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compositions (version 2.0-4)

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

2.0-4

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

January 5th, 2022

Functions in compositions (2.0-4)

Permeabilities of bayesite

Diagnostic probabilities

Steroid metabolite patterns in adults and children

Compositions of 25 specimens of kongite

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

Heuristics to find subpopulations of outliers

compositions-package

tools:::Rd_package_title("compositions")

Composition of glaciar sediments from the Aar massif (Switzerland)

Correlations of amounts and compositions

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Activity patterns of a statistician for 20 days

Compositions and total pebble counts of 92 glacial tills

Color-size compositions of 20 clam colonies from West Bay

Firework mixtures

Shifts of machine operators

Color-size compositions of 20 clam colonies from East Bay

Helper to compute confidence ellipsoids

Group amounts of parts

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

Internal functions: Parallel operations of single and multiple datasets

Honk Kong Pogo-Jumps Championship

Proportions of supervisor's statements assigned to different categories

SimulatedAmounts

Simulated amount datasets

Household Expenditures

Internal function: give a derived subclass to an object

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

gsi.isSingleRow

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

Treating binary and g-adic numbers

Centered log ratio transform

Class "amounts"

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

Closure of a composition

Bar charts of amounts

Class "aplus"

Classical Gauss Test

Aitchison compositions

Internal function: Convert to plain vector or matrix

Internal functions: Storing integers as reals

gsigetBalStruct

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

Internal functions of the compositions package

The geometric mean

Additive planar transform

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

Internal functions of the compositions package

Isometric log ratio transform

Isometric identity transform

logratioVariogram

Empirical variograms for compositions

Dendrogram representation of acomp or rcomp objects

arrows in 3D, based on package rgl

Internal functions of the compositions package

Three-dimensional biplots, based on package rgl

Power transform in the simplex

Compute balances for a compositional dataset.

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

Automatic common backtransformation for compositions

endmemberCoordinates

Recast amounts as mixtures of end-members

Isometric planar transform

Activity patterns of a statistician for 20 days

The arithmetic mean of rows or columns

outlierclassifier

Detect and classify compositional outliers.

Check for compositional data type

missingProjector

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

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

AnimalVegetation

Animal and vegetation measurement

Plot various graphics to analyse outliers.

plotmissingsummary

Plot a Missing Summary

Internal function: Compute a desired compositional margin

Measurement of skulls

AFM compositions of 23 aphyric Skye lavas

outliersInCompositions

Analysing outliers in compositions.

colorsForOutliers

Create a color/char palette or for groups of outliers

Creates a paneled plot like pairs for two different datasets.

Displaying compositions and amounts with box-plots

Internal functions of the compositions package

gsi.merge2signary

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

Principal component analysis for amounts in log geometry

Internal functions of the compositions package

Additive log ratio transform

Marginal compositions in Aitchison Compositions

Amounts analysed in log-scale

getdetectionlimit

Gets the detection limit stored in the data set

Compositional Ordinary Kriging

Density estimation on the simplex with Dirichlet kernel

The jura dataset

plot in 3D based on rgl

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

Classify and summarize missing values in a dataset

Compositional Goodness of fit test

Displaying amounts in scatterplots

Internal functions: A conditional drop

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

plotlogratioVariogram

Empirical variograms for compositions

vectorial arithmetic for data sets with aplus class

Compositional Goodness of fit test

Centered default transform

Dirichlet distribution

Compositions and depth of 25 specimens of boxite

Compositions of 25 specimens of hongite

Centered planar transform

Arithmetic operations for compositions in a real geometry

Aitchison Distribution

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

vectorial arithmetic for data sets with rplus class

Summary of compositions in real geometry

Distances in variouse approaches

The uniform distribution on the simplex

simulatemissings

Artifical simulation of various kinds of missings/polluted data

Simulate count compositions without overdispersion

Splitting datasets in groups given by factors

Hotellings T square distribution

Residual variance of a model

Environment containing the old gsi functions

Internal function: Invert a permutation

Internal function: Checking equality of IEEE special numbers

Compute the global projector to the observed subspace.

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

Fitting a Dirichlet distribution

Isometric default transform

Internal function: Solves singular and non square equation systems

Internal function: A panel displaying a label only

gsi.varwithlosts

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

Proportions of sand, silt and clay in sediments specimens

Axis for ternary diagrams

Compositional Goodness of fit test

Serum Protein compositions of blood samples

Principal component analysis for real compositions

Calling from a function with the own parameters

Internal functions of the compositions package

Internal function: row and column sums of matrices

Zero-replacement routine

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

gsi.expandrcomp

Internal function: Scaling rcomp

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

Principal component analysis for real data

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

Internal functions of the compositions package

Isometric log transform

Class "ccomp"

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

Yatquat fruit evaluation

Count compositions

kingTetrahedron

Ploting composition into rotable tetrahedron

Convert "compositions" classes to data frames or matrices

Class "acomp"

Compositional variogram model fitting

Variance covariance matrix of parameters in compositional regression

wrapped_functions

Standard R functions wrapped for compatibility

compositional-class

Class "compositional"

inner product for matrices and vectors

The names of the parts

IsMahalanobisOutlier

Checking for outliers

Internal functions of the compositions package

missing.compositions

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

Internal function: Recode missings with IEEE number and vice versa

Draws connected lines from point to point.

Vector space norm

Normalize vectors to norm 1

plot in 3D based on rgl

Principal component analysis for real amounts

Marginal compositions in real geometry

Read standard data files

Reads a data file in a geoeas format

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Loadings of relations of two amounts

3D-plot of compositional data

Class "rplus"

Draws straight lines from point to point.

simplemissingplot

Ternary diagrams

isoPortionLines

Isoportion- and Isoproportion-lines

acompscalarproduct

inner product for datasets with a vector space structure

Pairs plot method for compositions

Treating single compositions as one-row datasets

Class "rcomp"

inner product for datasets with vector scale

Simple treatment of real vectors

vectorial arithmetic for datasets in a classical vector scale

Variation matrices of amounts and compositions

Unique parametrisations for matrices.

3D-plot of positive data

plot in 3D based on rgl

Normal distributions on special spaces

Draws straight lines.

Mean amounts and mean compositions

Reads a data file in a mixR format

Variances and covariances of amounts and compositions

Metric summary statistics of real, amount or compositional data

Subsetting of compositions

Uncentered log transform

Ternary diagrams

Variogram functions

Perturbation of compositions

powerofpsdmatrix

power transform of a matrix

Principal component analysis for Aitchison compositions

Printing compositional data.

Compute distributions of empirical Mahalanobis distances based on simulations

Class "rmult"

Normal quantile plots for compositions and amounts

Plots of pairwise logratio against a covariable.

Parallel scalar products

Pairwise log ratio transform

Modify parameters of compositional plots.

Normalizing datasets by centering and scaling

The multivariate lognormal distribution

Summaries of amounts

Summarizing a compositional dataset in terms of ratios

Empirical variograms for compositions

Total sum of amounts

Compositions, depths and porosities of 25 specimens of coxite

Artic lake sediment samples of different water depth