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compositions (version 1.40-2)

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

9,016

Version

1.40-2

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

June 14th, 2018

Functions in compositions (1.40-2)

Measurement of skulls

CompLinModCoReg

Compositional Linear Model of Coregionalisation

Compositions, depths and porosities of 25 specimens of coxite

Serum Protein compositions of blood samples

Hotellings T square distribution

Additive planar transform

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

Centered default transform

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

Compositional Goodness of fit test

colorsForOutliers

Create a color/char palette or for groups of outliers

arrows in 3D, based on package rgl

Shifts of machine operators

Honk Kong Pogo-Jumps Championship

Compositional Ordinary Kriging

AFM compositions of 23 aphyric Skye lavas

Steroid metabolite patterns in adults and children

Household Expenditures

Amounts analysed in log-scale

Distances in variouse approaches

vectorial arithmetic for data sets with aplus class

Proportions of supervisor's statements assigned to different categories

The geometric mean

Treating binary and g-adic numbers

Proportions of sand, silt and clay in sediments specimens

compositions-package

Internal function: row and column sums of matrices

Three-dimensional biplots, based on package rgl

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

Aitchison compositions

missing.compositions

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

Environment containing the old gsi functions

Yatquat fruit evaluation

Compositions of 25 specimens of kongite

gsi.diagExtract

Internal functions: Get the diagonal of a matrix

Internal function: Invert a permutation

gsi.isSingleRow

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

Power transform in the simplex

getdetectionlimit

Gets the detection limit stored in the data set

Compute balances for a compositional dataset.

Displaying compositions and amounts with box-plots

Internal functions: Storing integers as reals

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

Isometric identity transform

Bar charts of amounts

Internal function: give a derived subclass to an object

Draws connected lines from point to point.

Isometric log ratio transform

Count compositions

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

Dendrogram representation of acomp or rcomp objects

Closure of a composition

fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model

Classical Gauss Test

Heuristics to find subpopulations of outliers

logratioVariogram

Empirical variograms for compositions

Internal functions: Parallel operations of single and multiple datasets

Internal functions: A conditional drop

Internal functions of the compositions package

gsi.diagGenerate

Internal functions: Generate a diagonal matrix

endmemberCoordinates

Recast amounts as mixtures of end-members

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

Internal functions of the compositions package

Fitting a Dirichlet distribution

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

Internal functions of the compositions package

gsi.expandrcomp

Internal function: Scaling rcomp

transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes

Reads a data file in a mixR format

Isometric log transform

Treating single compositions as one-row datasets

The jura dataset

Calling from a function with the own parameters

Internal function: Recode missings with IEEE number and vice versa

outlierclassifier

Detect and classify compositional outliers.

plot in 3D based on rgl

plotlogratioVariogram

Empirical variograms for compositions

kingTetrahedron

Ploting composition into rotable tetrahedron

Normal quantile plots for compositions and amounts

missingProjector

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

Modify parameters of compositional plots.

The multivariate lognormal distribution

Simulate count compositions without overdispersion

Centered log ratio transform

Internal functions of the compositions package

Internal functions of the compositions package

Correlations of amounts and compositions

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

Internal functions of the compositions package

Classify and summarize missing values in a dataset

Internal functions of the compositions package

Dirichlet distribution

Centered planar transform

Compositional Goodness of fit test

The uniform distribution on the simplex

Internal function: Checking equality of IEEE special numbers

Internal function: Compute a desired compositional margin

Internal variable: Negligible differences

Perturbation of compositions

gsi.merge2signary

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

MahalanobisDist

Compute Mahalanobis distances based von robust Estimations

Summary of compositions in real geometry

Variances and covariances of amounts and compositions

powerofpsdmatrix

power transform of a matrix

Group amounts of parts

Summaries of amounts

Ternary diagrams

gsi.varwithlosts

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

Variation matrices of amounts and compositions

Isometric default transform

Metric summary statistics of real, amount or compositional data

Check for compositional data type

Isometric planar transform

inner product for matrices and vectors

acompscalarproduct

inner product for datasets with a vector space structure

Principal component analysis for real data

gsigetBalStruct

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

Creates a paneled plot like pairs for two different datasets.

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

Principal component analysis for Aitchison compositions

Marginal compositions in real geometry

The names of the parts

Principal component analysis for real amounts

Read standard data files

Reads a data file in a geoeas format

Unique parametrisations for matrices.

Plot various graphics to analyse outliers.

3D-plot of positive data

Internal functions of the compositions package

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

plot in 3D based on rgl

Internal function: Convert to plain vector or matrix

outliersInCompositions

Analysing outliers in compositions.

Internal function: Solves singular and non square equation systems

Internal function: A panel displaying a label only

Printing compositional data.

IsMahalanobisOutlier

Checking for outliers

vectorial arithmetic for data sets with rplus class

plot in 3D based on rgl

3D-plot of compositional data

isoPortionLines

Isoportion- and Isoproportion-lines

Plots of pairwise logratio against a covariable.

Principal component analysis for amounts in log geometry

Principal component analysis for real compositions

vectorial arithmetic for datasets in a classical vector scale

Simple treatment of real vectors

inner product for datasets with vector scale

Compute distributions of empirical Mahalanobis distances based on simulations

Draws straight lines from point to point.

Parallel scalar products

Compute the global projector to the observed subspace.

simulatemissings

Artifical simulation of various kinds of missings/polluted data

Normalizing datasets by centering and scaling

Axis for ternary diagrams

Mean amounts and mean compositions

simplemissingplot

Ternary diagrams

Zero-replacement routine

Variogram functions

The arithmetic mean of rows or columns

Splitting datasets in groups given by factors

Draws straight lines.

Residual variance of a model

Summarizing a compositional dataset in terms of ratios

Vector space norm

Empirical variograms for compositions

plotmissingsummary

Plot a Missing Summary

Displaying amounts in scatterplots

Normalize vectors to norm 1

Uncentered log transform

Aitchison Distribution

Arithmetic operations for compositions in a real geometry

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

Loadings of relations of two amounts

Normal distributions on special spaces

Compositional Goodness of fit test

robustnessInCompositions

Handling robustness issues and outliers in compositions.

Total sum of amounts

Variance covariance matrix of parameters in compositional regression

Compositional variogram model fitting

Compositions and depth of 25 specimens of boxite

AnimalVegetation

Animal and vegetation measurement

Artic lake sediment samples of different water depth

Activity patterns of a statistician for 20 days

Activity patterns of a statistician for 20 days

Permeabilities of bayesite

Color-size compositions of 20 clam colonies from East Bay

Diagnostic probabilities

Firework mixtures

Compositions of 25 specimens of hongite

Color-size compositions of 20 clam colonies from West Bay

Compositions and total pebble counts of 92 glacial tills

Helper to compute confidence ellipsoids

SimulatedAmounts

Simulated amount datasets

Convert "compositions" classes to data frames

Marginal compositions in Aitchison Compositions

Additive log ratio transform