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compositions (version 2.0-8)

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

9,016

Version

2.0-8

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

January 31st, 2024

Functions in compositions (2.0-8)

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Compositions, depths and porosities of 25 specimens of coxite

Helper to compute confidence ellipsoids

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

Household Expenditures

Hotellings T square distribution

Compositions and total pebble counts of 92 glacial tills

Compositions of 25 specimens of hongite

Firework mixtures

Diagnostic probabilities

Compositions of 25 specimens of kongite

Measurement of skulls

Honk Kong Pogo-Jumps Championship

Yatquat fruit evaluation

SimulatedAmounts

Simulated amount datasets

Class "acomp"

Shifts of machine operators

Power transform in the simplex

Aitchison compositions

Additive log ratio transform

Steroid metabolite patterns in adults and children

Marginal compositions in Aitchison Compositions

Proportions of sand, silt and clay in sediments specimens

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

AFM compositions of 23 aphyric Skye lavas

Serum Protein compositions of blood samples

Proportions of supervisor's statements assigned to different categories

Additive planar transform

arrows in 3D, based on package rgl

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

Amounts analysed in log-scale

vectorial arithmetic for data sets with aplus class

Convert "compositions" classes to data frames or matrices

Automatic common backtransformation for compositions

Compute balances for a compositional dataset.

Class "amounts"

Class "aplus"

Bar charts of amounts

Displaying compositions and amounts with box-plots

Class "ccomp"

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

Count compositions

Compositional Goodness of fit test

Closure of a composition

Heuristics to find subpopulations of outliers

Centered log ratio transform

Three-dimensional biplots, based on package rgl

Centered default transform

Treating binary and g-adic numbers

Compositional Ordinary Kriging

Correlations of amounts and compositions

missing.compositions

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

Distances in variouse approaches

Centered planar transform

colorsForOutliers

Create a color/char palette or for groups of outliers

compositional-class

Class "compositional"

compositions-package

tools:::Rd_package_title("compositions")

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

Dendrogram representation of acomp or rcomp objects

Group amounts of parts

Compositional Goodness of fit test

getdetectionlimit

Gets the detection limit stored in the data set

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

The geometric mean

Fitting a Dirichlet distribution

Classical Gauss Test

Internal functions of the compositions package

Internal function: give a derived subclass to an object

Internal functions: Parallel operations of single and multiple datasets

endmemberCoordinates

Recast amounts as mixtures of end-members

Internal function: Compute a desired compositional margin

Calling from a function with the own parameters

Internal functions of the compositions package

gsi.merge2signary

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

gsi.expandrcomp

Internal function: Scaling rcomp

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

Internal function: Checking equality of IEEE special numbers

Internal function: Convert to plain vector or matrix

Internal functions of the compositions package

Internal functions: A conditional drop

Internal functions of the compositions package

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

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

gsigetBalStruct

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

Isometric planar transform

Internal function: row and column sums of matrices

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

Treating single compositions as one-row datasets

gsi.isSingleRow

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

Check for compositional data type

Internal function: Recode missings with IEEE number and vice versa

Normalize vectors to norm 1

Internal functions of the compositions package

Isometric identity transform

Isometric log ratio transform

The arithmetic mean of rows or columns

logratioVariogram

Empirical variograms for compositions

Internal functions: Storing integers as reals

Environment containing the old gsi functions

missingProjector

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

Internal function: Solves singular and non square equation systems

IsMahalanobisOutlier

Checking for outliers

Internal function: A panel displaying a label only

acompscalarproduct

inner product for datasets with a vector space structure

isoPortionLines

Isoportion- and Isoproportion-lines

Internal functions of the compositions package

gsi.varwithlosts

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

Mean amounts and mean compositions

Internal functions of the compositions package

Creates a paneled plot like pairs for two different datasets.

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

inner product for matrices and vectors

Isometric default transform

outliersInCompositions

Analysing outliers in compositions.

outlierclassifier

Detect and classify compositional outliers.

Reads a data file in a mixR format

Internal function: Invert a permutation

Metric summary statistics of real, amount or compositional data

Plot various graphics to analyse outliers.

Internal functions of the compositions package

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

Principal component analysis for amounts in log geometry

Perturbation of compositions

Ternary diagrams

Principal component analysis for real compositions

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

3D-plot of positive data

plot in 3D based on rgl

Density estimation on the simplex with Dirichlet kernel

The jura dataset

Isometric log transform

The names of the parts

Principal component analysis for real amounts

Vector space norm

Principal component analysis for real data

plot in 3D based on rgl

Normal quantile plots for compositions and amounts

Plots of pairwise logratio against a covariable.

plotlogratioVariogram

Empirical variograms for compositions

Loadings of relations of two amounts

Class "rcomp"

vectorial arithmetic for datasets in a classical vector scale

Class "rmult"

Marginal compositions in real geometry

Simple treatment of real vectors

Modify parameters of compositional plots.

Compute distributions of empirical Mahalanobis distances based on simulations

powerofpsdmatrix

power transform of a matrix

kingTetrahedron

Ploting composition into rotable tetrahedron

Read standard data files

Reads a data file in a geoeas format

The multivariate lognormal distribution

Pairs plot method for compositions

Draws connected lines from point to point.

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

3D-plot of compositional data

Classify and summarize missing values in a dataset

Unique parametrisations for matrices.

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

plotmissingsummary

Plot a Missing Summary

Principal component analysis for Aitchison compositions

plot in 3D based on rgl

The uniform distribution on the simplex

Dirichlet distribution

Simulate count compositions without overdispersion

Aitchison Distribution

Draws straight lines.

Subsetting of compositions

vectorial arithmetic for data sets with rplus class

Summary of compositions in real geometry

Class "rplus"

inner product for datasets with vector scale

Arithmetic operations for compositions in a real geometry

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

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Normal distributions on special spaces

Compute the global projector to the observed subspace.

Residual variance of a model

Total sum of amounts

Summarizing a compositional dataset in terms of ratios

Uncentered log transform

Empirical variograms for compositions

Variance covariance matrix of parameters in compositional regression

simulatemissings

Artifical simulation of various kinds of missings/polluted data

Zero-replacement routine

Splitting datasets in groups given by factors

Variances and covariances of amounts and compositions

Summaries of amounts

Variation matrices of amounts and compositions

Variogram functions

Displaying amounts in scatterplots

Parallel scalar products

Printing compositional data.

Pairwise log ratio transform

Normalizing datasets by centering and scaling

Axis for ternary diagrams

Draws straight lines from point to point.

simplemissingplot

Ternary diagrams

Compositional Goodness of fit test

Compositional variogram model fitting

wrapped_functions

Standard R functions wrapped for compatibility

Activity patterns of a statistician for 20 days

Compositions and depth of 25 specimens of boxite

AnimalVegetation

Animal and vegetation measurement

Composition of glaciar sediments from the Aar massif (Switzerland)

Color-size compositions of 20 clam colonies from West Bay

Color-size compositions of 20 clam colonies from East Bay

Artic lake sediment samples of different water depth

Activity patterns of a statistician for 20 days

Permeabilities of bayesite