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compositions (version 2.0-7)

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

16,601

Version

2.0-7

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

January 9th, 2024

Functions in compositions (2.0-7)

Activity patterns of a statistician for 20 days

Activity patterns of a statistician for 20 days

Firework mixtures

Compositions and depth of 25 specimens of boxite

Compositions and total pebble counts of 92 glacial tills

Composition of glaciar sediments from the Aar massif (Switzerland)

Compositions of 25 specimens of kongite

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Marginal compositions in Aitchison Compositions

Steroid metabolite patterns in adults and children

Helper to compute confidence ellipsoids

Compositions, depths and porosities of 25 specimens of coxite

Shifts of machine operators

Diagnostic probabilities

Additive log ratio transform

Compute balances for a compositional dataset.

AnimalVegetation

Animal and vegetation measurement

Automatic common backtransformation for compositions

SimulatedAmounts

Simulated amount datasets

Color-size compositions of 20 clam colonies from East Bay

Measurement of skulls

Compositions of 25 specimens of hongite

AFM compositions of 23 aphyric Skye lavas

Hotellings T square distribution

Class "amounts"

Color-size compositions of 20 clam colonies from West Bay

Aitchison compositions

Power transform in the simplex

Proportions of sand, silt and clay in sediments specimens

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

Household Expenditures

Honk Kong Pogo-Jumps Championship

Bar charts of amounts

Additive planar transform

Compositional Goodness of fit test

Yatquat fruit evaluation

Class "acomp"

Serum Protein compositions of blood samples

Fitting a Dirichlet distribution

Proportions of supervisor's statements assigned to different categories

Centered default transform

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

Treating binary and g-adic numbers

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

arrows in 3D, based on package rgl

Displaying compositions and amounts with box-plots

Three-dimensional biplots, based on package rgl

Class "aplus"

Convert "compositions" classes to data frames or matrices

Amounts analysed in log-scale

vectorial arithmetic for data sets with aplus class

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

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

Class "ccomp"

Count compositions

colorsForOutliers

Create a color/char palette or for groups of outliers

Isometric identity transform

Internal function: Solves singular and non square equation systems

Closure of a composition

Centered planar transform

Compositional Ordinary Kriging

Internal function: A panel displaying a label only

Isometric log ratio transform

Heuristics to find subpopulations of outliers

Distances in variouse approaches

Dendrogram representation of acomp or rcomp objects

compositions-package

tools:::Rd_package_title("compositions")

endmemberCoordinates

Recast amounts as mixtures of end-members

Internal functions of the compositions package

Internal functions of the compositions package

Group amounts of parts

Correlations of amounts and compositions

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

Internal function: Compute a desired compositional margin

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

missing.compositions

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

logratioVariogram

Empirical variograms for compositions

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

Centered log ratio transform

gsigetBalStruct

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

compositional-class

Class "compositional"

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

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

gsi.merge2signary

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

Classical Gauss Test

Classify and summarize missing values in a dataset

getdetectionlimit

Gets the detection limit stored in the data set

Internal functions of the compositions package

The geometric mean

Internal functions of the compositions package

Isometric log transform

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

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

Compositional Goodness of fit test

IsMahalanobisOutlier

Checking for outliers

isoPortionLines

Isoportion- and Isoproportion-lines

Internal functions: A conditional drop

Internal function: Checking equality of IEEE special numbers

The jura dataset

gsi.isSingleRow

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

outliersInCompositions

Analysing outliers in compositions.

kingTetrahedron

Ploting composition into rotable tetrahedron

Density estimation on the simplex with Dirichlet kernel

The arithmetic mean of rows or columns

Internal function: row and column sums of matrices

Internal functions of the compositions package

Creates a paneled plot like pairs for two different datasets.

missingProjector

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

Environment containing the old gsi functions

Draws connected lines from point to point.

Internal functions: Parallel operations of single and multiple datasets

Calling from a function with the own parameters

gsi.expandrcomp

Internal function: Scaling rcomp

Dirichlet distribution

Internal function: give a derived subclass to an object

Aitchison Distribution

Reads a data file in a mixR format

Internal functions: Storing integers as reals

Metric summary statistics of real, amount or compositional data

plot in 3D based on rgl

Internal function: Recode missings with IEEE number and vice versa

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

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

Internal functions of the compositions package

3D-plot of compositional data

inner product for matrices and vectors

Internal functions of the compositions package

Principal component analysis for amounts in log geometry

Internal function: Invert a permutation

Isometric planar transform

Check for compositional data type

Pairs plot method for compositions

gsi.varwithlosts

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

Internal function: Convert to plain vector or matrix

Internal functions of the compositions package

The names of the parts

acompscalarproduct

inner product for datasets with a vector space structure

Isometric default transform

plotmissingsummary

Plot a Missing Summary

Treating single compositions as one-row datasets

Normalize vectors to norm 1

Mean amounts and mean compositions

Principal component analysis for real compositions

simulatemissings

Artifical simulation of various kinds of missings/polluted data

Displaying amounts in scatterplots

Vector space norm

outlierclassifier

Detect and classify compositional outliers.

plotlogratioVariogram

Empirical variograms for compositions

Unique parametrisations for matrices.

plot in 3D based on rgl

Splitting datasets in groups given by factors

Plots of pairwise logratio against a covariable.

Principal component analysis for real data

Axis for ternary diagrams

Principal component analysis for real amounts

Compositional Goodness of fit test

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

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

Arithmetic operations for compositions in a real geometry

Modify parameters of compositional plots.

Normal quantile plots for compositions and amounts

The multivariate lognormal distribution

vectorial arithmetic for data sets with rplus class

Variation matrices of amounts and compositions

Draws straight lines.

powerofpsdmatrix

power transform of a matrix

inner product for datasets with vector scale

Plot various graphics to analyse outliers.

Normal distributions on special spaces

Principal component analysis for Aitchison compositions

Variance covariance matrix of parameters in compositional regression

Variogram functions

Subsetting of compositions

Residual variance of a model

Perturbation of compositions

3D-plot of positive data

Ternary diagrams

plot in 3D based on rgl

Marginal compositions in real geometry

Read standard data files

Reads a data file in a geoeas format

Loadings of relations of two amounts

Parallel scalar products

Class "rcomp"

Zero-replacement routine

Simple treatment of real vectors

Normalizing datasets by centering and scaling

Summarizing a compositional dataset in terms of ratios

Total sum of amounts

Summaries of amounts

Empirical variograms for compositions

vectorial arithmetic for datasets in a classical vector scale

Compute distributions of empirical Mahalanobis distances based on simulations

Pairwise log ratio transform

Printing compositional data.

Class "rplus"

Summary of compositions in real geometry

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Class "rmult"

The uniform distribution on the simplex

Compute the global projector to the observed subspace.

simplemissingplot

Ternary diagrams

Simulate count compositions without overdispersion

Draws straight lines from point to point.

Variances and covariances of amounts and compositions

Uncentered log transform

Compositional variogram model fitting

wrapped_functions

Standard R functions wrapped for compatibility

Permeabilities of bayesite

Artic lake sediment samples of different water depth