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"cptInv" ] }, { "page": "DiagnosticProb", "title": "Diagnostic probabilities", "topics": [ "Data17", "DiagnosticProb" ] }, { "page": "dist", "title": "Distances in variouse approaches", "topics": [ "dist", "dist.default" ] }, { "page": "ellipses", "title": "Draw ellipses", "topics": [ "ellipses", "ellipses.acomp", "ellipses.aplus", "ellipses.rcomp", "ellipses.rmult", "ellipses.rplus" ] }, { "page": "endmemberCoordinates", "title": "Recast amounts as mixtures of end-members", "topics": [ "endmemberCoordinates", "endmemberCoordinates.acomp", "endmemberCoordinates.aplus", "endmemberCoordinates.default", "endmemberCoordinates.rplus", "endmemberCoordinatesInv", "endmemberCoordinatesInv.acomp", "endmemberCoordinatesInv.aplus", "endmemberCoordinatesInv.rcomp", "endmemberCoordinatesInv.rmult", "endmemberCoordinatesInv.rplus" ] }, { "page": "Firework", "title": "Firework mixtures", "topics": [ "Data13", "Firework" ] }, { "page": "fitdirichlet", "title": "Fitting a Dirichlet distribution", "topics": [ "fitDirichlet" ] }, { "page": "fitsamemean", "title": "Fit Same Mean Different Variance Model", "topics": [ "fitSameMeanDifferentVarianceModel" ] }, { "page": "gausstest", "title": "Classical Gauss Test", "topics": [ "Gauss.test" ] }, { "page": "geometricmean", "title": "The geometric mean", "topics": [ "geometricmean", "geometricmeanCol", "geometricmeanRow", "gsi.geometricmean", "gsi.geometricmean.Col", "gsi.geometricmean.Row", "gsi.geometricmeanCol", "gsi.geometricmeanRow" ] }, { "page": "getdetectionlimit", "title": "Gets the detection limit stored in the data set", "topics": [ "getDetectionlimit" ] }, { "page": "Glacial", "title": "Compositions and total pebble counts of 92 glacial tills", "topics": [ "DATA18", "Glacial" ] }, { "page": "goftests", "title": "Compositional Goodness of fit test", "topics": [ "acompGOF.test", "acompGOF.test.formula", "acompGOF.test.list", "acompNormalGOF.test", "acompTwoSampleGOF.test", "gsi.acompUniformityGOF.test" ] }, { "page": "groupparts", "title": "Group amounts of parts", "topics": [ "groupparts", "groupparts.acomp", "groupparts.aplus", "groupparts.ccomp", "groupparts.rcomp", "groupparts.rplus" ] }, { "page": "Hongite", "title": "Compositions of 25 specimens of hongite", "topics": [ "Data01", "Hongite" ] }, { "page": "HotellingsTsq", "title": "Hotellings T square distribution", "topics": [ "pHotellingsTsq", "qHotellingsTsq" ] }, { "page": "HouseholdExp", "title": "Household Expenditures", "topics": [ "DATA08", "HEMF", "HouseholdExp" ] }, { "page": "Hydrochem", "title": "Hydrochemical composition data set of Llobregat river basin water (NE Spain)", "topics": [ "Hydrochem" ] }, { "page": "idt", "title": "Isometric default transform", "topics": [ "idt", "idt.acomp", "idt.aplus", "idt.ccomp", "idt.data.frame", "idt.default", "idt.factor", "idt.rcomp", "idt.rmult", "idt.rplus", "idtInv", "idtInv.acomp", "idtInv.aplus", "idtInv.ccomp", "idtInv.data.frame", "idtInv.default", "idtInv.factor", "idtInv.rcomp", "idtInv.rmult", "idtInv.rplus" ] }, { "page": "iit", "title": "Isometric identity transform", "topics": [ "iit", "iitInv" ] }, { "page": "ilr", "title": "Isometric log ratio transform", "topics": [ "ilr", "ilrInv" ] }, { "page": "ilrBase", "title": "The canonical basis in the clr plane used for ilr and ipt transforms.", "topics": [ "ilrBase", "ilrBaseList" ] }, { "page": "ilt", "title": "Isometric log transform", "topics": [ "ilt", "iltInv" ] }, { "page": "ipt", "title": "Isometric planar transform", "topics": [ "ipt", "iptInv", "uciptInv" ] }, { "page": "isAcomp", "title": "Check for compositional data type", "topics": [ "is.acomp", "is.aplus", "is.ccomp", "is.rcomp", "is.rmult", "is.rplus" ] }, { "page": "ismahalanobisoutlier", "title": "Checking for outliers", "topics": [ "IsMahalanobisOutlier" ] }, { "page": "isoportion", "title": "Isoportion- and Isoproportion-lines", "topics": [ "isoPortionLines", "isoPortionLines.acomp", "isoPortionLines.rcomp", "isoProportionLines", "isoProportionLines.acomp", "isoProportionLines.rcomp" ] }, { "page": "jura", "title": "The jura dataset", "topics": [ "jura259", "juraset" ] }, { "page": "kdeDirichlet", "title": "Density estimation on the simplex with Dirichlet kernel", "topics": [ "kdeDirichlet" ] }, { "page": "kingtetrahedron", "title": "Ploting composition into rotable tetrahedron", "topics": [ "kingTetrahedron" ] }, { "page": "Kongite", "title": "Compositions of 25 specimens of kongite", "topics": [ "Data02", "Kongite" ] }, { "page": "lines", "title": "Draws connected lines from point to point.", "topics": [ "lines.acomp", "lines.aplus", "lines.rcomp", "lines.rmult", "lines.rplus" ] }, { "page": "logratioVariogram", "title": "Empirical variograms for compositions", "topics": [ "logratioVariogram", "logratioVariogram.acomp" ] }, { "page": "lrvgram", "title": "vgram2lrvgram", "topics": [ "cgram2vgram", "vgram2lrvgram" ] }, { "page": "mahalanobisdist", "title": "Compute Mahalanobis distances based von robust Estimations", "topics": [ "MahalanobisDist", "MahalanobisDist.acomp", "MahalanobisDist.aplus", "MahalanobisDist.rcomp", "MahalanobisDist.rmult", "MahalanobisDist.rplus" ] }, { "page": "matmult", "title": "inner product for matrices and vectors", "topics": [ "%*%", "%*%.default" ] }, { "page": "meanAcomp", "title": "Mean amounts and mean compositions", "topics": [ "mean.acomp", "mean.aplus", "mean.ccomp", "mean.rcomp", "mean.rmult", "mean.rplus" ] }, { "page": "meanrow", "title": "The arithmetic mean of rows or columns", "topics": [ "mean.col", "mean.row", "meanCol", "meanRow" ] }, { "page": "Metabolites", "title": "Steroid metabolite patterns in adults and children", "topics": [ "Data09", "Metabolites" ] }, { "page": "compmiss", "title": "The policy of treatment of missing values in the \"compositions\" package", "topics": [ "BDL", "BDLvalue", "composition.missing", "composition.missings", "compositions.missing", "compositions.missings", "has.missings", "has.missings.default", "has.missings.rmult", "is.BDL", "is.MAR", "is.MNAR", "is.MNV", "is.NMV", "is.SZ", "is.WMNAR", "is.WZERO", "MAR", "MARvalue", "missings", "missingsInCompositions", "MNAR", "MNARvalue", "NMV", "SZ", "SZvalue" ] }, { "page": "missingProjector", "title": "Returns a projector the the observed space in case of missings.", "topics": [ "missingProjector", "missingProjector.acomp", "missingProjector.aplus", "missingProjector.rcomp", "missingProjector.rmult", "missingProjector.rplus" ] }, { "page": "missingsummary", "title": "Classify and summarize missing values in a dataset", "topics": [ "missingSummary", "missingType" ] }, { "page": "mixRead", "title": "Reads a data file in a mixR format", "topics": [ "mix.Read" ] }, { "page": "mvar", "title": "Metric summary statistics of real, amount or compositional data", "topics": [ "mcor", "mcor.default", "mcov", "mcov.default", "msd", "msd.default", "mvar", "mvar.default" ] }, { "page": "names", "title": "The names of the