compositions-package compositions $.acomp subsetting $.aplus subsetting $.ccomp subsetting $.rcomp subsetting $.rmult subsetting $.rplus subsetting %*% matmult %*%.acomp matmultacomp %*%.aplus matmultacomp %*%.default matmult %*%.rmult rmultmatmult *.acomp acomparith *.aplus aplusarithm *.rcomp rcomparithm *.rmult rmultarithm *.rplus rplusarithm +.acomp perturbe +.aplus aplusarithm +.rcomp rcomparithm +.rmult rmultarithm +.rplus rplusarithm -.acomp perturbe -.aplus aplusarithm -.rcomp rcomparithm -.rmult rmultarithm -.rplus rplusarithm /.acomp acomparith /.aplus aplusarithm /.rcomp rcomparithm /.rmult rmultarithm /.rplus rplusarithm Aar Aar acomp acomp acomp-class acomp-class acompGOF.test goftests acompGOF.test.formula goftests acompGOF.test.list goftests acompmargin acompmargin acompNormalGOF.test goftests acompNormalLocation.test tests acompTwoSampleGOF.test goftests Activity10 Activity10 Activity31 Activity31 AitchisonDistributionIntegrals raitchison alr alr alrInv alr amounts-class amounts-class AnimalVegetation AnimalVegetation anova wrapped_functions aplus aplus aplus-class aplus-class apt apt aptInv apt ArcticLake ArcticLake arrows3D arrows3d arrows3D.default arrows3d as.data.frame.acomp asdataframe as.data.frame.aplus asdataframe as.data.frame.ccomp asdataframe as.data.frame.rcomp asdataframe as.data.frame.rmult asdataframe as.data.frame.rplus asdataframe as.matrix.rmult asdataframe as.missingSummary plotmissingsummary axis3D axis3d backtransform backtransform backtransform.rmult backtransform balance balancebase balance.acomp balancebase balance.aplus balancebase balance.rcomp balancebase balance.rplus balancebase balance01 balancebase balance01.acomp balancebase balance01.rcomp balancebase balanceBase balancebase balanceBase.acomp balancebase balanceBase.aplus balancebase balanceBase.rcomp balancebase balanceBase.rplus balancebase barplot.acomp barplot barplot.aplus barplot barplot.ccomp barplot barplot.rcomp barplot barplot.rplus barplot Bayesite Bayesite BDL compmiss BDLvalue compmiss binary binary binary2logical binary biplot3D biplot3d biplot3D.default biplot3d biplot3D.princomp biplot3d bit binary bit.character binary bit.numeric binary bit<- binary bit<-.character binary bit<-.numeric binary bitCount binary Blood23 Blood23 Boxite Boxite boxplot.acomp boxplot boxplot.aplus boxplot boxplot.rcomp boxplot boxplot.rplus boxplot ccomp ccomp ccomp-class ccomp-class ccompMultinomialGOF.test ccompgof ccompPoissonGOF.test ccompgof cdt cdt cdt.acomp cdt cdt.aplus cdt cdt.ccomp cdt cdt.data.frame cdt cdt.default cdt cdt.factor cdt cdt.rcomp cdt cdt.rmult cdt cdt.rplus cdt cdtInv cdt cdtInv.acomp cdt cdtInv.aplus cdt cdtInv.ccomp cdt cdtInv.data.frame cdt cdtInv.default cdt cdtInv.factor cdt cdtInv.rcomp cdt cdtInv.rmult cdt cdtInv.rplus cdt cgram2vgram lrvgram ClamEast ClamEast ClamWest ClamWest clo clo clr clr clr2ilr clr2ilr clrInv clr clrvar2ilr clr2ilr clrvar2variation clr2ilr ClusterFinder1 clusterfinder ClusterFinder1.acomp clusterfinder CoDaDendrogram codadendrogram coerce,acomp,data.frame-method acomp-class