Package: compositions 2.0-8

K. Gerald van den Boogaart

compositions: Compositional Data Analysis

Provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.

Authors:K. Gerald van den Boogaart <[email protected]>, Raimon Tolosana-Delgado, Matevz Bren

compositions_2.0-8.tar.gz
compositions_2.0-8.tar.gz(r-4.5-noble)compositions_2.0-8.tar.gz(r-4.4-noble)
compositions_2.0-8.tgz(r-4.4-emscripten)compositions_2.0-8.tgz(r-4.3-emscripten)
compositions.pdf |compositions.html✨
compositions/json (API)

# Install 'compositions' in R:
install.packages('compositions', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openblas– Optimized BLAS
Datasets:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

556 exports 1 stars 5.39 score 7 dependencies 30 dependents 39 mentions 1.6k scripts 6.3k downloads

Last updated 8 months agofrom:1849b8d73f. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 01 2024
R-4.5-linux-x86_64NOTESep 01 2024

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Dependencies:bayesmDEoptimRMASSRcppRcppArmadillorobustbasetensorA

'compositions' v2.0: R classes for compositional analysis

Rendered fromcompositions_v2.Rmdusingknitr::rmarkdownon Sep 01 2024.

Last update: 2023-04-13
Started: 2020-07-14

Using Animal

Rendered fromUsingCompositions.rnwusingutils::Sweaveon Sep 01 2024.

