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compositions (version 1.10-1)

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

11,499

Version

1.10-1

License

GPL (>= 2)

Maintainer

K Gerald van den Boogaart

Last Published

December 7th, 2010

Functions in compositions (1.10-1)

gsireset3D

Internal functions of the compositions package
rcomp

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

Bar charts of amounts
rlnorm

The multivariate lognormal distribution
outlierplot

Plot various graphics to analyse outliers.
R2

R square
scale

Normalizing datasets by centering and scaling
straight

Draws straight lines.
CompLinModCoReg

Compositional Linear Model of Coregionalisation
AnimalVegetation

Animal and vegetation measurement
Kongite

Compositions of 25 specimens of kongite
ArcticLake

Artic lake sediment samples of different water depth
acomparith

Power transform in the simplex
Metabolites

Steroid metabolite patterns in adults and children
ClusterFinder1

Heuristics to find subpopulations of outliers
Coxite

Compositions, depths and porosities of 25 specimens of coxite
acomp

Aitchison compositions
clr2ilr

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

Yatquat fruit evaluation
ClamWest

Color-size compositions of 20 clam colonies from West Bay
ccompgof

Compositional Goodness of fit test
endmemberCoordinates

Recast amounts as mixtures of end-members
Hongite

Compositions of 25 specimens of hongite
balance

Compute balances for a compositional dataset.
clr

Centered log ratio transform
coloredBiplot

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

Simulated amount datasets
gsiinternal2

Internal functions of the compositions package
boxplot

Displaying compositions and amounts with box-plots
binary

Treating binary and g-adic numbers
WhiteCells

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

Additive planar transform
ellipses

Draw ellipses
Activity31

Activity patterns of a statistician for 20 days
missingsummary

Classify and summarize missing values in a dataset
Glacial

Compositions and total pebble counts of 92 glacial tills
DiagnosticProb

Diagnostic probabilities
compositions-package

library(compositions)
arrows3D

arrows in 3D, based on package rgl
Skulls

Measurement of skulls
gsiCoorInfo

Internal functions of the compositions package
axis3D

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

The geometric mean
ShiftOperators

Shifts of machine operators
gsi.csum

Internal function: row and column sums of matrices
clo

Closure of a composition
alr

Additive log ratio transform
Blood23

Blood samples
Sediments

Proportions of sand, silt and clay in sediments specimens
Firework

Firework mixtures
HouseholdExp

Household Expenditures
gsi.plain

Internal function: Convert to plain vector or matrix
gsigetBalStruct

An Auxiliary functions to compute user-defined ilr and ipt transforms.
biplot3D

Three-dimensional biplots, based on package rgl
ternaryAxis

Axis for ternary diagrams
cor.acomp

Correlations of amounts and compositions
gsi.mapin01

Internal functions: Storing integers as reals
jura

The jura dataset
as.data.frame

Convert "compositions" classes to data frames
plotlogratioVariogram

Empirical variograms for compositions
HotellingsTsq

Hotellings T square distribution
SerumProtein

Serum Protein compositions of blood samples
compOKriging

Compositional Ordinary Kriging
gsicall

Internal functions of the compositions package
missing.compositions

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

Compute Mahalanobis distances based von robust Estimations
SkyeAFM

AFM compositions of 23 aphyric Skye lavas
gsi.simshape

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

Honk Kong Pogo-Jumps Championship
gsi.eps

Internal variable: Negligible differences
aplusarithm

vectorial arithmetic for data sets with aplus class
rMahalanobis

Compute distributions of empirical Mahalanobis distances based on simulations
powerofpsdmatrix

power transform of a matrix
gsi.diagGenerate

Internal functions: Generate a diagonal matrix
ccomp

Count compositions
gsi.eq

Internal function: Checking equality of IEEE special numbers
iit

Isometric identity transform
aplus

Amounts analysed in log-scale
fitdirichlet

Fitting a Dirichlet distribution
names

The names of the parts
meanrow

The arithmetic mean of rows or columns
pairwiseplot

Creates a paneled plot like pairs for two different datasets.
gof

Compositional Goodness of fit test
gsi.getD

Interal function: Get number of samples and number of parts in a compositional object
plot3D

plot in 3D based on rgl
Supervisor

Proportions of supervisor's statements assigned to different categories
gsiinternal

Environment containing the the old gsi functions
mvar

Metric summary statistics of real, amount or compositional data
cdt

Centered default transform
simplemissingplot

Ternary diagrams
ipt

Isometric planar transform
summary.aplus

Summaries of amounts
gsi.drop

Internal functions: A conditional drop
dist

Distances in variouse approaches
ConfRadius

Helper to compute confidence ellipsoids
Hydrochem

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

Permeabilities of bayesite
cpt

Centered planar transform
ClamEast

Color-size compositions of 20 clam colonies from East Bay
gsi.diagExtract

Internal functions: Get the diagonal of a matrix
fitSameMeanDifferentVarianceModel