coerce,acomp,structure-method acomp-class coerce,aplus,data.frame-method aplus-class coerce,aplus,structure-method aplus-class coerce,ccomp,data.frame-method ccomp-class coerce,ccomp,structure-method ccomp-class coerce,rcomp,data.frame-method rcomp-class coerce,rcomp,structure-method rcomp-class coerce,rmult,data.frame-method rmult-class coerce,rmult,structure-method rmult-class coerce,rplus,data.frame-method rplus-class coerce,rplus,structure-method rplus-class coerce<-,acomp,data.frame-method acomp-class coerce<-,aplus,data.frame-method aplus-class coerce<-,ccomp,data.frame-method ccomp-class coerce<-,rcomp,data.frame-method rcomp-class coerce<-,rmult,data.frame-method rmult-class coerce<-,rplus,data.frame-method rplus-class coloredBiplot coloredbiplot coloredBiplot.default coloredbiplot coloredBiplot.prcomp coloredbiplot coloredBiplot.princomp coloredbiplot colorsForOutliers1 colorsforoutliers colorsForOutliers2 colorsforoutliers CompLinModCoReg CompLinModCo compOKriging compOKriging composition.missing compmiss composition.missings compmiss compositional-class compositional-class compositions compositions compositions.missing compmiss compositions.missings compmiss ConfRadius ConfRadius convex.rcomp rcomparithm cor cor cor.acomp cor cor.aplus cor cor.default cor cor.rcomp cor cor.rmult cor cor.rplus cor cov varAcomp cov.acomp varAcomp cov.aplus varAcomp cov.default varAcomp cov.rcomp varAcomp cov.rmult varAcomp cov.rplus varAcomp Coxite Coxite cpt cpt cptInv cpt dAitchison raitchison Data01 Hongite Data02 Kongite Data03 Boxite Data04 Coxite Data05 ArcticLake Data06 SkyeAFM Data07 Supervisor DATA08 HouseholdExp Data09 Metabolites DATA10 Activity10 Data11 WhiteCells Data12 Yatquat Data13 Firework Data14 ClamEast Data15 ClamWest Data16 SerumProtein Data17 DiagnosticProb DATA18 Glacial Data19 PogoJump Data20 Sediments Data21 Bayesite Data22 ShiftOperators Data23 Blood23 Data24 Skulls Data25 AnimalVegetation DATA31 Activity31 dDirichlet rDirichlet DiagnosticProb DiagnosticProb dist dist dist.default dist dlnorm.rplus rlnorm dnorm.acomp rnorm dnorm.aplus rnorm dnorm.rmult rnorm ellipses ellipses ellipses.acomp ellipses ellipses.aplus ellipses ellipses.rcomp ellipses ellipses.rmult ellipses ellipses.rplus ellipses endmemberCoordinates endmemberCoordinates endmemberCoordinates.acomp endmemberCoordinates endmemberCoordinates.aplus endmemberCoordinates endmemberCoordinates.default endmemberCoordinates endmemberCoordinates.rplus endmemberCoordinates endmemberCoordinatesInv endmemberCoordinates endmemberCoordinatesInv.acomp endmemberCoordinates endmemberCoordinatesInv.aplus endmemberCoordinates endmemberCoordinatesInv.rcomp endmemberCoordinates endmemberCoordinatesInv.rmult endmemberCoordinates endmemberCoordinatesInv.rplus endmemberCoordinates Firework Firework fit.lmc vgmFit fit.lmc.logratioVariogram vgmFit fitDirichlet fitdirichlet fitSameMeanDifferentVarianceModel fitsamemean gadic binary Gauss.test gausstest geometricmean geometricmean geometricmeanCol geometricmean geometricmeanRow geometricmean getDetectionlimit getdetectionlimit getStickyClassOption