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:
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')) |
- Aar - Composition of glaciar sediments from the Aar massif
- Activity10 - Activity patterns of a statistician for 20 days
- Activity31 - Activity patterns of a statistician for 20 days
- AnimalVegetation - Animal and vegetation measurement
- ArcticLake - Artic lake sediment samples of different water depth
- Bayesite - Permeabilities of bayesite
- Blood23 - Blood samples
- Boxite - Compositions and depth of 25 specimens of boxite
- ClamEast - Color-size compositions of 20 clam colonies from East Bay
- ClamWest - Color-size compositions of 20 clam colonies from West Bay
- Coxite - Compositions, depths and porosities of 25 specimens of coxite
- DiagnosticProb - Diagnostic probabilities
- Firework - Firework mixtures
- Glacial - Compositions and total pebble counts of 92 glacial tills
- Hongite - Compositions of 25 specimens of hongite
- HouseholdExp - Household Expenditures
- Hydrochem - Hydrochemical composition data set of Llobregat river basin water
- Kongite - Compositions of 25 specimens of kongite
- Metabolites - Steroid metabolite patterns in adults and children
- PogoJump - Honk Kong Pogo-Jumps Championship
- Sediments - Proportions of sand, silt and clay in sediments specimens
- SerumProtein - Serum Protein compositions of blood samples
- ShiftOperators - Shifts of machine operators
- Skulls - Measurement of skulls
- SkyeAFM - AFM compositions of 23 aphyric Skye lavas
- Supervisor - Proportions of supervisor's statements assigned to different categories
- WhiteCells - White-cell composition of 30 blood samples by two different methods
- Yatquat - Yatquat fruit evaluation
- jura259 - The jura dataset
- juraset - The jura dataset
- sa.dirichlet - Simulated amount datasets
- sa.dirichlet.dil - Simulated amount datasets
- sa.dirichlet.mix - Simulated amount datasets
- sa.dirichlet5 - Simulated amount datasets
- sa.dirichlet5.dil - Simulated amount datasets
- sa.dirichlet5.mix - Simulated amount datasets
- sa.groups - Simulated amount datasets
- sa.groups.area - Simulated amount datasets
- sa.groups.dil - Simulated amount datasets
- sa.groups.mix - Simulated amount datasets
- sa.groups5 - Simulated amount datasets
- sa.groups5.area - Simulated amount datasets
- sa.groups5.dil - Simulated amount datasets
- sa.groups5.mix - Simulated amount datasets
- sa.lognormals - Simulated amount datasets
- sa.lognormals.dil - Simulated amount datasets
- sa.lognormals.mix - Simulated amount datasets
- sa.lognormals5 - Simulated amount datasets
- sa.lognormals5.dil - Simulated amount datasets
- sa.lognormals5.mix - Simulated amount datasets
- sa.missings - Simulated amount datasets
- sa.missings5 - Simulated amount datasets
- sa.outliers1 - Simulated amount datasets
- sa.outliers2 - Simulated amount datasets
- sa.outliers3 - Simulated amount datasets
- sa.outliers4 - Simulated amount datasets
- sa.outliers5 - Simulated amount datasets
- sa.outliers6 - Simulated amount datasets
- sa.tnormals - Simulated amount datasets
- sa.tnormals.dil - Simulated amount datasets
- sa.tnormals.mix - Simulated amount datasets
- sa.tnormals5 - Simulated amount datasets
- sa.tnormals5.dil - Simulated amount datasets
- sa.tnormals5.mix - Simulated amount datasets
- sa.uniform - Simulated amount datasets
- sa.uniform.dil - Simulated amount datasets
- sa.uniform.mix - Simulated amount datasets
- sa.uniform5 - Simulated amount datasets
- sa.uniform5.dil - Simulated amount datasets
- sa.uniform5.mix - Simulated amount datasets
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 11 months agofrom:1849b8d73f. Checks:OK: 1 NOTE: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 13 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 13 2024 |
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Dependencies:bayesmDEoptimRMASSRcppRcppArmadillorobustbasetensorA
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compositional Data Analysis | compositions-package compositions |
| Composition of glaciar sediments from the Aar massif (Switzerland) | Aar |
| Aitchison compositions | acomp |
