Learn R Programming

⚠️There's a newer version (2.0-8) of this package.Take me there.

compositions (version 2.0-6)

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.

Copy Link

Version

Install

install.packages('compositions')

Monthly Downloads

9,116

Version

2.0-6

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

April 13th, 2023

Functions in compositions (2.0-6)

Color-size compositions of 20 clam colonies from West Bay

Artic lake sediment samples of different water depth

Compositions and depth of 25 specimens of boxite

Permeabilities of bayesite

Composition of glaciar sediments from the Aar massif (Switzerland)

Activity patterns of a statistician for 20 days

Activity patterns of a statistician for 20 days

Color-size compositions of 20 clam colonies from East Bay

AnimalVegetation

Animal and vegetation measurement

Firework mixtures

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Compositions and total pebble counts of 92 glacial tills

Helper to compute confidence ellipsoids

Diagnostic probabilities

Compositions, depths and porosities of 25 specimens of coxite

Household Expenditures

Proportions of sand, silt and clay in sediments specimens

Serum Protein compositions of blood samples

Steroid metabolite patterns in adults and children

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

Compositions of 25 specimens of kongite

Measurement of skulls

Compositions of 25 specimens of hongite

Proportions of supervisor's statements assigned to different categories

Yatquat fruit evaluation

AFM compositions of 23 aphyric Skye lavas

Class "amounts"

Shifts of machine operators

Class "acomp"

Hotellings T square distribution

Honk Kong Pogo-Jumps Championship

Power transform in the simplex

Convert "compositions" classes to data frames or matrices

Aitchison compositions

SimulatedAmounts

Simulated amount datasets

Class "aplus"

Amounts analysed in log-scale

Additive planar transform

Marginal compositions in Aitchison Compositions

Additive log ratio transform

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

Three-dimensional biplots, based on package rgl

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

Displaying compositions and amounts with box-plots

Automatic common backtransformation for compositions

vectorial arithmetic for data sets with aplus class

arrows in 3D, based on package rgl

Compute balances for a compositional dataset.

colorsForOutliers

Create a color/char palette or for groups of outliers

Compositional Ordinary Kriging

Class "ccomp"

Dendrogram representation of acomp or rcomp objects

Closure of a composition

Compositional Goodness of fit test

Centered log ratio transform

Bar charts of amounts

Group amounts of parts

Centered default transform

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

Internal functions of the compositions package

getdetectionlimit

Gets the detection limit stored in the data set

compositional-class

Class "compositional"

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

Treating binary and g-adic numbers

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

Compositional Goodness of fit test

Classical Gauss Test

Internal functions: Parallel operations of single and multiple datasets

compositions-package

tools:::Rd_package_title("compositions")

Heuristics to find subpopulations of outliers

The geometric mean

Correlations of amounts and compositions

Fitting a Dirichlet distribution

Centered planar transform

Internal function: give a derived subclass to an object

Count compositions

Internal functions of the compositions package

Internal functions of the compositions package

Internal functions of the compositions package

gsi.expandrcomp

Internal function: Scaling rcomp

Distances in variouse approaches

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

Internal function: row and column sums of matrices

gsi.varwithlosts

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

endmemberCoordinates

Recast amounts as mixtures of end-members

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

Internal functions of the compositions package

Calling from a function with the own parameters

Internal function: Compute a desired compositional margin

Environment containing the old gsi functions

Internal functions of the compositions package

Internal function: Convert to plain vector or matrix

gsigetBalStruct

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

Isometric planar transform

Internal function: Invert a permutation

gsi.merge2signary

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

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

Isometric identity transform

Internal function: Solves singular and non square equation systems

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

Internal function: A panel displaying a label only

Internal function: Checking equality of IEEE special numbers

Internal functions: A conditional drop

Isometric default transform

gsi.isSingleRow

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

Density estimation on the simplex with Dirichlet kernel

The jura dataset

Isometric log ratio transform

Check for compositional data type

Mean amounts and mean compositions

The arithmetic mean of rows or columns

acompscalarproduct

inner product for datasets with a vector space structure

Internal functions of the compositions package

missingProjector

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

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

inner product for matrices and vectors

IsMahalanobisOutlier

Checking for outliers

Pairs plot method for compositions

Unique parametrisations for matrices.

Internal functions: Storing integers as reals

3D-plot of positive data

isoPortionLines

Isoportion- and Isoproportion-lines

Reads a data file in a mixR format

Metric summary statistics of real, amount or compositional data

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

Internal function: Recode missings with IEEE number and vice versa

Internal functions of the compositions package

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

Isometric log transform

plot in 3D based on rgl

Dirichlet distribution

Classify and summarize missing values in a dataset

logratioVariogram

Empirical variograms for compositions

Ternary diagrams

Perturbation of compositions

Principal component analysis for amounts in log geometry

plot in 3D based on rgl

Principal component analysis for real data

Principal component analysis for real amounts

Read standard data files

Reads a data file in a geoeas format

Marginal compositions in real geometry

Vector space norm

The names of the parts

kingTetrahedron

Ploting composition into rotable tetrahedron

Draws connected lines from point to point.

outliersInCompositions

Analysing outliers in compositions.

Principal component analysis for real compositions

3D-plot of compositional data

plotlogratioVariogram

Empirical variograms for compositions

plot in 3D based on rgl

Aitchison Distribution

Creates a paneled plot like pairs for two different datasets.

Arithmetic operations for compositions in a real geometry

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

Plots of pairwise logratio against a covariable.

Loadings of relations of two amounts

Normal quantile plots for compositions and amounts

powerofpsdmatrix

power transform of a matrix

Class "rcomp"

Parallel scalar products

Normalizing datasets by centering and scaling

Simulate count compositions without overdispersion

Principal component analysis for Aitchison compositions

The uniform distribution on the simplex

Summary of compositions in real geometry

Treating single compositions as one-row datasets

inner product for datasets with vector scale

Normalize vectors to norm 1

Compute the global projector to the observed subspace.

outlierclassifier

Detect and classify compositional outliers.

Plot various graphics to analyse outliers.

plotmissingsummary

Plot a Missing Summary

Simple treatment of real vectors

Printing compositional data.

Pairwise log ratio transform

Displaying amounts in scatterplots

Normal distributions on special spaces

Modify parameters of compositional plots.

vectorial arithmetic for datasets in a classical vector scale

Class "rmult"

Compute distributions of empirical Mahalanobis distances based on simulations

The multivariate lognormal distribution

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

Compositional variogram model fitting

Compositional Goodness of fit test

Axis for ternary diagrams

simulatemissings

Artifical simulation of various kinds of missings/polluted data

robustnessInCompositions

Handling robustness issues and outliers in compositions.

wrapped_functions

Standard R functions wrapped for compatibility

Class "rplus"

Draws straight lines.

Subsetting of compositions

Variation matrices of amounts and compositions

Summarizing a compositional dataset in terms of ratios

Splitting datasets in groups given by factors

Residual variance of a model

Variogram functions

Zero-replacement routine

Summaries of amounts

vectorial arithmetic for data sets with rplus class

Variance covariance matrix of parameters in compositional regression

Uncentered log transform

simplemissingplot

Ternary diagrams

Draws straight lines from point to point.

Empirical variograms for compositions

Total sum of amounts

Variances and covariances of amounts and compositions