Last update: 2023-02-04
Started: 2018-06-14

Readme and manuals

Help Manual

Help pageTopics
Compositional Data Analysiscompositions-package compositions
Composition of glaciar sediments from the Aar massif (Switzerland)Aar
Aitchison compositionsacomp
Class '"acomp"'acomp-class coerce,acomp,data.frame-method coerce,acomp,structure-method coerce<-,acomp,data.frame-method
Power transform in the simplex*.acomp /.acomp power.acomp
Marginal compositions in Aitchison Compositionsacompmargin
inner product for datasets with a vector space structure%*%.acomp %*%.aplus
Activity patterns of a statistician for 20 daysActivity10 DATA10
Activity patterns of a statistician for 20 daysActivity31 DATA31
Additive log ratio transformalr alrInv
Class '"amounts"'amounts-class
Animal and vegetation measurementAnimalVegetation Data25
Amounts analysed in log-scaleaplus
Class '"aplus"'aplus-class coerce,aplus,data.frame-method coerce,aplus,structure-method coerce<-,aplus,data.frame-method
vectorial arithmetic for data sets with aplus class*.aplus +.aplus -.aplus /.aplus perturbe.aplus power.aplus
Additive planar transformapt aptInv
Artic lake sediment samples of different water depthArcticLake Data05
arrows in 3D, based on package rglarrows3D arrows3D.default
Convert "compositions" classes to data frames or matricesas.data.frame.acomp as.data.frame.aplus as.data.frame.ccomp as.data.frame.rcomp as.data.frame.rmult as.data.frame.rplus as.matrix.rmult
Drawing a 3D coordiante system to a plot, based on package rglaxis3D
Automatic common backtransformation for compositionsbacktransform backtransform.rmult gsi.getV gsi.orig
Compute balances for a compositional dataset.balance balance.acomp balance.aplus balance.rcomp balance.rplus balance01 balance01.acomp balance01.rcomp balanceBase balanceBase.acomp balanceBase.aplus balanceBase.rcomp balanceBase.rplus
Bar charts of amountsbarplot.acomp barplot.aplus barplot.ccomp barplot.rcomp barplot.rplus
Permeabilities of bayesiteBayesite Data21
Treating binary and g-adic numbersbinary binary2logical bit bit.character bit.numeric bit<- bit<-.character bit<-.numeric bitCount gadic gsi.orSum maxBit maxBit.character maxBit.numeric unbinary whichBits
Three-dimensional biplots, based on package rglbiplot3D biplot3D.default biplot3D.princomp
Blood samplesBlood23 Data23
Compositions and depth of 25 specimens of boxiteBoxite Data03
Displaying compositions and amounts with box-plotsboxplot.acomp boxplot.aplus boxplot.rcomp boxplot.rplus vp.boxplot vp.logboxplot
Count compositionsccomp
Class '"ccomp"'ccomp-class coerce,ccomp,data.frame-method coerce,ccomp,structure-method coerce<-,ccomp,data.frame-method
Compositional Goodness of fit testccompMultinomialGOF.test ccompPoissonGOF.test PoissonGOF.test
Centered default transformcdt cdt.acomp cdt.aplus cdt.ccomp cdt.data.frame cdt.default cdt.factor cdt.rcomp cdt.rmult cdt.rplus cdtInv cdtInv.acomp cdtInv.aplus cdtInv.ccomp cdtInv.data.frame cdtInv.default cdtInv.factor cdtInv.rcomp cdtInv.rmult cdtInv.rplus
Color-size compositions of 20 clam colonies from East BayClamEast Data14
Color-size compositions of 20 clam colonies from West BayClamWest Data15
Closure of a compositionclo
Centered log ratio transformclr clrInv
Convert between clr and ilr, and between cpt and ipt.clr2ilr clrvar2ilr clrvar2variation ilr2clr ilrvar2clr is.clrvar is.ilrvar variation2clrvar
Heuristics to find subpopulations of outliersClusterFinder1 ClusterFinder1.acomp
Dendrogram representation of acomp or rcomp objectsCoDaDendrogram
A biplot providing somewhat easier access to details of the plot.coloredBiplot coloredBiplot.default coloredBiplot.prcomp coloredBiplot.princomp
Create a color/char palette or for groups of outlierscolorsForOutliers1 colorsForOutliers2 pchForOutliers1
Compositional Linear Model of CoregionalisationCompLinModCoReg
Compositional Ordinary KrigingcompOKriging
Class '"compositional"'compositional-class
Helper to compute confidence ellipsoidsConfRadius
Correlations of amounts and compositionscor cor.acomp cor.aplus cor.default cor.rcomp cor.rmult cor.rplus
Compositions, depths and porosities of 25 specimens of coxiteCoxite Data04
Centered planar transformcpt cptInv
Diagnostic probabilitiesData17 DiagnosticProb
Distances in variouse approachesdist dist.default
Draw ellipsesellipses ellipses.acomp ellipses.aplus ellipses.rcomp ellipses.rmult ellipses.rplus
Recast amounts as mixtures of end-membersendmemberCoordinates endmemberCoordinates.acomp endmemberCoordinates.aplus endmemberCoordinates.default endmemberCoordinates.rplus endmemberCoordinatesInv endmemberCoordinatesInv.acomp endmemberCoordinatesInv.aplus endmemberCoordinatesInv.rcomp endmemberCoordinatesInv.rmult endmemberCoordinatesInv.rplus
Firework mixturesData13 Firework
Fitting a Dirichlet distributionfitDirichlet
Fit Same Mean Different Variance ModelfitSameMeanDifferentVarianceModel
Classical Gauss TestGauss.test
The geometric meangeometricmean geometricmeanCol geometricmeanRow gsi.geometricmean gsi.geometricmean.Col gsi.geometricmean.Row gsi.geometricmeanCol gsi.geometricmeanRow
Gets the detection limit stored in the data setgetDetectionlimit