| 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 Compositions | acompmargin |
| inner product for datasets with a vector space structure | %*%.acomp %*%.aplus |
| Activity patterns of a statistician for 20 days | Activity10 DATA10 |
| Activity patterns of a statistician for 20 days | Activity31 DATA31 |
| Additive log ratio transform | alr alrInv |
| Class '"amounts"' | amounts-class |
| Animal and vegetation measurement | AnimalVegetation Data25 |
| Amounts analysed in log-scale | aplus |
| 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 transform | apt aptInv |
| Artic lake sediment samples of different water depth | ArcticLake Data05 |
| arrows in 3D, based on package rgl | arrows3D arrows3D.default |
| Convert "compositions" classes to data frames or matrices | as.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 rgl | axis3D |
| Automatic common backtransformation for compositions | backtransform 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 amounts | barplot.acomp barplot.aplus barplot.ccomp barplot.rcomp barplot.rplus |
| Permeabilities of bayesite | Bayesite Data21 |
| Treating binary and g-adic numbers | binary 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 rgl | biplot3D biplot3D.default biplot3D.princomp |
| Blood samples | Blood23 Data23 |
| Compositions and depth of 25 specimens of boxite | Boxite Data03 |
| Displaying compositions and amounts with box-plots | boxplot.acomp boxplot.aplus boxplot.rcomp boxplot.rplus vp.boxplot vp.logboxplot |
| Count compositions | ccomp |
| Class '"ccomp"' | ccomp-class coerce,ccomp,data.frame-method coerce,ccomp,structure-method coerce<-,ccomp,data.frame-method |
| Compositional Goodness of fit test | ccompMultinomialGOF.test ccompPoissonGOF.test PoissonGOF.test |
| Centered default transform | cdt 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 Bay | ClamEast Data14 |
| Color-size compositions of 20 clam colonies from West Bay | ClamWest Data15 |
| Closure of a composition | clo |
| Centered log ratio transform | clr 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 outliers | ClusterFinder1 ClusterFinder1.acomp |
| Dendrogram representation of acomp or rcomp objects | CoDaDendrogram |
| 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 outliers | colorsForOutliers1 colorsForOutliers2 pchForOutliers1 |
| Compositional Linear Model of Coregionalisation | CompLinModCoReg |
| Compositional Ordinary Kriging | compOKriging |
| Class '"compositional"' | compositional-class |
| Helper to compute confidence ellipsoids | ConfRadius |
| Correlations of amounts and compositions | cor cor.acomp cor.aplus cor.default cor.rcomp cor.rmult cor.rplus |
| Compositions, depths and porosities of 25 specimens of coxite | Coxite Data04 |
| Centered planar transform | cpt cptInv |
| Diagnostic probabilities | Data17 DiagnosticProb |
| Distances in variouse approaches | dist dist.default |
| Draw ellipses | ellipses ellipses.acomp ellipses.aplus ellipses.rcomp ellipses.rmult ellipses.rplus |
| Recast amounts as mixtures of end-members | endmemberCoordinates endmemberCoordinates.acomp endmemberCoordinates.aplus endmemberCoordinates.default endmemberCoordinates.rplus endmemberCoordinatesInv endmemberCoordinatesInv.acomp endmemberCoordinatesInv.aplus endmemberCoordinatesInv.rcomp endmemberCoordinatesInv.rmult endmemberCoordinatesInv.rplus |
| Firework mixtures | Data13 Firework |
| Fitting a Dirichlet distribution | fitDirichlet |
| Fit Same Mean Different Variance Model | fitSameMeanDifferentVarianceModel |
| Classical Gauss Test | Gauss.test |
| The geometric mean | geometricmean geometricmeanCol geometricmeanRow gsi.geometricmean gsi.geometricmean.Col gsi.geometricmean.Row gsi.geometricmeanCol gsi.geometricmeanRow |
| Gets the detection limit stored in the data set | getDetectionlimit |
| Compositions and total pebble counts of 92 glacial tills | DATA18 Glacial |
| Compositional Goodness of fit test | acompGOF.test acompGOF.test.formula acompGOF.test.list acompNormalGOF.test acompTwoSampleGOF.test gsi.acompUniformityGOF.test |
