "page": "randtest.between", "title": "Monte-Carlo Test on the between-groups inertia percentage (in C).", "topics": [ "randtest.between" ] }, { "page": "randtest.coinertia", "title": "Monte-Carlo test on a Co-inertia analysis (in C).", "topics": [ "randtest.coinertia" ] }, { "page": "randtest.discrimin", "title": "Monte-Carlo Test on a Discriminant Analysis (in C).", "topics": [ "randtest.discrimin" ] }, { "page": "randtest.dpcoa", "title": "Permutation test for double principal coordinate analysis (DPCoA)", "topics": [ "randtest.dpcoa" ] }, { "page": "randtest.pcaiv", "title": "Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia", "topics": [ "randtest.pcaiv", "randtest.pcaivortho" ] }, { "page": "randxval", "title": "Two-fold cross-validation", "topics": [ "as.krandxval", "as.randxval", "krandxval", "print.krandxval", "print.randxval", "randxval" ] }, { "page": "rankrock", "title": "Ordination Table", "topics": [ "rankrock" ] }, { "page": "reconst", "title": "Reconstitution of Data from a Duality Diagram", "topics": [ "reconst", "reconst.coa", "reconst.pca" ] }, { "page": "rhizobium", "title": "Genetic structure of two nitrogen fixing bacteria influenced by geographical isolation and host specialization", "topics": [ "rhizobium" ] }, { "page": "rhone", "title": "Physico-Chemistry Data", "topics": [ "rhone" ] }, { "page": "rlq", "title": "RLQ analysis", "topics": [ "plot.rlq", "print.rlq", "randtest.rlq", "rlq", "summary.rlq" ] }, { "page": "rpjdl", "title": "Avifauna and Vegetation", "topics": [ "rpjdl" ] }, { "page": "rtest", "title": "Class of the Permutation Tests (in R).", "topics": [ "rtest" ] }, { "page": "rtest.between", "title": "Monte-Carlo Test on the between-groups inertia percentage (in R).", "topics": [ "rtest.between" ] }, { "page": "rtest.discrimin", "title": "Monte-Carlo Test on a Discriminant Analysis (in R).", "topics": [ "rtest.discrimin" ] }, { "page": "RV.randtest", "title": "Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in C++ with Rcpp).", "topics": [ "RV.randtest" ] }, { "page": "RV.rtest", "title": "Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in R).", "topics": [ "RV.rtest" ] }, { "page": "RVdist.randtest", "title": "Tests of randomization on the correlation between two distance matrices (in R).", "topics": [ "RVdist.randtest" ] }, { "page": "RVintra.randtest", "title": "Monte-Carlo Test on the sum of eigenvalues of a within-class co-inertia analysis (in C++ with Rcpp).", "topics": [ "RVintra.randtest" ] }, { "page": "s.arrow", "title": "Plot of the factorial maps for the projection of a vector basis", "topics": [ "s.arrow" ] }, { "page": "s.chull", "title": "Plot of the factorial maps with polygons of contour by level of a factor", "topics": [ "s.chull" ] }, { "page": "s.class", "title": "Plot of factorial maps with representation of point classes", "topics": [ "s.class" ] }, { "page": "s.corcircle", "title": "Plot of the factorial maps of a correlation circle", "topics": [ "s.corcircle" ] }, { "page": "s.distri", "title": "Plot of a frequency distribution", "topics": [ "s.distri" ] }, { "page": "s.hist", "title": "Display of a scatterplot and its two marginal histograms", "topics": [ "s.hist" ] }, { "page": "s.image", "title": "Graph of a variable using image and contour", "topics": [ "s.image" ] }, { "page": "s.kde2d", "title": "Scatter 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