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compositions (version 2.0-9)

Compositional Data Analysis

Description

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.

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Install

install.packages('compositions')

Monthly Downloads

10,007

Version

2.0-9

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

August 21st, 2025

Functions in compositions (2.0-9)

Firework mixtures

Diagnostic probabilities

Hotellings T square distribution

Compositions and total pebble counts of 92 glacial tills

Compositions, depths and porosities of 25 specimens of coxite

Household Expenditures

Hydrochemical composition data set of Llobregat river basin water (NE Spain)

Compositions of 25 specimens of hongite

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Helper to compute confidence ellipsoids

Proportions of sand, silt and clay in sediments specimens

Steroid metabolite patterns in adults and children

Honk Kong Pogo-Jumps Championship

AFM compositions of 23 aphyric Skye lavas

Serum Protein compositions of blood samples

Measurement of skulls

Compositions of 25 specimens of kongite

Shifts of machine operators

SimulatedAmounts

Simulated amount datasets

Power transform in the simplex

Proportions of supervisor's statements assigned to different categories

White-cell composition of 30 blood samples by two different methods

Marginal compositions in Aitchison Compositions

Class "acomp"

Yatquat fruit evaluation

Aitchison compositions

Class "amounts"

Additive log ratio transform

Class "aplus"

arrows in 3D, based on package rgl

Treating binary and g-adic numbers

Bar charts of amounts

Amounts analysed in log-scale

Drawing a 3D coordiante system to a plot, based on package rgl

vectorial arithmetic for data sets with aplus class

Compute balances for a compositional dataset.

Centered default transform

Convert between clr and ilr, and between cpt and ipt.

Additive planar transform

Automatic common backtransformation for compositions

Count compositions

Convert "compositions" classes to data frames or matrices

Three-dimensional biplots, based on package rgl

Heuristics to find subpopulations of outliers

Displaying compositions and amounts with box-plots

Closure of a composition

Centered log ratio transform

Class "ccomp"

Compositional Goodness of fit test

compositional-class

Class "compositional"

A biplot providing somewhat easier access to details of the plot.

colorsForOutliers

Create a color/char palette or for groups of outliers

Centered planar transform

Dendrogram representation of acomp or rcomp objects

compositions-package

tools:::Rd_package_title("compositions")

missing.compositions

The policy of treatment of missing values in the "compositions" package

Compositional Ordinary Kriging

Distances in variouse approaches

Correlations of amounts and compositions

endmemberCoordinates

Recast amounts as mixtures of end-members

Classical Gauss Test

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

Group amounts of parts

Internal functions of the compositions package

Internal functions of the compositions package

gsi.isSingleRow

Internal function: Can something be considered as a single multivariate data item?

Internal functions: A conditional drop

Internal functions of the compositions package

Fitting a Dirichlet distribution

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

gsi.expandrcomp

Internal function: Scaling rcomp

Compositional Goodness of fit test

Internal function: Compute a desired compositional margin

Interal function: Get number of samples and number of parts in a compositional object

Environment containing the old gsi functions

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

gsigetBalStruct

An auxiliary functions to compute user-defined ilr and ipt transforms.

Internal functions: Storing integers as reals

The canonical basis in the clr plane used for ilr and ipt transforms.

gsi.merge2signary

Auxiliary functions to compute user-defined ilr and ipt transforms.

The geometric mean

Internal functions: Parallel operations of single and multiple datasets

getdetectionlimit

Gets the detection limit stored in the data set

Calling from a function with the own parameters

Internal function: Invert a permutation

Internal function: row and column sums of matrices

Internal function: give a derived subclass to an object

Internal function: Checking equality of IEEE special numbers

Internal function: Reshape an object to the shape type of another

Internal functions of the compositions package

Internal functions of the compositions package

Internal function: Recode missings with IEEE number and vice versa

Internal function: Convert to plain vector or matrix

Internal functions of the compositions package

Internal functions of the compositions package

Internal function: A panel displaying a label only

Internal functions of the compositions package

Internal function: Solves singular and non square equation systems

The canonical basis in the clr plane used for ilr and ipt transforms.

