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compositions (version 2.0-2)

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

2.0-2

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

July 14th, 2021

Functions in compositions (2.0-2)

Activity patterns of a statistician for 20 days

Color-size compositions of 20 clam colonies from West Bay

AnimalVegetation

Animal and vegetation measurement

Color-size compositions of 20 clam colonies from East Bay

Compositions and depth of 25 specimens of boxite

Activity patterns of a statistician for 20 days

Composition of glaciar sediments from the Aar massif (Switzerland)

Permeabilities of bayesite

Artic lake sediment samples of different water depth

Household Expenditures

Compositions, depths and porosities of 25 specimens of coxite

Steroid metabolite patterns in adults and children

Firework mixtures

Compositions of 25 specimens of hongite

Compositions and total pebble counts of 92 glacial tills

Compositions of 25 specimens of kongite

Hotellings T square distribution

Diagnostic probabilities

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Helper to compute confidence ellipsoids

Shifts of machine operators

SimulatedAmounts

Simulated amount datasets

Yatquat fruit evaluation

Serum Protein compositions of blood samples

Proportions of sand, silt and clay in sediments specimens

Class "amounts"

Aitchison compositions

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

Proportions of supervisor's statements assigned to different categories

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

AFM compositions of 23 aphyric Skye lavas

Measurement of skulls

Class "acomp"

Convert "compositions" classes to data frames

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

Class "aplus"

Power transform in the simplex

Automatic common backtransformation for compositions

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

Amounts analysed in log-scale

Compute balances for a compositional dataset.

Centered planar transform

Closure of a composition

Centered log ratio transform

Additive planar transform

Three-dimensional biplots, based on package rgl

Heuristics to find subpopulations of outliers

arrows in 3D, based on package rgl

colorsForOutliers

Create a color/char palette or for groups of outliers

Compositional Ordinary Kriging

Distances in variouse approaches

Internal functions of the compositions package

Group amounts of parts

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

Fitting a Dirichlet distribution

Internal function: row and column sums of matrices

Internal functions: A conditional drop

Environment containing the old gsi functions

Internal function: Checking equality of IEEE special numbers

Internal functions of the compositions package

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

Internal functions of the compositions package

gsi.varwithlosts

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

compositional-class

Class "compositional"

Displaying compositions and amounts with box-plots

missing.compositions

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

Compositional Goodness of fit test

vectorial arithmetic for data sets with aplus class

Centered default transform

Isometric default transform

Compositional Goodness of fit test

getdetectionlimit

Gets the detection limit stored in the data set

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

Internal function: Invert a permutation

Dendrogram representation of acomp or rcomp objects

Draws connected lines from point to point.

Internal function: Convert to plain vector or matrix

Honk Kong Pogo-Jumps Championship

Marginal compositions in Aitchison Compositions

Internal functions: Parallel operations of single and multiple datasets

Classical Gauss Test

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

The geometric mean

Internal function: give a derived subclass to an object

Additive log ratio transform

gsi.expandrcomp

Internal function: Scaling rcomp

Internal functions of the compositions package

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

Isometric log transform

logratioVariogram

Empirical variograms for compositions

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

missingProjector

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

Calling from a function with the own parameters

Internal function: Compute a desired compositional margin

gsi.merge2signary

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

Mean amounts and mean compositions

Check for compositional data type

The arithmetic mean of rows or columns

Isometric planar transform

Internal function: Recode missings with IEEE number and vice versa

Classify and summarize missing values in a dataset

gsi.isSingleRow

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

Ternary diagrams

Internal functions of the compositions package

Internal functions: Storing integers as reals

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

Internal functions of the compositions package

Isometric identity transform

Unique parametrisations for matrices.

Perturbation of compositions

plotmissingsummary

Plot a Missing Summary

Isometric log ratio transform

Reads a data file in a mixR format

plotlogratioVariogram

Empirical variograms for compositions

Treating single compositions as one-row datasets

Aitchison Distribution

plot in 3D based on rgl

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

Principal component analysis for real amounts

Loadings of relations of two amounts

vectorial arithmetic for datasets in a classical vector scale

3D-plot of positive data

outlierclassifier

Detect and classify compositional outliers.

Bar charts of amounts

3D-plot of compositional data

Displaying amounts in scatterplots

powerofpsdmatrix

power transform of a matrix

Class "rmult"

Normal quantile plots for compositions and amounts

Printing compositional data.

inner product for datasets with vector scale

vectorial arithmetic for data sets with rplus class

Splitting datasets in groups given by factors

Simulate count compositions without overdispersion

Dirichlet distribution

Treating binary and g-adic numbers

Count compositions

compositions-package

Correlations of amounts and compositions

Class "ccomp"

Principal component analysis for real data

Pairwise log ratio transform

Principal component analysis for real compositions

Plots of pairwise logratio against a covariable.

Draws straight lines.

Normalizing datasets by centering and scaling

kingTetrahedron

Ploting composition into rotable tetrahedron

Vector space norm

Marginal compositions in real geometry

The jura dataset

Draws straight lines from point to point.

endmemberCoordinates

Recast amounts as mixtures of end-members

Summary of compositions in real geometry

Arithmetic operations for compositions in a real geometry

Summaries of amounts

The uniform distribution on the simplex

Internal functions of the compositions package

Parallel scalar products

wrapped_functions

Standard R functions wrapped for compatibility

Zero-replacement routine

Normalize vectors to norm 1

Principal component analysis for Aitchison compositions

Principal component analysis for amounts in log geometry

Creates a paneled plot like pairs for two different datasets.

Pairs plot method for compositions

The multivariate lognormal distribution

Normal distributions on special spaces

Simple treatment of real vectors

Compute distributions of empirical Mahalanobis distances based on simulations

Variogram functions

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Residual variance of a model

Uncentered log transform

Internal function: A panel displaying a label only

Internal functions of the compositions package

Empirical variograms for compositions

Subsetting of compositions

gsigetBalStruct

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

Internal function: Solves singular and non square equation systems

IsMahalanobisOutlier

Checking for outliers

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

Class "rplus"

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

isoPortionLines

Isoportion- and Isoproportion-lines

Summarizing a compositional dataset in terms of ratios

Variance covariance matrix of parameters in compositional regression

Compositional variogram model fitting

Variation matrices of amounts and compositions

acompscalarproduct

inner product for datasets with a vector space structure

inner product for matrices and vectors

Variances and covariances of amounts and compositions

simplemissingplot

Ternary diagrams

simulatemissings

Artifical simulation of various kinds of missings/polluted data

outliersInCompositions

Analysing outliers in compositions.

The names of the parts

Plot various graphics to analyse outliers.

Metric summary statistics of real, amount or compositional data

plot in 3D based on rgl

Class "rcomp"

plot in 3D based on rgl

Compute the global projector to the observed subspace.

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

Modify parameters of compositional plots.

Axis for ternary diagrams

Compositional Goodness of fit test

Total sum of amounts