Compositions and total pebble counts of 92 glacial tillsDATA18 Glacial
Compositional Goodness of fit testacompGOF.test acompGOF.test.formula acompGOF.test.list acompNormalGOF.test acompTwoSampleGOF.test gsi.acompUniformityGOF.test
Group amounts of partsgroupparts groupparts.acomp groupparts.aplus groupparts.ccomp groupparts.rcomp groupparts.rplus
Compositions of 25 specimens of hongiteData01 Hongite
Hotellings T square distributionpHotellingsTsq qHotellingsTsq
Household ExpendituresDATA08 HEMF HouseholdExp
Hydrochemical composition data set of Llobregat river basin water (NE Spain)Hydrochem
Isometric default transformidt 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
Isometric identity transformiit iitInv
Isometric log ratio transformilr ilrInv
The canonical basis in the clr plane used for ilr and ipt transforms.ilrBase ilrBaseList
Isometric log transformilt iltInv
Isometric planar transformipt iptInv uciptInv
Check for compositional data typeis.acomp is.aplus is.ccomp is.rcomp is.rmult is.rplus
Checking for outliersIsMahalanobisOutlier
Isoportion- and Isoproportion-linesisoPortionLines isoPortionLines.acomp isoPortionLines.rcomp isoProportionLines isoProportionLines.acomp isoProportionLines.rcomp
The jura datasetjura259 juraset
Density estimation on the simplex with Dirichlet kernelkdeDirichlet
Ploting composition into rotable tetrahedronkingTetrahedron
Compositions of 25 specimens of kongiteData02 Kongite
Draws connected lines from point to point.lines.acomp lines.aplus lines.rcomp lines.rmult lines.rplus
Empirical variograms for compositionslogratioVariogram logratioVariogram.acomp
vgram2lrvgramcgram2vgram vgram2lrvgram
Compute Mahalanobis distances based von robust EstimationsMahalanobisDist MahalanobisDist.acomp MahalanobisDist.aplus MahalanobisDist.rcomp MahalanobisDist.rmult MahalanobisDist.rplus
inner product for matrices and vectors%*% %*%.default
Mean amounts and mean compositionsmean.acomp mean.aplus mean.ccomp mean.rcomp mean.rmult mean.rplus
The arithmetic mean of rows or columnsmean.col mean.row meanCol meanRow
Steroid metabolite patterns in adults and childrenData09 Metabolites
The policy of treatment of missing values in the "compositions" packageBDL 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
Returns a projector the the observed space in case of missings.missingProjector missingProjector.acomp missingProjector.aplus missingProjector.rcomp missingProjector.rmult missingProjector.rplus
Classify and summarize missing values in a datasetmissingSummary missingType
Reads a data file in a mixR formatmix.Read
Metric summary statistics of real, amount or compositional datamcor mcor.default mcov mcov.default msd msd.default mvar mvar.default
The names of the partsnames.acomp names.aplus names.ccomp names.rcomp names.rmult names.rplus names<-.acomp names<-.aplus names<-.ccomp names<-.rcomp names<-.rmult names<-.rplus
Vector space normnorm norm.acomp norm.aplus norm.default norm.matrix norm.rcomp norm.rmult norm.rplus
Normalize vectors to norm 1normalize normalize.default
Compositional Goodness of fit testacompNormalLocation.test
Treating single compositions as one-row datasetsoneOrDataset
Detect and classify compositional outliers.OutlierClassifier1 OutlierClassifier1.acomp
Plot various graphics to analyse outliers.outlierplot outlierplot.acomp
Analysing outliers in compositions.outliersInCompositions
Pairs plot method for compositionspairs.acomp pairs.rcomp vp.diffdensityplot vp.kde2dplot vp.lrboxplot vp.lrdensityplot
Creates a paneled plot like pairs for two different datasets.pairwisePlot pairwisePlot.default
Unique parametrisations for matrices.parameterPosdefClrMat parameterPosdefMat parameterRank1ClrMat parameterRank1Mat parametricPosdefClrMat parametricPosdefMat parametricRank1ClrMat parametricRank1Mat
Perturbation of compositions+.acomp -.acomp perturbe
Ternary diagramsplot.acomp plot.ccomp plot.rcomp
Displaying amounts in scatterplotsplot.aplus plot.rmult plot.rplus
plot in 3D based on rglplot3D plot3D.default
3D-plot of compositional dataplot3D.acomp plot3D.rcomp
3D-plot of positive dataplot3D.aplus
plot in 3D based on rglplot3D.rmult
plot in 3D based on rglplot3D.rplus
Empirical variograms for compositionsplot.logratioVariogram
Plot a Missing Summaryas.missingSummary plot.missingSummary
Honk Kong Pogo-Jumps ChampionshipData19 PogoJump
power transform of a matrixpowerofpsdmatrix
Principal component analysis for Aitchison compositionsplot.princomp.acomp predict.princomp.acomp princomp.acomp print.princomp.acomp
Principal component analysis for amounts in log geometryplot.princomp.aplus predict.princomp.aplus princomp.aplus print.princomp.aplus
Principal component analysis for real compositionsplot.princomp.rcomp predict.princomp.rcomp princomp.rcomp print.princomp.rcomp
Principal component analysis for real dataprincomp.rmult
Principal component analysis for real amountsplot.princomp.rplus predict.princomp.rplus princomp.rplus print.princomp.rplus
Printing compositional data.print.acomp print.aplus print.rcomp print.rplus
Pairwise log ratio transformpwlr pwlrInv
Plots of pairwise logratio against a covariable.pwlrPlot pwlrplot