parts", "topics": [ "names.acomp", "names.aplus", "names.ccomp", "names.rcomp", "names.rmult", "names.rplus", "names<-.acomp", "names<-.aplus", "names<-.ccomp", "names<-.rcomp", "names<-.rmult", "names<-.rplus" ] }, { "page": "norm", "title": "Vector space norm", "topics": [ "norm", "norm.acomp", "norm.aplus", "norm.default", "norm.matrix", "norm.rcomp", "norm.rmult", "norm.rplus" ] }, { "page": "normalize", "title": "Normalize vectors to norm 1", "topics": [ "normalize", "normalize.default" ] }, { "page": "tests", "title": "Compositional Goodness of fit test", "topics": [ "acompNormalLocation.test" ] }, { "page": "oneOrDataset", "title": "Treating single compositions as one-row datasets", "topics": [ "oneOrDataset" ] }, { "page": "outlierclassifier", "title": "Detect and classify compositional outliers.", "topics": [ "OutlierClassifier1", "OutlierClassifier1.acomp" ] }, { "page": "outlierplot", "title": "Plot various graphics to analyse outliers.", "topics": [ "outlierplot", "outlierplot.acomp" ] }, { "page": "outliers", "title": "Analysing outliers in compositions.", "topics": [ "outliersInCompositions" ] }, { "page": "panelAcomp", "title": "Pairs plot method for compositions", "topics": [ "pairs.acomp", "pairs.rcomp", "vp.diffdensityplot", "vp.kde2dplot", "vp.lrboxplot", "vp.lrdensityplot" ] }, { "page": "pairwisePlot", "title": "Creates a paneled plot like pairs for two different datasets.", "topics": [ "pairwisePlot", "pairwisePlot.default" ] }, { "page": "parametricMat", "title": "Unique parametrisations for matrices.", "topics": [ "parameterPosdefClrMat", "parameterPosdefMat", "parameterRank1ClrMat", "parameterRank1Mat", "parametricPosdefClrMat", "parametricPosdefMat", "parametricRank1ClrMat", "parametricRank1Mat" ] }, { "page": "perturbe", "title": "Perturbation of compositions", "topics": [ "+.acomp", "-.acomp", "perturbe" ] }, { "page": "plot", "title": "Ternary diagrams", "topics": [ "plot.acomp", "plot.ccomp", "plot.rcomp" ] }, { "page": "plotpos", "title": "Displaying amounts in scatterplots", "topics": [ "plot.aplus", "plot.rmult", "plot.rplus" ] }, { "page": "plot3d", "title": "plot in 3D based on rgl", "topics": [ "plot3D", "plot3D.default" ] }, { "page": "plot3dacomp", "title": "3D-plot of compositional data", "topics": [ "plot3D.acomp", "plot3D.rcomp" ] }, { "page": "plot3daplus", "title": "3D-plot of positive data", "topics": [ "plot3D.aplus" ] }, { "page": "plot3drmult", "title": "plot in 3D based on rgl", "topics": [ "plot3D.rmult" ] }, { "page": "plot3drplus", "title": "plot in 3D based on rgl", "topics": [ "plot3D.rplus" ] }, { "page": "plotlogratioVariogram", "title": "Empirical variograms for compositions", "topics": [ "plot.logratioVariogram" ] }, { "page": "plotmissingsummary", "title": "Plot a Missing Summary", "topics": [ "as.missingSummary", "plot.missingSummary" ] }, { "page": "PogoJump", "title": "Honk Kong Pogo-Jumps Championship", "topics": [ "Data19", "PogoJump" ] }, { "page": "powerofmatrix", "title": "power transform of a matrix", "topics": [ "powerofpsdmatrix" ] }, { "page": "princompacomp", "title": "Principal component analysis for Aitchison compositions", "topics": [ "plot.princomp.acomp", "predict.princomp.acomp", "princomp.acomp", "print.princomp.acomp" ] }, { "page": "princompaplus", "title": "Principal component analysis for amounts in log geometry", "topics": [ "plot.princomp.aplus", "predict.princomp.aplus", "princomp.aplus", "print.princomp.aplus" ] }, { "page": "princomprcomp", "title": "Principal