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compositions (version 1.40-5)

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

10,267

Version

1.40-5

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

April 8th, 2020

Functions in compositions (1.40-5)

Composition of glaciar sediments from the Aar massif (Switzerland)

Color-size compositions of 20 clam colonies from East Bay

Household Expenditures

Compositions and total pebble counts of 92 glacial tills

AnimalVegetation

Animal and vegetation measurement

Activity patterns of a statistician for 20 days

Color-size compositions of 20 clam colonies from West Bay

Firework mixtures

Compositions and depth of 25 specimens of boxite

Permeabilities of bayesite

CompLinModCoReg

Compositional Linear Model of Coregionalisation

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

Diagnostic probabilities

Additive log ratio transform

Helper to compute confidence ellipsoids

Compositions, depths and porosities of 25 specimens of coxite

Compositions of 25 specimens of kongite

Measurement of skulls

AFM compositions of 23 aphyric Skye lavas

Steroid metabolite patterns in adults and children

Honk Kong Pogo-Jumps Championship

Shifts of machine operators

Centered log ratio transform

Classical Gauss Test

SimulatedAmounts

Simulated amount datasets

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

Power transform in the simplex

Three-dimensional biplots, based on package rgl

Yatquat fruit evaluation

The geometric mean

Amounts analysed in log-scale

Displaying compositions and amounts with box-plots

Marginal compositions in Aitchison Compositions

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

getdetectionlimit

Gets the detection limit stored in the data set

Compositions of 25 specimens of hongite

Heuristics to find subpopulations of outliers

Dendrogram representation of acomp or rcomp objects

Aitchison compositions

Compositional Goodness of fit test

Count compositions

Internal functions of the compositions package

Compute balances for a compositional dataset.

gsi.expandrcomp

Internal function: Scaling rcomp

Calling from a function with the own parameters

Hotellings T square distribution

vectorial arithmetic for data sets with aplus class

Additive planar transform

Internal functions of the compositions package

Isometric identity transform

Proportions of sand, silt and clay in sediments specimens

Isometric log ratio transform

Compositional Goodness of fit test

compositions-package

Serum Protein compositions of blood samples

Bar charts of amounts

The jura dataset

Compositional Ordinary Kriging

kingTetrahedron

Ploting composition into rotable tetrahedron

Classify and summarize missing values in a dataset

Proportions of supervisor's statements assigned to different categories

Internal functions: Parallel operations of single and multiple datasets

missing.compositions

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

missingProjector

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

Internal function: give a derived subclass to an object

Correlations of amounts and compositions

Convert "compositions" classes to data frames

Treating binary and g-adic numbers

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

arrows in 3D, based on package rgl

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

Plot various graphics to analyse outliers.

outliersInCompositions

Analysing outliers in compositions.

plot in 3D based on rgl

Internal function: Compute a desired compositional margin

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

plot in 3D based on rgl

gsigetBalStruct

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

Centered default transform

Principal component analysis for real compositions

Aitchison Distribution

endmemberCoordinates

Recast amounts as mixtures of end-members

Group amounts of parts

Loadings of relations of two amounts

Closure of a composition

Centered planar transform

Principal component analysis for real data

colorsForOutliers

Create a color/char palette or for groups of outliers

Internal functions of the compositions package

Distances in variouse approaches

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

Internal functions: A conditional drop

Internal functions of the compositions package

Internal functions of the compositions package

Internal function: row and column sums of matrices

gsi.merge2signary

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

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

vectorial arithmetic for data sets with rplus class

Fitting a Dirichlet distribution

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

Environment containing the old gsi functions

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

Internal function: Checking equality of IEEE special numbers

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

Compute the global projector to the observed subspace.

Internal function: Invert a permutation

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

Axis for ternary diagrams

gsi.isSingleRow

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

Internal function: Convert to plain vector or matrix

Internal function: Recode missings with IEEE number and vice versa

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

Isometric log transform

Internal functions: Storing integers as reals

Internal functions of the compositions package

gsi.varwithlosts

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

Internal function: Solves singular and non square equation systems

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

Variance covariance matrix of parameters in compositional regression

Isometric default transform

Internal functions of the compositions package

Draws connected lines from point to point.

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

Internal functions of the compositions package

Internal function: A panel displaying a label only

Compositional variogram model fitting

IsMahalanobisOutlier

Checking for outliers

logratioVariogram

Empirical variograms for compositions

Reads a data file in a mixR format

plotmissingsummary

Plot a Missing Summary

Perturbation of compositions

Unique parametrisations for matrices.

plotlogratioVariogram

Empirical variograms for compositions

inner product for matrices and vectors

Normal quantile plots for compositions and amounts

acompscalarproduct

inner product for datasets with a vector space structure

Dirichlet distribution

Isometric planar transform

Mean amounts and mean compositions

Vector space norm

The arithmetic mean of rows or columns

Check for compositional data type

Ternary diagrams

Principal component analysis for Aitchison compositions

Creates a paneled plot like pairs for two different datasets.

plot in 3D based on rgl

Normalize vectors to norm 1

Pairs plot method for compositions

isoPortionLines

Isoportion- and Isoproportion-lines

Parallel scalar products

Normalizing datasets by centering and scaling

Summaries of amounts

3D-plot of compositional data

Summary of compositions in real geometry

The names of the parts

The multivariate lognormal distribution

Principal component analysis for amounts in log geometry

Read standard data files

Reads a data file in a geoeas format

Treating single compositions as one-row datasets

Metric summary statistics of real, amount or compositional data

Modify parameters of compositional plots.

Marginal compositions in real geometry

Empirical variograms for compositions

Uncentered log transform

outlierclassifier

Detect and classify compositional outliers.

3D-plot of positive data

vectorial arithmetic for datasets in a classical vector scale

Zero-replacement routine

Pairwise log ratio transform

Draws straight lines from point to point.

inner product for datasets with vector scale

Displaying amounts in scatterplots

Plots of pairwise logratio against a covariable.

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

Compositional Goodness of fit test

simplemissingplot

Ternary diagrams

Simulate count compositions without overdispersion

Printing compositional data.

The uniform distribution on the simplex

Principal component analysis for real amounts

Arithmetic operations for compositions in a real geometry

Total sum of amounts

powerofpsdmatrix

power transform of a matrix

Compute distributions of empirical Mahalanobis distances based on simulations

simulatemissings

Artifical simulation of various kinds of missings/polluted data

Simple treatment of real vectors

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Normal distributions on special spaces

Draws straight lines.

Splitting datasets in groups given by factors

Summarizing a compositional dataset in terms of ratios

Residual variance of a model

Variances and covariances of amounts and compositions

Variogram functions

Variation matrices of amounts and compositions

Artic lake sediment samples of different water depth

Activity patterns of a statistician for 20 days