subsetting Glacial Glacial groupparts groupparts groupparts.acomp groupparts groupparts.aplus groupparts groupparts.ccomp groupparts groupparts.rcomp groupparts groupparts.rplus groupparts gsi gsiinternal gsi.acompUniformityGOF.test goftests gsi.add gsiadd gsi.add2pairs gsipairs gsi.addclass gsiaddclass gsi.addCoorInfo gsicoorinfo gsi.buildilrBase gsimerge2signary gsi.call gsicall gsi.cleanR gsirecode gsi.closespread gsiclosespread gsi.coorInfo gsicoorinfo gsi.csum gsicsum gsi.diagExtract gsidiagExtract gsi.diagGenerate gsidiagGenerate gsi.div gsiadd gsi.drop gsidrop gsi.eq gsieq gsi.expandrcomp gsiexpandrcomp gsi.filtercall gsifiltercall gsi.geometricmean geometricmean gsi.geometricmean.Col geometricmean gsi.geometricmean.Row geometricmean gsi.geometricmeanCol geometricmean gsi.geometricmeanRow geometricmean gsi.getBalStruct gsigetbalstruct gsi.getCoorInfo gsicoorinfo gsi.getD gsigetD gsi.getN gsigetD gsi.getV backtransform gsi.ilrBase2signary gsimerge2signary gsi.isSingleRow gsiisSingleRow gsi.mapfrom01 gsimap01 gsi.mapin01 gsimap01 gsi.mapmax gsimap01 gsi.mapmin gsimap01 gsi.margin gsimargin gsi.margin.acomp gsimargin gsi.margin.aplus gsimargin gsi.margin.rcomp gsimargin gsi.margin.rplus gsimargin gsi.merge2signary gsimerge2signary gsi.mul gsiadd gsi.optimalilrBase gsimerge2signary gsi.OrderIlr gsimerge2signary gsi.orig backtransform gsi.orSum binary gsi.pairrelativeMatrix gsipairrelativeMatrix gsi.pairs gsipairs gsi.plain gsiplain gsi.plotmargin gsiplotmargin gsi.plots gsipairs gsi.PrinBal gsiPrinBal gsi.pStore rmahalanobis gsi.recodeC2M gsirecode gsi.recodeM2C gsirecode gsi.recodeM2Clean gsirecode gsi.reset3D gsireset3d gsi.rsum gsicsum gsi.setCoorInfo gsicoorinfo gsi.signary2ilrBase gsimerge2signary gsi.simshape gsisimshape gsi.spreadToIsoSpace gsispreadToIsoSpace gsi.sub gsiadd gsi.svdsolve gsisvdsolve gsi.textpanel gsitextpanel gsi.varwithlosts gsivarwithlosts gsi2.invperm gsiinvperm has.missings compmiss has.missings.default compmiss has.missings.rmult compmiss HEMF HouseholdExp Hongite Hongite HouseholdExp HouseholdExp Hydrochem Hydrochem idt idt idt.acomp idt idt.aplus idt idt.ccomp idt idt.data.frame idt idt.default idt idt.factor idt idt.rcomp idt idt.rmult idt idt.rplus idt idtInv idt idtInv.acomp idt idtInv.aplus idt idtInv.ccomp idt idtInv.data.frame idt idtInv.default idt idtInv.factor idt idtInv.rcomp idt idtInv.rmult idt idtInv.rplus idt iit iit iitInv iit ilr ilr ilr2clr clr2ilr ilrBase ilrBase ilrBaseList ilrBase ilrInv ilr ilrvar2clr clr2ilr ilt ilt iltInv ilt ipt ipt iptInv ipt is.acomp isAcomp is.aplus isAcomp is.BDL compmiss is.ccomp isAcomp is.clrvar clr2ilr is.ilrvar clr2ilr is.MAR compmiss is.MNAR compmiss is.MNV compmiss is.NMV compmiss is.rcomp isAcomp is.rmult isAcomp is.rplus isAcomp is.SZ compmiss is.variation variation is.WMNAR compmiss is.WZERO compmiss IsMahalanobisOutlier ismahalanobisoutlier isoPortionLines isoportion isoPortionLines.acomp isoportion isoPortionLines.rcomp isoportion isoProportionLines isoportion isoProportionLines.acomp isoportion isoProportionLines.rcomp isoportion jura259 