R: Compositional Data Analysis

# Compositional Data Analysis

## Documentation for package ‘compositions’ version 2.0-8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.

## Help Pages

A B C D E F G H I J K L M N O P Q R S T U V W Y Z misc

compositions-package | Compositional Data Analysis

## -- A --

Aar | Composition of glaciar sediments from the Aar massif (Switzerland)
acomp | Aitchison compositions
acomp-class | Class '"acomp"'
acompGOF.test | Compositional Goodness of fit test
acompGOF.test.formula | Compositional Goodness of fit test
acompGOF.test.list | Compositional Goodness of fit test
acompmargin | Marginal compositions in Aitchison Compositions
acompNormalGOF.test | Compositional Goodness of fit test
acompNormalLocation.test | Compositional Goodness of fit test
acompTwoSampleGOF.test | Compositional Goodness of fit test
Activity10 | Activity patterns of a statistician for 20 days
Activity31 | Activity patterns of a statistician for 20 days
AitchisonDistributionIntegrals | Aitchison Distribution
alr | Additive log ratio transform
alrInv | Additive log ratio transform
amounts-class | Class '"amounts"'
AnimalVegetation | Animal and vegetation measurement
anova | Standard R functions wrapped for compatibility
aplus | Amounts analysed in log-scale
aplus-class | Class '"aplus"'
apt | Additive planar transform
aptInv | Additive planar transform
ArcticLake | Artic lake sediment samples of different water depth
arrows3D | arrows in 3D, based on package rgl
arrows3D.default | arrows in 3D, based on package rgl
as.data.frame.acomp | Convert "compositions" classes to data frames or matrices
as.data.frame.aplus | Convert "compositions" classes to data frames or matrices
as.data.frame.ccomp | Convert "compositions" classes to data frames or matrices
as.data.frame.rcomp | Convert "compositions" classes to data frames or matrices
as.data.frame.rmult | Convert "compositions" classes to data frames or matrices
as.data.frame.rplus | Convert "compositions" classes to data frames or matrices
as.matrix.rmult | Convert "compositions" classes to data frames or matrices
as.missingSummary | Plot a Missing Summary
axis3D | Drawing a 3D coordiante system to a plot, based on package rgl

## -- B --

backtransform | Automatic common backtransformation for compositions
backtransform.rmult | Automatic common backtransformation for compositions
balance | Compute balances for a compositional dataset.
balance.acomp | Compute balances for a compositional dataset.
balance.aplus | Compute balances for a compositional dataset.
balance.rcomp | Compute balances for a compositional dataset.
balance.rplus | Compute balances for a compositional dataset.
balance01 | Compute balances for a compositional dataset.
balance01.acomp | Compute balances for a compositional dataset.
balance01.rcomp | Compute balances for a compositional dataset.
balanceBase | Compute balances for a compositional dataset.
balanceBase.acomp | Compute balances for a compositional dataset.
balanceBase.aplus | Compute balances for a compositional dataset.
balanceBase.rcomp | Compute balances for a compositional dataset.
balanceBase.rplus | Compute balances for a compositional dataset.
barplot.acomp | Bar charts of amounts
barplot.aplus | Bar charts of amounts
barplot.ccomp | Bar charts of amounts
barplot.rcomp | Bar charts of amounts
barplot.rplus | Bar charts of amounts
Bayesite | Permeabilities of bayesite
BDL | The policy of treatment of missing values in the "compositions" package
BDLvalue | The policy of treatment of missing values in the "compositions" package
binary | Treating binary and g-adic numbers
binary2logical | Treating binary and g-adic numbers
biplot3D | Three-dimensional biplots, based on package rgl
biplot3D.default | Three-dimensional biplots, based on package rgl
biplot3D.princomp | Three-dimensional biplots, based on package rgl
bit | Treating binary and g-adic numbers
bit.character | Treating binary and g-adic numbers
bit.numeric | Treating binary and g-adic numbers
bit<- | Treating binary and g-adic numbers
bit<-.character | Treating binary and g-adic numbers
bit<-.numeric | Treating binary and g-adic numbers
bitCount | Treating binary and g-adic numbers
Blood23 | Blood samples
Boxite | Compositions and depth of 25 specimens of boxite
boxplot.acomp | Displaying compositions and amounts with box-plots
boxplot.aplus | Displaying compositions and amounts with box-plots
boxplot.rcomp | Displaying compositions and amounts with box-plots
boxplot.rplus | Displaying compositions and amounts with box-plots