component analysis for real compositions", "topics": [ "plot.princomp.rcomp", "predict.princomp.rcomp", "princomp.rcomp", "print.princomp.rcomp" ] }, { "page": "princomprmult", "title": "Principal component analysis for real data", "topics": [ "princomp.rmult" ] }, { "page": "princomprplus", "title": "Principal component analysis for real amounts", "topics": [ "plot.princomp.rplus", "predict.princomp.rplus", "princomp.rplus", "print.princomp.rplus" ] }, { "page": "print", "title": "Printing compositional data.", "topics": [ "print.acomp", "print.aplus", "print.rcomp", "print.rplus" ] }, { "page": "pwlr", "title": "Pairwise log ratio transform", "topics": [ "pwlr", "pwlrInv" ] }, { "page": "pwlrPlot", "title": "Plots of pairwise logratio against a covariable.", "topics": [ "pwlrPlot", "pwlrplot" ] }, { "page": "qqnorm", "title": "Normal quantile plots for compositions and amounts", "topics": [ "qqnorm.acomp", "qqnorm.aplus", "qqnorm.rcomp", "qqnorm.rplus", "vp.qqnorm" ] }, { "page": "R2", "title": "R square", "topics": [ "R2", "R2.default", "R2.lm", "Rsquare" ] }, { "page": "raitchison", "title": "Aitchison Distribution", "topics": [ "AitchisonDistributionIntegrals", "dAitchison", "rAitchison" ] }, { "page": "ratioLoadings", "title": "Loadings of relations of two amounts", "topics": [ "plot.relativeLoadings.princomp.acomp", "plot.relativeLoadings.princomp.aplus", "plot.relativeLoadings.princomp.rcomp", "plot.relativeLoadings.princomp.rplus", "print.relativeLoadings.princomp.acomp", "print.relativeLoadings.princomp.aplus", "print.relativeLoadings.princomp.rcomp", "print.relativeLoadings.princomp.rplus", "relativeLoadings", "relativeLoadings.princomp.acomp", "relativeLoadings.princomp.aplus", "relativeLoadings.princomp.rcomp", "relativeLoadings.princomp.rplus" ] }, { "page": "rcomp", "title": "Compositions as elements of the simplex embedded in the D-dimensional real space", "topics": [ "rcomp" ] }, { "page": "rcomp-class", "title": "Class '\"rcomp\"'", "topics": [ "coerce,rcomp,data.frame-method", "coerce,rcomp,structure-method", "coerce<-,rcomp,data.frame-method", "rcomp-class" ] }, { "page": "rcomparithm", "title": "Arithmetic operations for compositions in a real geometry", "topics": [ "*.rcomp", "+.rcomp", "-.rcomp", "/.rcomp", "convex.rcomp" ] }, { "page": "rcompmargin", "title": "Marginal compositions in real geometry", "topics": [ "rcompmargin" ] }, { "page": "rDirichlet", "title": "Dirichlet distribution", "topics": [ "dDirichlet", "rDirichlet", "rDirichlet.acomp", "rDirichlet.rcomp" ] }, { "page": "readgeoeas", "title": "Reads a data file in a geoeas format", "topics": [ "read.geoEAS", "read.geoeas" ] }, { "page": "replot", "title": "Modify parameters of compositional plots.", "topics": [ "noreplot", "replot", "replotable" ] }, { "page": "rlnorm", "title": "The multivariate lognormal distribution", "topics": [ "dlnorm.rplus", "rlnorm.rplus" ] }, { "page": "rmahalanobis", "title": "Compute distributions of empirical Mahalanobis distances based on simulations", "topics": [ "gsi.pStore", "pEmpiricalMahalanobis", "pMaxMahalanobis", "pPortionMahalanobis", "pQuantileMahalanobis", "qEmpiricalMahalanobis", "qMaxMahalanobis", "qPortionMahalanobis", "rEmpiricalMahalanobis", "rMaxMahalanobis", "rPortionMahalanobis" ] }, { "page": "rmult", "title": "Simple treatment of real vectors", "topics": [ "print.rmult", "rmult" ] }, { "page": "rmult-class", "title": "Class '\"rmult\"'", "topics": [ "coerce,rmult,data.frame-method", "coerce,rmult,structure-method", "coerce<-,rmult,data.frame-method", "rmult-class" ] }, { "page": "rmultarithm", "title": "vectorial arithmetic for datasets in a classical vector scale", "topics": [ "*.rmult", "+.rmult", "-.rmult", "/.rmult" ] }, { "page": "rmultmatmult", "title": "inner product for datasets with vector scale", "topics": [ "%*%.rmult" ] }, { "page": "rnorm", "title": "Normal distributions on special spaces", "topics": [ "dnorm.acomp", "dnorm.aplus", "dnorm.rmult", "rnorm.acomp", "rnorm.aplus", "rnorm.ccomp", "rnorm.rcomp", "rnorm.rmult", "rnorm.rplus" ] }, { "page": "robustness", "title": "Handling robustness issues and outliers in compositions.", "topics": [ "robust", "robustnessInCompositions" ] }, { "page": "rplus", "title": "Amounts i.e. positive numbers analysed as objects of the real vector space", "topics": [ "rplus" ] }, { "page": "rplus-class", "title": "Class '\"rplus\"'", "topics": [ "coerce,rplus,data.frame-method", "coerce,rplus,structure-method", "coerce<-,rplus,data.frame-method", "rplus-class" ] }, { "page": "rplusarithm", "title": "vectorial arithmetic for data sets with rplus class", "topics": [ "*.rplus", "+.rplus", "-.rplus", "/.rplus", "mul.rplus" ] }, { "page": "rpois", "title": "Simulate count compositions without overdispersion", "topics": [ "rmultinom.ccomp", "rpois.ccomp" ] }, { "page": "runif", "title": "The uniform distribution on the simplex", "topics": [ "runif.acomp", "runif.rcomp" ] }, { "page": "scalar", "title": "Parallel scalar products", "topics": [ "scalar", "scalar.default" ] }, { "page": "scale", "title": "Normalizing datasets by centering and scaling", "topics": [ "scale", "scale.acomp", "scale.aplus", "scale.default", "scale.rcomp", "scale.rmult", "scale.rplus" ] }, { "page": "Sediments", "title": "Proportions of sand, silt and clay in sediments specimens", "topics": [ "Data20", "Sediments" ] }, { "page": "segments", "title": "Draws straight lines from point to point.", "topics": [ "segments", "segments.acomp", "segments.aplus", "segments.default", "segments.rcomp", "segments.rmult", "segments.rplus" ] }, { "page": "SerumProtein", "title": "Serum Protein compositions of blood samples", "topics": [ "Data16", "SerumProtein" ] }, { "page": "ShiftOperators", "title": "Shifts of machine operators", "topics": [ "Data22", "ShiftOperators" ] }, { "page": "simplemissingplot", "title": "Ternary diagrams", "topics": [ "simpleMissingSubplot" ] }, { "page": "SimulatedAmounts", "title": "Simulated amount datasets", "topics": [ "sa.dirichlet", "sa.dirichlet.dil", "sa.dirichlet.mix", "sa.dirichlet5", "sa.dirichlet5.dil", "sa.dirichlet5.mix", "sa.groups", "sa.groups.area", "sa.groups.dil", "sa.groups.mix", "sa.groups5", "sa.groups5.area", "sa.groups5.dil", "sa.groups5.mix", "sa.lognormals", "sa.lognormals.dil", "sa.lognormals.mix", "sa.lognormals5", "sa.lognormals5.dil", "sa.lognormals5.mix", "sa.missings", "sa.missings5", "sa.outliers1", "sa.outliers2", "sa.outliers3", "sa.outliers4", "sa.outliers5", "sa.outliers6", "sa.tnormals", "sa.tnormals.dil", "sa.tnormals.mix", "sa.tnormals5", "sa.tnormals5.dil", "sa.tnormals5.mix", "sa.uniform", "sa.uniform.dil", "sa.uniform.mix", "sa.uniform5", "sa.uniform5.dil", "sa.uniform5.mix", "SimulatedAmounts" ] }, { "page": "simulatemissing", "title": "Artifical simulation of various kinds of missings/polluted data", "topics": [ "observeWithAdditiveError", "observeWithDetectionLimit", "observeWithDetectionlimit", "simulateMissings" ] }, { "page": "Skulls", "title": "Measurement