jura juraset jura Kappa ult kdeDirichlet kdeDirichlet kingTetrahedron kingtetrahedron Kongite Kongite lines.acomp lines lines.aplus lines lines.rcomp lines lines.rmult lines lines.rplus lines logratioVariogram logratioVariogram logratioVariogram.acomp logratioVariogram MahalanobisDist mahalanobisdist MahalanobisDist.acomp mahalanobisdist MahalanobisDist.aplus mahalanobisdist MahalanobisDist.rcomp mahalanobisdist MahalanobisDist.rmult mahalanobisdist MahalanobisDist.rplus mahalanobisdist MAR compmiss MARvalue compmiss maxBit binary maxBit.character binary maxBit.numeric binary mcor mvar mcor.default mvar mcov mvar mcov.default mvar mean.acomp meanAcomp mean.aplus meanAcomp mean.ccomp meanAcomp mean.col meanrow mean.rcomp meanAcomp mean.rmult meanAcomp mean.row meanrow mean.rplus meanAcomp meanCol meanrow meanRow meanrow Metabolites Metabolites missingProjector missingProjector missingProjector.acomp missingProjector missingProjector.aplus missingProjector missingProjector.rcomp missingProjector missingProjector.rmult missingProjector missingProjector.rplus missingProjector missings compmiss missingsInCompositions compmiss missingSummary missingsummary missingType missingsummary mix.2acomp mix2compositions mix.2aplus mix2compositions mix.2rcomp mix2compositions mix.2rmult mix2compositions mix.2rplus mix2compositions mix.Read mixRead MNAR compmiss MNARvalue compmiss msd mvar msd.default mvar mul.rplus rplusarithm mvar mvar mvar.default mvar names.acomp names names.aplus names names.ccomp names names.rcomp names names.rmult names names.rplus names names<-.acomp names names<-.aplus names names<-.ccomp names names<-.rcomp names names<-.rmult names names<-.rplus names NMV compmiss noreplot replot norm norm norm.acomp norm norm.aplus norm norm.default norm norm.matrix norm norm.rcomp norm norm.rmult norm norm.rplus norm normalize normalize normalize.default normalize observeWithAdditiveError simulatemissing observeWithDetectionLimit simulatemissing observeWithDetectionlimit simulatemissing oneOrDataset oneOrDataset OutlierClassifier1 outlierclassifier OutlierClassifier1.acomp outlierclassifier outlierplot outlierplot outlierplot.acomp outlierplot outliersInCompositions outliers pairs.acomp panelAcomp pairs.rcomp panelAcomp pairwisePlot pairwisePlot pairwisePlot.default pairwisePlot parameterPosdefClrMat parametricMat parameterPosdefMat parametricMat parameterRank1ClrMat parametricMat parameterRank1Mat parametricMat parametricPosdefClrMat parametricMat parametricPosdefMat parametricMat parametricRank1ClrMat parametricMat parametricRank1Mat parametricMat pchForOutliers1 colorsforoutliers pEmpiricalMahalanobis rmahalanobis perturbe perturbe perturbe.aplus aplusarithm pHotellingsTsq HotellingsTsq plot.acomp plot plot.aplus plotpos plot.ccomp plot plot.logratioVariogram plotlogratioVariogram plot.missingSummary plotmissingsummary plot.princomp.acomp princompacomp plot.princomp.aplus princompaplus plot.princomp.rcomp princomprcomp plot.princomp.rplus princomprplus plot.rcomp plot plot.relativeLoadings.princomp.acomp ratioLoadings plot.relativeLoadings.princomp.aplus