| Group amounts of parts | groupparts groupparts.acomp groupparts.aplus groupparts.ccomp groupparts.rcomp groupparts.rplus |
| Compositions of 25 specimens of hongite | Data01 Hongite |
| Hotellings T square distribution | pHotellingsTsq qHotellingsTsq |
| Household Expenditures | DATA08 HEMF HouseholdExp |
| Hydrochemical composition data set of Llobregat river basin water (NE Spain) | Hydrochem |
| Isometric default transform | 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 |
| Isometric identity transform | iit iitInv |
| Isometric log ratio transform | ilr ilrInv |
| The canonical basis in the clr plane used for ilr and ipt transforms. | ilrBase ilrBaseList |
| Isometric log transform | ilt iltInv |
| Isometric planar transform | ipt iptInv uciptInv |
| Check for compositional data type | is.acomp is.aplus is.ccomp is.rcomp is.rmult is.rplus |
| Checking for outliers | IsMahalanobisOutlier |
| Isoportion- and Isoproportion-lines | isoPortionLines isoPortionLines.acomp isoPortionLines.rcomp isoProportionLines isoProportionLines.acomp isoProportionLines.rcomp |
| The jura dataset | jura259 juraset |
| Density estimation on the simplex with Dirichlet kernel | kdeDirichlet |
| Ploting composition into rotable tetrahedron | kingTetrahedron |
| Compositions of 25 specimens of kongite | Data02 Kongite |
| Draws connected lines from point to point. | lines.acomp lines.aplus lines.rcomp lines.rmult lines.rplus |
| Empirical variograms for compositions | logratioVariogram logratioVariogram.acomp |
| vgram2lrvgram | cgram2vgram vgram2lrvgram |
| Compute Mahalanobis distances based von robust Estimations | MahalanobisDist MahalanobisDist.acomp MahalanobisDist.aplus MahalanobisDist.rcomp MahalanobisDist.rmult MahalanobisDist.rplus |
| inner product for matrices and vectors | %*% %*%.default |
| Mean amounts and mean compositions | mean.acomp mean.aplus mean.ccomp mean.rcomp mean.rmult mean.rplus |
| The arithmetic mean of rows or columns | mean.col mean.row meanCol meanRow |
| Steroid metabolite patterns in adults and children | Data09 Metabolites |
| The policy of treatment of missing values in the "compositions" package | 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 |
| 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 dataset | missingSummary missingType |
| Reads a data file in a mixR format | mix.Read |
| Metric summary statistics of real, amount or compositional data | mcor mcor.default mcov mcov.default msd msd.default mvar mvar.default |
| The names of the parts | names.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 norm | norm norm.acomp norm.aplus norm.default norm.matrix norm.rcomp norm.rmult norm.rplus |
| Normalize vectors to norm 1 | normalize normalize.default |
| Compositional Goodness of fit test | acompNormalLocation.test |
| Treating single compositions as one-row datasets | oneOrDataset |
| 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 compositions | pairs.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 diagrams | plot.acomp plot.ccomp plot.rcomp |
| Displaying amounts in scatterplots | plot.aplus plot.rmult plot.rplus |
| plot in 3D based on rgl | plot3D plot3D.default |
| 3D-plot of compositional data | plot3D.acomp plot3D.rcomp |
| 3D-plot of positive data | plot3D.aplus |
| plot in 3D based on rgl | plot3D.rmult |
| plot in 3D based on rgl | plot3D.rplus |
| Empirical variograms for compositions | plot.logratioVariogram |
| Plot a Missing Summary | as.missingSummary plot.missingSummary |
| Honk Kong Pogo-Jumps Championship | Data19 PogoJump |
| power transform of a matrix | powerofpsdmatrix |
| Principal component analysis for Aitchison compositions | plot.princomp.acomp predict.princomp.acomp princomp.acomp print.princomp.acomp |
| Principal component analysis for amounts in log geometry | plot.princomp.aplus predict.princomp.aplus princomp.aplus print.princomp.aplus |
| Principal component analysis for real compositions | plot.princomp.rcomp predict.princomp.rcomp princomp.rcomp print.princomp.rcomp |
| Principal component analysis for real data | princomp.rmult |
| Principal component analysis for real amounts | plot.princomp.rplus predict.princomp.rplus princomp.rplus print.princomp.rplus |