of skulls", "topics": [ "Data24", "Skulls" ] }, { "page": "SkyeAFM", "title": "AFM compositions of 23 aphyric Skye lavas", "topics": [ "Data06", "SkyeAFM" ] }, { "page": "split", "title": "Splitting datasets in groups given by factors", "topics": [ "split.acomp", "split.aplus", "split.ccomp", "split.rcomp", "split.rmult", "split.rplus" ] }, { "page": "straight", "title": "Draws straight lines.", "topics": [ "straight", "straight.acomp", "straight.aplus", "straight.rcomp", "straight.rmult", "straight.rplus" ] }, { "page": "subsetting", "title": "Subsetting of compositions", "topics": [ "$.acomp", "$.aplus", "$.ccomp", "$.rcomp", "$.rmult", "$.rplus", "getStickyClassOption", "setStickyClassOption", "[.acomp", "[.aplus", "[.ccomp", "[.rcomp", "[.rmult", "[.rplus" ] }, { "page": "summaryAcomp", "title": "Summarizing a compositional dataset in terms of ratios", "topics": [ "summary.acomp" ] }, { "page": "summaryAplus", "title": "Summaries of amounts", "topics": [ "summary.aplus", "summary.rmult", "summary.rplus" ] }, { "page": "summaryRcomp", "title": "Summary of compositions in real geometry", "topics": [ "summary.rcomp" ] }, { "page": "sumprojector", "title": "Compute the global projector to the observed subspace.", "topics": [ "sumMissingProjector", "sumMissingProjector.acomp", "sumMissingProjector.aplus", "sumMissingProjector.rcomp", "sumMissingProjector.rmult", "sumMissingProjector.rplus" ] }, { "page": "Supervisor", "title": "Proportions of supervisor's statements assigned to different categories", "topics": [ "Data07", "Supervisor" ] }, { "page": "ternaryAxis", "title": "Axis for ternary diagrams", "topics": [ "ternaryAxis" ] }, { "page": "totals", "title": "Total sum of amounts", "topics": [ "totals", "totals.acomp", "totals.aplus", "totals.ccomp", "totals.rcomp", "totals.rplus" ] }, { "page": "mix2compositions", "title": "Transformations from 'mixtures' to 'compositions' classes", "topics": [ "mix.2acomp", "mix.2aplus", "mix.2rcomp", "mix.2rmult", "mix.2rplus" ] }, { "page": "tryDebugger", "title": "Empirical variograms for compositions", "topics": [ "tryDebugger" ] }, { "page": "ult", "title": "Uncentered log transform", "topics": [ "Kappa", "ult", "ultInv" ] }, { "page": "varAcomp", "title": "Variances and covariances of amounts and compositions", "topics": [ "cov", "cov.acomp", "cov.aplus", "cov.default", "cov.rcomp", "cov.rmult", "cov.rplus", "var", "var.acomp", "var.aplus", "var.default", "var.rcomp", "var.rmult", "var.rplus" ] }, { "page": "variation", "title": "Variation matrices of amounts and compositions", "topics": [ "is.variation", "variation", "variation.acomp", "variation.aplus", "variation.default", "variation.rcomp", "variation.rmult", "variation.rplus" ] }, { "page": "variograms", "title": "Variogram functions", "topics": [ "vgram.cardsin", "vgram.exp", "vgram.gauss", "vgram.lin", "vgram.nugget", "vgram.pow", "vgram.sph" ] }, { "page": "varmlm", "title": "Residual variance of a model", "topics": [ "var.lm", "var.mlm" ] }, { "page": "vcovAcomp", "title": "Variance covariance matrix of parameters in compositional regression", "topics": [ "vcovAcomp" ] }, { "page": "vgmFit", "title": "Compositional variogram model fitting", "topics": [ "fit.lmc", "fit.lmc.logratioVariogram", "vgmFit", "vgmFit2lrv", "vgmGetParameters", "vgmGof", "vgmSetParameters" ] }, { "page": "WhiteCells", "title": "White-cell composition of 30 blood samples by two 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