ratioLoadings plot.relativeLoadings.princomp.rcomp ratioLoadings plot.relativeLoadings.princomp.rplus ratioLoadings plot.rmult plotpos plot.rplus plotpos plot3D plot3d plot3D.acomp plot3dacomp plot3D.aplus plot3daplus plot3D.default plot3d plot3D.rcomp plot3dacomp plot3D.rmult plot3drmult plot3D.rplus plot3drplus pMaxMahalanobis rmahalanobis PogoJump PogoJump PoissonGOF.test ccompgof power.acomp acomparith power.aplus aplusarithm powerofpsdmatrix powerofmatrix pPortionMahalanobis rmahalanobis pQuantileMahalanobis rmahalanobis predict.princomp.acomp princompacomp predict.princomp.aplus princompaplus predict.princomp.rcomp princomprcomp predict.princomp.rplus princomprplus princomp.acomp princompacomp princomp.aplus princompaplus princomp.rcomp princomprcomp princomp.rmult princomprmult princomp.rplus princomprplus print.acomp print print.aplus print print.princomp.acomp princompacomp print.princomp.aplus princompaplus print.princomp.rcomp princomprcomp print.princomp.rplus princomprplus print.rcomp print print.relativeLoadings.princomp.acomp ratioLoadings print.relativeLoadings.princomp.aplus ratioLoadings print.relativeLoadings.princomp.rcomp ratioLoadings print.relativeLoadings.princomp.rplus ratioLoadings print.rmult rmult print.rplus print pwlr pwlr pwlrInv pwlr pwlrPlot pwlrPlot pwlrplot pwlrPlot qEmpiricalMahalanobis rmahalanobis qHotellingsTsq HotellingsTsq qMaxMahalanobis rmahalanobis qPortionMahalanobis rmahalanobis qqnorm.acomp qqnorm qqnorm.aplus qqnorm qqnorm.rcomp qqnorm qqnorm.rplus qqnorm R2 R2 R2.default R2 R2.lm R2 rAitchison raitchison rcomp rcomp rcomp-class rcomp-class rcompmargin rcompmargin rDirichlet rDirichlet rDirichlet.acomp rDirichlet rDirichlet.rcomp rDirichlet read.geoEAS readgeoeas read.geoeas readgeoeas relativeLoadings ratioLoadings relativeLoadings.princomp.acomp ratioLoadings relativeLoadings.princomp.aplus ratioLoadings relativeLoadings.princomp.rcomp ratioLoadings relativeLoadings.princomp.rplus ratioLoadings rEmpiricalMahalanobis rmahalanobis replot replot replotable replot rlnorm.rplus rlnorm rMaxMahalanobis rmahalanobis rmult rmult rmult-class rmult-class rmultinom.ccomp rpois rnorm.acomp rnorm rnorm.aplus rnorm rnorm.ccomp rnorm rnorm.rcomp rnorm rnorm.rmult rnorm rnorm.rplus rnorm robust robustness robustnessInCompositions robustness rplus rplus rplus-class rplus-class rpois.ccomp rpois rPortionMahalanobis rmahalanobis Rsquare R2 runif.acomp runif runif.rcomp runif sa.dirichlet SimulatedAmounts sa.dirichlet.dil SimulatedAmounts sa.dirichlet.mix SimulatedAmounts sa.dirichlet5 SimulatedAmounts sa.dirichlet5.dil SimulatedAmounts sa.dirichlet5.mix SimulatedAmounts sa.groups SimulatedAmounts sa.groups.area SimulatedAmounts sa.groups.dil SimulatedAmounts sa.groups.mix SimulatedAmounts sa.groups5 SimulatedAmounts sa.groups5.area SimulatedAmounts sa.groups5.dil SimulatedAmounts sa.groups5.mix SimulatedAmounts sa.lognormals SimulatedAmounts sa.lognormals.dil SimulatedAmounts sa.lognormals.mix SimulatedAmounts sa.lognormals5 SimulatedAmounts sa.lognormals5.dil SimulatedAmounts sa.lognormals5.mix