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compositions (version 1.01-1)

Compositional Data Analysis

Description

The package 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 Aitchison and Pawlowsky-Glahn.

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Version

Install

install.packages('compositions')

Monthly Downloads

10,852

Version

1.01-1

License

GPL version 2 or newer

Maintainer

K Gerald van den Boogaart

Last Published

February 1st, 2024

Functions in compositions (1.01-1)

gsi.varwithlosts

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

Internal functions of the compositions package

The names of the parts

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

Diagnostic probabilities

vectorial arithmetic for datasets in a classical vector scale

Serum Protein compositions of blood samples

Compute balances for a compositional dataset.

Activity patterns of a statistician for 20 days

Compositions of 25 specimens of hongite

gsi.expandrcomp

Internal function: Scaling rcomp

arrows in 3D, based on package rgl

gsi.isSingleRow

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

Closure of a composition

Additive planar transform

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

Centered planar transform

Internal functions: A conditional drop

Heuristics to find subpopulations of outliers

Proportions of sand, silt and clay in sediments specimens

Centered default transform

Dendrogram representation of acomp or rcomp objects

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

Internal functions of the compositions package

Environment containing the the old gsi functions

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

endmemberCoordinates

Recast amounts as mixtures of end-members

Internal variable: Negligible differences

Internal functions: Storing integers as reals

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

Internal function: give a derived subclass to an object

Vector space norm

Internal function: Convert to plain vector or matrix

vectorial arithmetic for data sets with rplus class

getdetectionlimit

Gets the detection limit stored in the data set

Isometric planar transform

Principal component analysis for amounts in log geometry

Compute distributions of empirical Mahalanobis distances based on simulations

Internal functions of the compositions package

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

Compositions, depths and porosities of 25 specimens of coxite

Activity patterns of a statistician for 20 days

Distances in variouse approaches

Variances and covariances of amounts and compositions

Principal component analysis for real amounts

Modify parameters of compositional plots.

Read standard data files

Reads a data file in a geoeas format

Compositions and depth of 25 specimens of boxite

AFM compositions of 23 aphyric Skye lavas

Internal functions of the compositions package

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

Color-size compositions of 20 clam colonies from East Bay

Amounts analysed in log-scale

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

Additive log ratio transform

Internal functions of the compositions package

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

Normal distributions on special spaces

Color-size compositions of 20 clam colonies from West Bay

Shifts of machine operators

Honk Kong Pogo-Jumps Championship

Compositions and total pebble counts of 92 glacial tills

Internal functions of the compositions package

Isometric log transform

Plot various graphics to analyse outliers.

Power transform in the simplex

Internal function: Invert a permutation

Axis for ternary diagrams

IsMahalanobisOutlier

Checking for outliers

Compositions of 25 specimens of kongite

gsi.merge2signary

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

Measurement of skulls

Internal functions: Parallel operations of single and multiple datasets

inner product for matrices and vectors

outliersInCompositions

Analysing outliers in compositions.

Parallel scalar products

Proportions of supervisor's statements assigned to different categories

Firework mixtures

Bar charts of amounts

Isometric log ratio transform

Artic lake sediment samples of different water depth

missingProjector

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

Internal function: row and column sums of matrices

Principal component analysis for Aitchison compositions

missing.compositions

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

Marginal compositions in Aitchison Compositions

Steroid metabolite patterns in adults and children

3D-plot of positive data

simplemissingplot

Ternary diagrams

Three-dimensional biplots, based on package rgl

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

Splitting datasets in groups given by factors

Normalizing datasets by centering and scaling

gsigetBalStruct

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

Draws straight lines from point to point.

Yatquat fruit evaluation

Mean amounts and mean compositions

Internal function: A panel displaying a label only

powerofpsdmatrix

power transform of a matrix

plot in 3D based on rgl

SimulatedAmounts

Simulated amount datasets

Aitchison compositions

Internal function: Compute a desired compositional margin

kingTetrahedron

Ploting composition into rotable tetrahedron

Principal component analysis for real compositions

Internal function: Solves singular and non square equation systems

outlierclassifier

Detect and classify compositional outliers.

Reads a data file in a mixR format

Correlations of amounts and compositions

Internal functions of the compositions package

Check for compositional data type

Isometric identity transform

Creates a paneled plot like pairs for two different datasets.

Summarizing a compositional dataset in terms of ratios

Convert "compositions" classes to data frames

Draws connected lines from point to point.

Ternary diagrams

Internal function: Recode missings with IEEE number and vice versa

Classify and summarize missing values in a dataset

Summary of compositions in real geometry

Normal quantile plots for compositions and amounts

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

plotmissingsummary

Plot a Missing Summary

Marginal compositions in real geometry

AnimalVegetation

Animal and vegetation measurement

The multivariate lognormal distribution

Displaying compositions and amounts with box-plots

Treating single compositions as one-row datasets

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

Simple treatment of real vectors

Metric summary statistics of real, amount or compositional data

Draws straight lines.

acompscalarproduct

inner product for datasets with a vector space structure

inner product for datasets with vector scale

Permeabilities of bayesite

Loadings of relations of two amounts

vectorial arithmetic for data sets with aplus class

Internal function: Checking equality of IEEE special numbers

Zero-replacement routine

Normalize vectors to norm 1

Treating binary and g-adic numbers

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Printing compositional data.

isoPortionLines

Isoportion- and Isoproportion-lines

The arithmetic mean of rows or columns

plot in 3D based on rgl

Summaries of amounts

Displaying amounts in scatterplots

Arithmetic operations for compositions in a real geometry

Principal component analysis for real data

Household Expenditures

Dirichlet distribution

simulatemissings

Artifical simulation of various kinds of missings

Total sum of amounts

Variation matrices of amounts and compositions

Centered log ratio transform

Calling from a function with the own parameters

Uncentered log transform

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

colorsForOutliers

Create a color/char palette or for groups of outliers

Perturbation of compositions

The uniform distribution on the simplex

The geometric mean

compositions-package

library(compositions)

Group amounts of parts

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

Isometric default transform

Compute the global projector to the observed subspace.