gsi.varwithlosts

Internal function: computes variance of compositional data set with missing/zero values

Isometric planar transform

Isometric default transform

IsMahalanobisOutlier

Checking for outliers

Isometric log ratio transform

Isometric identity transform

Check for compositional data type

isoPortionLines

Isoportion- and Isoproportion-lines

Isometric log transform

Density estimation on the simplex with Dirichlet kernel

Mean amounts and mean compositions

The jura dataset

kingTetrahedron

Ploting composition into rotable tetrahedron

acompscalarproduct

inner product for datasets with a vector space structure

inner product for matrices and vectors

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

logratioVariogram

Empirical variograms for compositions

Draws connected lines from point to point.

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

missingProjector

Returns a projector the the observed space in case of missings.

Reads a data file in a mixR format

Treating single compositions as one-row datasets

Normalize vectors to norm 1

The arithmetic mean of rows or columns

Classify and summarize missing values in a dataset

Vector space norm

Metric summary statistics of real, amount or compositional data

The names of the parts

outliersInCompositions

Analysing outliers in compositions.

outlierclassifier

Detect and classify compositional outliers.

plot in 3D based on rgl

Perturbation of compositions

Plot various graphics to analyse outliers.

Unique parametrisations for matrices.

Creates a paneled plot like pairs for two different datasets.

Pairs plot method for compositions

Ternary diagrams

3D-plot of compositional data

plotmissingsummary

Plot a Missing Summary

plotlogratioVariogram

Empirical variograms for compositions

plot in 3D based on rgl

powerofpsdmatrix

power transform of a matrix

plot in 3D based on rgl

Displaying amounts in scatterplots

3D-plot of positive data

Principal component analysis for amounts in log geometry

Principal component analysis for real compositions

Principal component analysis for Aitchison compositions

Normal quantile plots for compositions and amounts

Class "rcomp"

Loadings of relations of two amounts

Principal component analysis for real amounts

Principal component analysis for real data

Pairwise log ratio transform

Dirichlet distribution

Printing compositional data.

Aitchison Distribution

Plots of pairwise logratio against a covariable.

Marginal compositions in real geometry

vectorial arithmetic for datasets in a classical vector scale

Modify parameters of compositional plots.

Compositions as elements of the simplex embedded in the D-dimensional real space

Read standard data files

Reads a data file in a geoeas format

Arithmetic operations for compositions in a real geometry

The multivariate lognormal distribution

Simple treatment of real vectors

Compute distributions of empirical Mahalanobis distances based on simulations

Class "rmult"

The uniform distribution on the simplex

Class "rplus"

Normal distributions on special spaces

Amounts i.e. positive numbers analysed as objects of the real vector space

inner product for datasets with vector scale

Normalizing datasets by centering and scaling

Parallel scalar products

Simulate count compositions without overdispersion

robustnessInCompositions

Handling robustness issues and outliers in compositions.

vectorial arithmetic for data sets with rplus class

Compute the global projector to the observed subspace.

Summary of compositions in real geometry

simplemissingplot

Ternary diagrams

Draws straight lines.

simulatemissings

Artifical simulation of various kinds of missings/polluted data

Splitting datasets in groups given by factors

Draws straight lines from point to point.

Summaries of amounts

Subsetting of compositions

Summarizing a compositional dataset in terms of ratios

Axis for ternary diagrams

Compositional Goodness of fit test

Variogram functions

Uncentered log transform

Variance covariance matrix of parameters in compositional regression

Variation matrices of amounts and compositions

Variances and covariances of amounts and compositions

Residual variance of a model

Total sum of amounts

Empirical variograms for compositions

wrapped_functions

Standard R functions wrapped for compatibility

Compositional variogram model fitting

Zero-replacement routine

Artic lake sediment samples of different water depth

Activity patterns of a statistician for 20 days

Composition of glaciar sediments from the Aar massif (Switzerland)

Activity patterns of a statistician for 20 days

Permeabilities of bayesite

Color-size compositions of 20 clam colonies from East Bay

Color-size compositions of 20 clam colonies from West Bay

Compositions and depth of 25 specimens of boxite

AnimalVegetation

Animal and vegetation measurement