SimulatedAmounts sa.missings SimulatedAmounts sa.missings5 SimulatedAmounts sa.outliers1 SimulatedAmounts sa.outliers2 SimulatedAmounts sa.outliers3 SimulatedAmounts sa.outliers4 SimulatedAmounts sa.outliers5 SimulatedAmounts sa.outliers6 SimulatedAmounts sa.tnormals SimulatedAmounts sa.tnormals.dil SimulatedAmounts sa.tnormals.mix SimulatedAmounts sa.tnormals5 SimulatedAmounts sa.tnormals5.dil SimulatedAmounts sa.tnormals5.mix SimulatedAmounts sa.uniform SimulatedAmounts sa.uniform.dil SimulatedAmounts sa.uniform.mix SimulatedAmounts sa.uniform5 SimulatedAmounts sa.uniform5.dil SimulatedAmounts sa.uniform5.mix SimulatedAmounts scalar scalar scalar.default scalar scale scale scale.acomp scale scale.aplus scale scale.default scale scale.rcomp scale scale.rmult scale scale.rplus scale Sediments Sediments segments segments segments.acomp segments segments.aplus segments segments.default segments segments.rcomp segments segments.rmult segments segments.rplus segments SerumProtein SerumProtein setStickyClassOption subsetting ShiftOperators ShiftOperators simpleMissingSubplot simplemissingplot SimulatedAmounts SimulatedAmounts simulateMissings simulatemissing Skulls Skulls SkyeAFM SkyeAFM split.acomp split split.aplus split split.ccomp split split.rcomp split split.rmult split split.rplus split straight straight straight.acomp straight straight.aplus straight straight.rcomp straight straight.rmult straight straight.rplus straight summary.acomp summaryAcomp summary.aplus summaryAplus summary.rcomp summaryRcomp summary.rmult summaryAplus summary.rplus summaryAplus sumMissingProjector sumprojector sumMissingProjector.acomp sumprojector sumMissingProjector.aplus sumprojector sumMissingProjector.rcomp sumprojector sumMissingProjector.rmult sumprojector sumMissingProjector.rplus sumprojector Supervisor Supervisor SZ compmiss SZvalue compmiss ternaryAxis ternaryAxis totals totals totals.acomp totals totals.aplus totals totals.ccomp totals totals.rcomp totals totals.rplus totals tryDebugger tryDebugger uciptInv ipt ult ult ultInv ult unbinary binary var varAcomp var.acomp varAcomp var.aplus varAcomp var.default varAcomp var.lm varmlm var.mlm varmlm var.rcomp varAcomp var.rmult varAcomp var.rplus varAcomp variation variation variation.acomp variation variation.aplus variation variation.default variation variation.rcomp variation variation.rmult variation variation.rplus variation variation2clrvar clr2ilr vcovAcomp vcovAcomp vgmFit vgmFit vgmFit2lrv vgmFit vgmGetParameters vgmFit vgmGof vgmFit vgmSetParameters vgmFit vgram.cardsin variograms vgram.exp variograms vgram.gauss variograms vgram.lin variograms vgram.nugget variograms vgram.pow variograms vgram.sph variograms vgram2lrvgram lrvgram vp.boxplot boxplot vp.diffdensityplot panelAcomp vp.kde2dplot panelAcomp vp.logboxplot boxplot vp.lrboxplot panelAcomp vp.lrdensityplot panelAcomp vp.qqnorm qqnorm whichBits binary WhiteCells WhiteCells Yatquat Yatquat zeroreplace zeroreplace [.acomp subsetting [.aplus subsetting [.ccomp subsetting [.rcomp subsetting [.rmult subsetting [.rplus subsetting