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compositions (version 2.0-1)

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

10,267

Version

2.0-1

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

January 8th, 2021

Functions in compositions (2.0-1)

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

Activity patterns of a statistician for 20 days

Artic lake sediment samples of different water depth

Color-size compositions of 20 clam colonies from East Bay

Activity patterns of a statistician for 20 days

Permeabilities of bayesite

Compositions of 25 specimens of hongite

Hotellings T square distribution

SimulatedAmounts

Simulated amount datasets

Yatquat fruit evaluation

Shifts of machine operators

Class "aplus"

Helper to compute confidence ellipsoids

Class "amounts"

Steroid metabolite patterns in adults and children

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Class "acomp"

Compositions of 25 specimens of kongite

Household Expenditures

Firework mixtures

Compositions, depths and porosities of 25 specimens of coxite

Compositions and total pebble counts of 92 glacial tills

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

Convert "compositions" classes to data frames

vectorial arithmetic for data sets with aplus class

Honk Kong Pogo-Jumps Championship

Power transform in the simplex

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

Bar charts of amounts

Treating binary and g-adic numbers

Additive planar transform

Amounts analysed in log-scale

Proportions of sand, silt and clay in sediments specimens

Aitchison compositions

Closure of a composition

Class "ccomp"

Centered log ratio transform

Count compositions

Three-dimensional biplots, based on package rgl

arrows in 3D, based on package rgl

Displaying compositions and amounts with box-plots

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

Diagnostic probabilities

Measurement of skulls

Proportions of supervisor's statements assigned to different categories

Serum Protein compositions of blood samples

Marginal compositions in Aitchison Compositions

AFM compositions of 23 aphyric Skye lavas

Additive log ratio transform

Dendrogram representation of acomp or rcomp objects

Compositional Goodness of fit test

Centered planar transform

Automatic common backtransformation for compositions

Compute balances for a compositional dataset.

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

Distances in variouse approaches

compositional-class

Class "compositional"

missing.compositions

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

Centered default transform

colorsForOutliers

Create a color/char palette or for groups of outliers

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

Fitting a Dirichlet distribution

getdetectionlimit

Gets the detection limit stored in the data set

Compositional Goodness of fit test

Internal functions of the compositions package

Internal functions of the compositions package

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

compositions-package

Internal functions: Parallel operations of single and multiple datasets

Internal function: give a derived subclass to an object

Compositional Ordinary Kriging

Correlations of amounts and compositions

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

Environment containing the old gsi functions

Internal function: row and column sums of matrices

Classical Gauss Test

gsi.expandrcomp

Internal function: Scaling rcomp

The geometric mean

Heuristics to find subpopulations of outliers

Internal functions of the compositions package

Group amounts of parts

Internal function: Recode missings with IEEE number and vice versa

Internal function: Convert to plain vector or matrix

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

gsigetBalStruct

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

endmemberCoordinates

Recast amounts as mixtures of end-members

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

Isometric log transform

Internal functions of the compositions package

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

gsi.varwithlosts

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

Calling from a function with the own parameters

Internal functions of the compositions package

Internal functions of the compositions package

Internal function: Compute a desired compositional margin

Internal function: Checking equality of IEEE special numbers

Internal functions: A conditional drop

gsi.merge2signary

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

Internal functions of the compositions package

Internal functions of the compositions package

Isometric identity transform

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

Internal function: A panel displaying a label only

Internal function: Solves singular and non square equation systems

Internal functions: Storing integers as reals

gsi.isSingleRow

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

IsMahalanobisOutlier

Checking for outliers

Isometric default transform

Isometric log ratio transform

Vector space norm

Internal function: Invert a permutation

isoPortionLines

Isoportion- and Isoproportion-lines

kingTetrahedron

Ploting composition into rotable tetrahedron

The jura dataset

Unique parametrisations for matrices.

Draws connected lines from point to point.

inner product for matrices and vectors

acompscalarproduct

inner product for datasets with a vector space structure

Isometric planar transform

Perturbation of compositions

Check for compositional data type

Principal component analysis for Aitchison compositions

plotlogratioVariogram

Empirical variograms for compositions

plotmissingsummary

Plot a Missing Summary

Normalize vectors to norm 1

Principal component analysis for amounts in log geometry

Classify and summarize missing values in a dataset

Principal component analysis for real compositions

Plot various graphics to analyse outliers.

missingProjector

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

outliersInCompositions

Analysing outliers in compositions.

Reads a data file in a mixR format

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

logratioVariogram

Empirical variograms for compositions

Printing compositional data.

Principal component analysis for real amounts

Ternary diagrams

Mean amounts and mean compositions

Pairwise log ratio transform

Plots of pairwise logratio against a covariable.

Principal component analysis for real data

The arithmetic mean of rows or columns

Metric summary statistics of real, amount or compositional data

The names of the parts

Creates a paneled plot like pairs for two different datasets.

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

Pairs plot method for compositions

Normal quantile plots for compositions and amounts

Class "rmult"

Dirichlet distribution

plot in 3D based on rgl

Marginal compositions in real geometry

Arithmetic operations for compositions in a real geometry

Parallel scalar products

The uniform distribution on the simplex

Splitting datasets in groups given by factors

Draws straight lines.

Simple treatment of real vectors

outlierclassifier

Detect and classify compositional outliers.

3D-plot of compositional data

Treating single compositions as one-row datasets

3D-plot of positive data

Variance covariance matrix of parameters in compositional regression

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Normal distributions on special spaces

vectorial arithmetic for data sets with rplus class

Simulate count compositions without overdispersion

Read standard data files

Reads a data file in a geoeas format

Class "rcomp"

powerofpsdmatrix

power transform of a matrix

Displaying amounts in scatterplots

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

Compositional variogram model fitting

Modify parameters of compositional plots.

Summarizing a compositional dataset in terms of ratios

Subsetting of compositions

Compute distributions of empirical Mahalanobis distances based on simulations

The multivariate lognormal distribution

Variogram functions

Summary of compositions in real geometry

Normalizing datasets by centering and scaling

Summaries of amounts

Compositional Goodness of fit test

Total sum of amounts

Residual variance of a model

Variation matrices of amounts and compositions

Variances and covariances of amounts and compositions

Zero-replacement routine

Loadings of relations of two amounts

plot in 3D based on rgl

plot in 3D based on rgl

Aitchison Distribution

inner product for datasets with vector scale

vectorial arithmetic for datasets in a classical vector scale

Class "rplus"

Draws straight lines from point to point.

Compute the global projector to the observed subspace.

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

Axis for ternary diagrams

simplemissingplot

Ternary diagrams

Empirical variograms for compositions

Uncentered log transform

simulatemissings

Artifical simulation of various kinds of missings/polluted data