Normal quantile plots for compositions and amountsqqnorm.acomp qqnorm.aplus qqnorm.rcomp qqnorm.rplus vp.qqnorm
R squareR2 R2.default R2.lm Rsquare
Aitchison DistributionAitchisonDistributionIntegrals dAitchison rAitchison
Loadings of relations of two amountsplot.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
Compositions as elements of the simplex embedded in the D-dimensional real spacercomp
Class '"rcomp"'coerce,rcomp,data.frame-method coerce,rcomp,structure-method coerce<-,rcomp,data.frame-method rcomp-class
Arithmetic operations for compositions in a real geometry*.rcomp +.rcomp -.rcomp /.rcomp convex.rcomp
Marginal compositions in real geometryrcompmargin
Dirichlet distributiondDirichlet rDirichlet rDirichlet.acomp rDirichlet.rcomp
Reads a data file in a geoeas formatread.geoEAS read.geoeas
Modify parameters of compositional plots.noreplot replot replotable
The multivariate lognormal distributiondlnorm.rplus rlnorm.rplus
Compute distributions of empirical Mahalanobis distances based on simulationsgsi.pStore pEmpiricalMahalanobis pMaxMahalanobis pPortionMahalanobis pQuantileMahalanobis qEmpiricalMahalanobis qMaxMahalanobis qPortionMahalanobis rEmpiricalMahalanobis rMaxMahalanobis rPortionMahalanobis
Simple treatment of real vectorsprint.rmult rmult
Class '"rmult"'coerce,rmult,data.frame-method coerce,rmult,structure-method coerce<-,rmult,data.frame-method rmult-class
vectorial arithmetic for datasets in a classical vector scale*.rmult +.rmult -.rmult /.rmult
inner product for datasets with vector scale%*%.rmult
Normal distributions on special spacesdnorm.acomp dnorm.aplus dnorm.rmult rnorm.acomp rnorm.aplus rnorm.ccomp rnorm.rcomp rnorm.rmult rnorm.rplus
Handling robustness issues and outliers in compositions.robust robustnessInCompositions
Amounts i.e. positive numbers analysed as objects of the real vector spacerplus
Class '"rplus"'coerce,rplus,data.frame-method coerce,rplus,structure-method coerce<-,rplus,data.frame-method rplus-class
vectorial arithmetic for data sets with rplus class*.rplus +.rplus -.rplus /.rplus mul.rplus
Simulate count compositions without overdispersionrmultinom.ccomp rpois.ccomp
The uniform distribution on the simplexrunif.acomp runif.rcomp
Parallel scalar productsscalar scalar.default
Normalizing datasets by centering and scalingscale scale.acomp scale.aplus scale.default scale.rcomp scale.rmult scale.rplus
Proportions of sand, silt and clay in sediments specimensData20 Sediments
Draws straight lines from point to point.segments segments.acomp segments.aplus segments.default segments.rcomp segments.rmult segments.rplus
Serum Protein compositions of blood samplesData16 SerumProtein
Shifts of machine operatorsData22 ShiftOperators
Ternary diagramssimpleMissingSubplot
Simulated amount datasetssa.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
Artifical simulation of various kinds of missings/polluted dataobserveWithAdditiveError observeWithDetectionLimit observeWithDetectionlimit simulateMissings
Measurement of skullsData24 Skulls
AFM compositions of 23 aphyric Skye lavasData06 SkyeAFM
Splitting datasets in groups given by factorssplit.acomp split.aplus split.ccomp split.rcomp split.rmult split.rplus
Draws straight lines.straight straight.acomp straight.aplus straight.rcomp straight.rmult straight.rplus
Subsetting of compositions$.acomp $.aplus $.ccomp $.rcomp $.rmult $.rplus getStickyClassOption setStickyClassOption [.acomp [.aplus [.ccomp [.rcomp [.rmult [.rplus
Summarizing a compositional dataset in terms of ratiossummary.acomp
Summaries of amountssummary.aplus summary.rmult summary.rplus
Summary of compositions in real geometrysummary.rcomp
Compute the global projector to the observed subspace.sumMissingProjector sumMissingProjector.acomp sumMissingProjector.aplus sumMissingProjector.rcomp sumMissingProjector.rmult sumMissingProjector.rplus
Proportions of supervisor's statements assigned to different categoriesData07 Supervisor
Axis for ternary diagramsternaryAxis
Total sum of amountstotals totals.acomp totals.aplus totals.ccomp totals.rcomp totals.rplus
Transformations from 'mixtures' to 'compositions' classesmix.2acomp mix.2aplus mix.2rcomp mix.2rmult mix.2rplus
Empirical variograms for compositionstryDebugger
Uncentered log transformKappa ult ultInv
Variances and covariances of amounts and compositionscov 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
Variation matrices of amounts and compositionsis.variation variation variation.acomp variation.aplus variation.default variation.rcomp variation.rmult variation.rplus
Variogram functionsvgram.cardsin vgram.exp vgram.gauss vgram.lin vgram.nugget vgram.pow vgram.sph
Residual variance of a modelvar.lm var.mlm
Variance covariance matrix of parameters in compositional regressionvcovAcomp
Compositional variogram model fittingfit.lmc fit.lmc.logratioVariogram vgmFit vgmFit2lrv vgmGetParameters vgmGof vgmSetParameters
White-cell composition of 30 blood samples by two different methodsData11 WhiteCells
Standard R functions wrapped for compatibilityanova
Yatquat fruit evaluationData12 Yatquat
Zero-replacement routinezeroreplace