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compositions (version 2.0-5)

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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Version

Install

install.packages('compositions')

Monthly Downloads

9,946

Version

2.0-5

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

February 4th, 2023

Functions in compositions (2.0-5)

Color-size compositions of 20 clam colonies from West Bay

Activity patterns of a statistician for 20 days

Permeabilities of bayesite

Color-size compositions of 20 clam colonies from East Bay

AnimalVegetation

Animal and vegetation measurement

Compositions and depth of 25 specimens of boxite

Firework mixtures

Activity patterns of a statistician for 20 days

Artic lake sediment samples of different water depth

Compositions and total pebble counts of 92 glacial tills

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Compositions, depths and porosities of 25 specimens of coxite

Hotellings T square distribution

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

Compositions of 25 specimens of hongite

Household Expenditures

Diagnostic probabilities

Helper to compute confidence ellipsoids

Compositions of 25 specimens of kongite

Shifts of machine operators

Steroid metabolite patterns in adults and children

Honk Kong Pogo-Jumps Championship

Measurement of skulls

AFM compositions of 23 aphyric Skye lavas

Proportions of sand, silt and clay in sediments specimens

Serum Protein compositions of blood samples

Proportions of supervisor's statements assigned to different categories

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

Class "aplus"

Class "amounts"

Marginal compositions in Aitchison Compositions

SimulatedAmounts

Simulated amount datasets

Additive log ratio transform

Power transform in the simplex

arrows in 3D, based on package rgl

Additive planar transform

Aitchison compositions

Amounts analysed in log-scale

vectorial arithmetic for data sets with aplus class

Treating binary and g-adic numbers

Bar charts of amounts

Centered default transform

Class "ccomp"

Count compositions

Compositional Goodness of fit test

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

Three-dimensional biplots, based on package rgl

Centered log ratio transform

Closure of a composition

Displaying compositions and amounts with box-plots

Convert "compositions" classes to data frames or matrices

Heuristics to find subpopulations of outliers

Compute balances for a compositional dataset.

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

Class "acomp"

Automatic common backtransformation for compositions

Yatquat fruit evaluation

Correlations of amounts and compositions

Centered planar transform

compositions-package

tools:::Rd_package_title("compositions")

missing.compositions

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

colorsForOutliers

Create a color/char palette or for groups of outliers

compositional-class

Class "compositional"

Compositional Ordinary Kriging

Compositional Goodness of fit test

getdetectionlimit

Gets the detection limit stored in the data set

Group amounts of parts

Distances in variouse approaches

Internal functions of the compositions package

Internal functions of the compositions package

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

Internal functions: A conditional drop

Internal function: Checking equality of IEEE special numbers

Fitting a Dirichlet distribution

Internal functions: Parallel operations of single and multiple datasets

Internal function: give a derived subclass to an object

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

Classical Gauss Test

Internal function: Compute a desired compositional margin

Environment containing the old gsi functions

gsi.merge2signary

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

endmemberCoordinates

Recast amounts as mixtures of end-members

The geometric mean

Dendrogram representation of acomp or rcomp objects

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

Internal functions of the compositions package

gsigetBalStruct

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

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

Internal functions of the compositions package

Internal function: row and column sums of matrices

Internal function: Invert a permutation

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

Internal function: Solves singular and non square equation systems

Internal function: Recode missings with IEEE number and vice versa

Calling from a function with the own parameters

gsi.expandrcomp

Internal function: Scaling rcomp

Internal functions of the compositions package

gsi.isSingleRow

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

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

Isometric identity transform

Internal function: Convert to plain vector or matrix

Internal functions of the compositions package

Internal functions of the compositions package

Internal functions: Storing integers as reals

logratioVariogram

Empirical variograms for compositions

Internal functions of the compositions package

isoPortionLines

Isoportion- and Isoproportion-lines

Isometric log transform

IsMahalanobisOutlier

Checking for outliers

inner product for matrices and vectors

Isometric log ratio transform

gsi.varwithlosts

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

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

Check for compositional data type

Vector space norm

missingProjector

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

The arithmetic mean of rows or columns

The names of the parts

Classify and summarize missing values in a dataset

kingTetrahedron

Ploting composition into rotable tetrahedron

Isometric planar transform

Internal function: A panel displaying a label only

Normalize vectors to norm 1

Treating single compositions as one-row datasets

Draws connected lines from point to point.

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

acompscalarproduct

inner product for datasets with a vector space structure

Mean amounts and mean compositions

Perturbation of compositions

Ternary diagrams

outliersInCompositions

Analysing outliers in compositions.

The jura dataset

Density estimation on the simplex with Dirichlet kernel

3D-plot of compositional data

plot in 3D based on rgl

Isometric default transform

Reads a data file in a mixR format

Metric summary statistics of real, amount or compositional data

outlierclassifier

Detect and classify compositional outliers.

3D-plot of positive data

plotmissingsummary

Plot a Missing Summary

plot in 3D based on rgl

Displaying amounts in scatterplots

plot in 3D based on rgl

plotlogratioVariogram

Empirical variograms for compositions

Creates a paneled plot like pairs for two different datasets.

Class "rcomp"

Compute distributions of empirical Mahalanobis distances based on simulations

Loadings of relations of two amounts

Principal component analysis for real data

Plot various graphics to analyse outliers.

Principal component analysis for real amounts

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

Principal component analysis for amounts in log geometry

Arithmetic operations for compositions in a real geometry

Class "rmult"

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Pairs plot method for compositions

Class "rplus"

vectorial arithmetic for datasets in a classical vector scale

Simple treatment of real vectors

Summary of compositions in real geometry

Plots of pairwise logratio against a covariable.

Normal quantile plots for compositions and amounts

Parallel scalar products

simplemissingplot

Ternary diagrams

Normalizing datasets by centering and scaling

Draws straight lines from point to point.

powerofpsdmatrix

power transform of a matrix

Principal component analysis for Aitchison compositions

Dirichlet distribution

Printing compositional data.

Compute the global projector to the observed subspace.

Principal component analysis for real compositions

Unique parametrisations for matrices.

Uncentered log transform

Pairwise log ratio transform

Variances and covariances of amounts and compositions

Aitchison Distribution

Marginal compositions in real geometry

Draws straight lines.

Read standard data files

Reads a data file in a geoeas format

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

Simulate count compositions without overdispersion

Total sum of amounts

The uniform distribution on the simplex

vectorial arithmetic for data sets with rplus class

Summarizing a compositional dataset in terms of ratios

wrapped_functions

Standard R functions wrapped for compatibility

Empirical variograms for compositions

Compositional variogram model fitting

Normal distributions on special spaces

Modify parameters of compositional plots.

simulatemissings

Artifical simulation of various kinds of missings/polluted data

Subsetting of compositions

Splitting datasets in groups given by factors

The multivariate lognormal distribution

inner product for datasets with vector scale

Summaries of amounts

Variogram functions

Variation matrices of amounts and compositions

Zero-replacement routine

Residual variance of a model

Variance covariance matrix of parameters in compositional regression

Compositional Goodness of fit test

Axis for ternary diagrams

Composition of glaciar sediments from the Aar massif (Switzerland)