Fit Same Mean Different Variance Model
groupparts

Group amounts of parts
plot.aplus

Displaying amounts in scatterplots
gsi.addclass

Internal function: give a derived subclass to an object
gsi.isSingleRow

Internal function: Can something be considered as a single multivariate data item?
plot3Daplus

3D-plot of positive data
logratioVariogram

Empirical variograms for compositions
gsiinternal1

Internal functions of the compositions package
gsi.margin

Internal function: Compute a desired compositional margin
gausstest

Classical Gauss Test
lines

Draws connected lines from point to point.
gsiplotmargin

Internal functions of the compositions package
gsi.expandrcomp

Internal function: Scaling rcomp
rnorm

Normal distributions on special spaces
is.acomp

Check for compositional data type
perturbe

Perturbation of compositions
acompscalarproduct

inner product for datasets with a vector space structure
ilrBase

The canonical basis in the clr plane used for ilr and ipt transforms.
Read standard data files

Reads a data file in a geoeas format
gsipairs

Internal functions of the compositions package
gsi.merge2signary

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

Loadings of relations of two amounts
IsMahalanobisOutlier

Checking for outliers
norm

Vector space norm
gsi.varwithlosts

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

Draws straight lines from point to point.
normalize

Normalize vectors to norm 1
mean.acomp

Mean amounts and mean compositions
oneOrDataset

Treating single compositions as one-row datasets
rAitchison

Aitchison Distribution
gsiinternal3

Internal functions of the compositions package
parametricMat

Unique parametrisations for matrices.
outliersInCompositions

Analysing outliers in compositions.
robustnessInCompositions

Handling robustness issues and outliers in compositions.
idt

Isometric default transform
rmult

Simple treatment of real vectors
gsi2.invperm

Internal function: Invert a permutation
gsi.svdsolve

Internal function: Solves singular and non square equation systems
gsi.textpanel

Internal function: A panel displaying a label only
mix.Read

Reads a data file in a mixR format
princomp.aplus

Principal component analysis for amounts in log geometry
summary.acomp

Summarizing a compositional dataset in terms of ratios
lrvgram

vgram2lrvgram
princomp.rcomp

Principal component analysis for real compositions
rmultmatmult

inner product for datasets with vector scale
plot3Dacomp

3D-plot of compositional data
rcomparithm

Arithmetic operations for compositions in a real geometry
rcompmargin

Marginal compositions in real geometry
plot.acomp

Ternary diagrams
ilt

Isometric log transform
princomp.rplus

Principal component analysis for real amounts
princomp.acomp

Principal component analysis for Aitchison compositions
matmult

inner product for matrices and vectors
gsifiltercall

Calling from a function with the own parameters
isoPortionLines

Isoportion- and Isoproportion-lines
princomp.rmult

Principal component analysis for real data
plot3Drplus

plot in 3D based on rgl
plotmissingsummary

Plot a Missing Summary
rmultarithm

vectorial arithmetic for datasets in a classical vector scale
print.acomp

Printing compositional data.
split

Splitting datasets in groups given by factors
rplus

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

Artifical simulation of various kinds of missings
rplusarithm

vectorial arithmetic for data sets with rplus class
summary.rcomp

Summary of compositions in real geometry
rDirichlet

Dirichlet distribution
runif

The uniform distribution on the simplex
variation

Variation matrices of amounts and compositions
scalar

Parallel scalar products
sumprojector

Compute the global projector to the observed subspace.
totals

Total sum of amounts
rpois

Simulate count compositions without overdispersion
vcovAcomp

Variance covariance matrix of parameters in compositional regression
zeroreplace

Zero-replacement routine
varmlm

Residual variance of a model
NormalTests

Compositional Goodness of fit test
var.acomp

Variances and covariances of amounts and compositions
vgmFit

Compositional variogram model fitting
variograms

Variogram functions
ult

Uncentered log transform
replot

Modify parameters of compositional plots.
acompmargin

Marginal compositions in Aitchison Compositions
colorsForOutliers

Create a color/char palette or for groups of outliers
gsi.add

Internal functions: Parallel operations of single and multiple datasets
gsi.recode

Internal function: Recode missings with IEEE number and vice versa
kingTetrahedron

Ploting composition into rotable tetrahedron
ilr

Isometric log ratio transform
outlierclassifier

Detect and classify compositional outliers.
plot3Drmult

plot in 3D based on rgl
Activity10

Activity patterns of a statistician for 20 days
Boxite

Compositions and depth of 25 specimens of boxite
CoDaDendrogram

Dendrogram representation of acomp or rcomp objects
getdetectionlimit

Gets the detection limit stored in the data set
transformations from 'mixtures' to 'compositions' classes

Transformations from 'mixtures' to 'compositions' classes
missingProjector

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

Normal quantile plots for compositions and amounts
tryDebugger

Empirical variograms for compositions