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compositions (version 2.0-0)

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

9,016

Version

2.0-0

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

July 14th, 2020

Functions in compositions (2.0-0)

Activity patterns of a statistician for 20 days

Artic lake sediment samples of different water depth

AnimalVegetation

Animal and vegetation measurement

Activity patterns of a statistician for 20 days

Compositions and depth of 25 specimens of boxite

Composition of glaciar sediments from the Aar massif (Switzerland)

Permeabilities of bayesite

Compositions of 25 specimens of hongite

Compositions, depths and porosities of 25 specimens of coxite

Color-size compositions of 20 clam colonies from East Bay

Firework mixtures

Color-size compositions of 20 clam colonies from West Bay

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

Household Expenditures

Hotellings T square distribution

Steroid metabolite patterns in adults and children

Compositions and total pebble counts of 92 glacial tills

Diagnostic probabilities

Proportions of sand, silt and clay in sediments specimens

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Compositions of 25 specimens of kongite

Helper to compute confidence ellipsoids

SimulatedAmounts

Simulated amount datasets

Shifts of machine operators

Honk Kong Pogo-Jumps Championship

Class "amounts"

Power transform in the simplex

Amounts analysed in log-scale

Aitchison compositions

Measurement of skulls

vectorial arithmetic for data sets with aplus class

Serum Protein compositions of blood samples

Closure of a composition

Centered log ratio transform

Bar charts of amounts

Additive log ratio transform

Treating binary and g-adic numbers

AFM compositions of 23 aphyric Skye lavas

Marginal compositions in Aitchison Compositions

Class "aplus"

Three-dimensional biplots, based on package rgl

Convert "compositions" classes to data frames

colorsForOutliers

Create a color/char palette or for groups of outliers

Compositional Ordinary Kriging

Count compositions

Class "ccomp"

Proportions of supervisor's statements assigned to different categories

Centered planar transform

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

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

Compositional Goodness of fit test

Classical Gauss Test

Distances in variouse approaches

Additive planar transform

Correlations of amounts and compositions

Yatquat fruit evaluation

The geometric mean

arrows in 3D, based on package rgl

Dendrogram representation of acomp or rcomp objects

Centered default transform

compositions-package

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

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

Fitting a Dirichlet distribution

Class "acomp"

Internal functions of the compositions package

Internal functions of the compositions package

endmemberCoordinates

Recast amounts as mixtures of end-members

Internal function: Compute a desired compositional margin

Internal functions of the compositions package

gsi.merge2signary

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

Internal function: row and column sums of matrices

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

gsigetBalStruct

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

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

gsi.isSingleRow

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

Internal functions of the compositions package

Internal functions of the compositions package

gsi.varwithlosts

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

Isometric default transform

kingTetrahedron

Ploting composition into rotable tetrahedron

Treating single compositions as one-row datasets

The jura dataset

Internal functions: Storing integers as reals

Displaying compositions and amounts with box-plots

Group amounts of parts

outlierclassifier

Detect and classify compositional outliers.

Internal functions of the compositions package

Heuristics to find subpopulations of outliers

Compute balances for a compositional dataset.

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

Automatic common backtransformation for compositions

Check for compositional data type

Isometric planar transform

Compositional Goodness of fit test

getdetectionlimit

Gets the detection limit stored in the data set

Internal functions: Parallel operations of single and multiple datasets

Environment containing the old gsi functions

Internal function: Solves singular and non square equation systems

Internal function: Invert a permutation

Internal function: A panel displaying a label only

Internal function: give a derived subclass to an object

Isometric log ratio transform

Isometric identity transform

IsMahalanobisOutlier

Checking for outliers

Mean amounts and mean compositions

The arithmetic mean of rows or columns

Creates a paneled plot like pairs for two different datasets.

inner product for matrices and vectors

outliersInCompositions

Analysing outliers in compositions.

Dirichlet distribution

acompscalarproduct

inner product for datasets with a vector space structure

Normal quantile plots for compositions and amounts

Plot various graphics to analyse outliers.

Metric summary statistics of real, amount or compositional data

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

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

missing.compositions

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

compositional-class

Class "compositional"

Internal function: Convert to plain vector or matrix

Internal functions of the compositions package

Internal functions: A conditional drop

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Internal function: Checking equality of IEEE special numbers

Read standard data files

Reads a data file in a geoeas format

gsi.expandrcomp

Internal function: Scaling rcomp

Normal distributions on special spaces

Modify parameters of compositional plots.

isoPortionLines

Isoportion- and Isoproportion-lines

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

Pairs plot method for compositions

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

The names of the parts

plot in 3D based on rgl

Calling from a function with the own parameters

Isometric log transform

plot in 3D based on rgl

Draws connected lines from point to point.

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

Pairwise log ratio transform

logratioVariogram

Empirical variograms for compositions

Vector space norm

powerofpsdmatrix

power transform of a matrix

Displaying amounts in scatterplots

Unique parametrisations for matrices.

Perturbation of compositions

Compositional Goodness of fit test

Internal function: Recode missings with IEEE number and vice versa

Simple treatment of real vectors

Internal functions of the compositions package

Class "rmult"

Plots of pairwise logratio against a covariable.

Zero-replacement routine

Normalize vectors to norm 1

The uniform distribution on the simplex

Total sum of amounts

Principal component analysis for amounts in log geometry

Reads a data file in a mixR format

Principal component analysis for real amounts

Ternary diagrams

Parallel scalar products

Principal component analysis for Aitchison compositions

Classify and summarize missing values in a dataset

plot in 3D based on rgl

3D-plot of positive data

Printing compositional data.

missingProjector

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

Arithmetic operations for compositions in a real geometry

Principal component analysis for real data

Marginal compositions in real geometry

Principal component analysis for real compositions

3D-plot of compositional data

Normalizing datasets by centering and scaling

Class "rplus"

Summaries of amounts

plotlogratioVariogram

Empirical variograms for compositions

Summary of compositions in real geometry

Class "rcomp"

Draws straight lines from point to point.

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

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

inner product for datasets with vector scale

Variogram functions

vectorial arithmetic for datasets in a classical vector scale

plotmissingsummary

Plot a Missing Summary

Compute the global projector to the observed subspace.

The multivariate lognormal distribution

Loadings of relations of two amounts

Axis for ternary diagrams

Compute distributions of empirical Mahalanobis distances based on simulations

Aitchison Distribution

Subsetting of compositions

Residual variance of a model

Summarizing a compositional dataset in terms of ratios

Uncentered log transform

Empirical variograms for compositions

vectorial arithmetic for data sets with rplus class

Splitting datasets in groups given by factors

Draws straight lines.

Simulate count compositions without overdispersion

Variances and covariances of amounts and compositions

simplemissingplot

Ternary diagrams

Variation matrices of amounts and compositions

simulatemissings

Artifical simulation of various kinds of missings/polluted data

Compositional variogram model fitting

Variance covariance matrix of parameters in compositional regression