| Printing compositional data. | print.acomp print.aplus print.rcomp print.rplus |
| Pairwise log ratio transform | pwlr pwlrInv |
| Plots of pairwise logratio against a covariable. | pwlrPlot pwlrplot |
| Normal quantile plots for compositions and amounts | qqnorm.acomp qqnorm.aplus qqnorm.rcomp qqnorm.rplus vp.qqnorm |
| R square | R2 R2.default R2.lm Rsquare |
| Aitchison Distribution | AitchisonDistributionIntegrals dAitchison rAitchison |
| Loadings of relations of two amounts | 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 |
| Compositions as elements of the simplex embedded in the D-dimensional real space | rcomp |
| 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 geometry | rcompmargin |
| Dirichlet distribution | dDirichlet rDirichlet rDirichlet.acomp rDirichlet.rcomp |
| Reads a data file in a geoeas format | read.geoEAS read.geoeas |
| Modify parameters of compositional plots. | noreplot replot replotable |
| The multivariate lognormal distribution | dlnorm.rplus rlnorm.rplus |
| Compute distributions of empirical Mahalanobis distances based on simulations | gsi.pStore pEmpiricalMahalanobis pMaxMahalanobis pPortionMahalanobis pQuantileMahalanobis qEmpiricalMahalanobis qMaxMahalanobis qPortionMahalanobis rEmpiricalMahalanobis rMaxMahalanobis rPortionMahalanobis |
| Simple treatment of real vectors | print.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 spaces | dnorm.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 space | rplus |
| 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 overdispersion | rmultinom.ccomp rpois.ccomp |
| The uniform distribution on the simplex | runif.acomp runif.rcomp |
| Parallel scalar products | scalar scalar.default |
| Normalizing datasets by centering and scaling | scale scale.acomp scale.aplus scale.default scale.rcomp scale.rmult scale.rplus |
| Proportions of sand, silt and clay in sediments specimens | Data20 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 samples | Data16 SerumProtein |
| Shifts of machine operators | Data22 ShiftOperators |
| Ternary diagrams | simpleMissingSubplot |
| Simulated amount datasets | 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 |
| Artifical simulation of various kinds of missings/polluted data | observeWithAdditiveError observeWithDetectionLimit observeWithDetectionlimit simulateMissings |
| Measurement of skulls | Data24 Skulls |
| AFM compositions of 23 aphyric Skye lavas | Data06 SkyeAFM |
| Splitting datasets in groups given by factors | split.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 ratios | summary.acomp |
| Summaries of amounts | summary.aplus summary.rmult summary.rplus |
| Summary of compositions in real geometry | summary.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 categories | Data07 Supervisor |
| Axis for ternary diagrams | ternaryAxis |
| Total sum of amounts | totals totals.acomp totals.aplus totals.ccomp totals.rcomp totals.rplus |
| Transformations from 'mixtures' to 'compositions' classes | mix.2acomp mix.2aplus mix.2rcomp mix.2rmult mix.2rplus |
| Empirical variograms for compositions | tryDebugger |
| Uncentered log transform | Kappa ult ultInv |
| Variances and covariances of amounts and compositions | 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 |
| Variation matrices of amounts and compositions | is.variation variation variation.acomp variation.aplus variation.default variation.rcomp variation.rmult variation.rplus |
| Variogram functions | vgram.cardsin vgram.exp vgram.gauss vgram.lin vgram.nugget vgram.pow vgram.sph |
| Residual variance of a model | var.lm var.mlm |
| Variance covariance matrix of parameters in compositional regression | vcovAcomp |
| Compositional variogram model fitting | fit.lmc fit.lmc.logratioVariogram vgmFit vgmFit2lrv vgmGetParameters vgmGof vgmSetParameters |
| White-cell composition of 30 blood samples by two different methods | Data11 WhiteCells |
| Standard R functions wrapped for compatibility | anova |
| Yatquat fruit evaluation | Data12 Yatquat |
| Zero-replacement routine | zeroreplace |