## -- C --

ccomp | Count compositions
ccomp-class | Class '"ccomp"'
ccompMultinomialGOF.test | Compositional Goodness of fit test
ccompPoissonGOF.test | Compositional Goodness of fit test
cdt | Centered default transform
cdt.acomp | Centered default transform
cdt.aplus | Centered default transform
cdt.ccomp | Centered default transform
cdt.data.frame | Centered default transform
cdt.default | Centered default transform
cdt.factor | Centered default transform
cdt.rcomp | Centered default transform
cdt.rmult | Centered default transform
cdt.rplus | Centered default transform
cdtInv | Centered default transform
cdtInv.acomp | Centered default transform
cdtInv.aplus | Centered default transform
cdtInv.ccomp | Centered default transform
cdtInv.data.frame | Centered default transform
cdtInv.default | Centered default transform
cdtInv.factor | Centered default transform
cdtInv.rcomp | Centered default transform
cdtInv.rmult | Centered default transform
cdtInv.rplus | Centered default transform
cgram2vgram | vgram2lrvgram
ClamEast | Color-size compositions of 20 clam colonies from East Bay
ClamWest | Color-size compositions of 20 clam colonies from West Bay
clo | Closure of a composition
clr | Centered log ratio transform
clr2ilr | Convert between clr and ilr, and between cpt and ipt.
clrInv | Centered log ratio transform
clrvar2ilr | Convert between clr and ilr, and between cpt and ipt.
clrvar2variation | Convert between clr and ilr, and between cpt and ipt.
ClusterFinder1 | Heuristics to find subpopulations of outliers
ClusterFinder1.acomp | Heuristics to find subpopulations of outliers
CoDaDendrogram | Dendrogram representation of acomp or rcomp objects
coerce-method | Class '"acomp"'
coerce-method | Class '"aplus"'
coerce-method | Class '"ccomp"'
coerce-method | Class '"rcomp"'
coerce-method | Class '"rmult"'
coerce-method | Class '"rplus"'
coerce<--method | Class '"acomp"'
coerce<--method | Class '"aplus"'
coerce<--method | Class '"ccomp"'
coerce<--method | Class '"rcomp"'
coerce<--method | Class '"rmult"'
coerce<--method | Class '"rplus"'
coloredBiplot | A biplot providing somewhat easier access to details of the plot.
coloredBiplot.default | A biplot providing somewhat easier access to details of the plot.
coloredBiplot.prcomp | A biplot providing somewhat easier access to details of the plot.
coloredBiplot.princomp | A biplot providing somewhat easier access to details of the plot.
colorsForOutliers1 | Create a color/char palette or for groups of outliers
colorsForOutliers2 | Create a color/char palette or for groups of outliers
CompLinModCoReg | Compositional Linear Model of Coregionalisation
compOKriging | Compositional Ordinary Kriging
composition.missing | The policy of treatment of missing values in the "compositions" package
composition.missings | The policy of treatment of missing values in the "compositions" package
compositional-class | Class '"compositional"'
compositions | Compositional Data Analysis
compositions.missing | The policy of treatment of missing values in the "compositions" package
compositions.missings | The policy of treatment of missing values in the "compositions" package
ConfRadius | Helper to compute confidence ellipsoids
convex.rcomp | Arithmetic operations for compositions in a real geometry
cor | Correlations of amounts and compositions
cor.acomp | Correlations of amounts and compositions
cor.aplus | Correlations of amounts and compositions
cor.default | Correlations of amounts and compositions
cor.rcomp | Correlations of amounts and compositions
cor.rmult | Correlations of amounts and compositions
cor.rplus | Correlations of amounts and compositions
cov | Variances and covariances of amounts and compositions
cov.acomp | Variances and covariances of amounts and compositions
cov.aplus | Variances and covariances of amounts and compositions
cov.default | Variances and covariances of amounts and compositions
cov.rcomp | Variances and covariances of amounts and compositions
cov.rmult | Variances and covariances of amounts and compositions
cov.rplus | Variances and covariances of amounts and compositions
Coxite | Compositions, depths and porosities of 25 specimens of coxite
cpt | Centered planar transform
cptInv | Centered planar transform

## -- D --

dAitchison | Aitchison Distribution
Data01 | Compositions of 25 specimens of hongite
Data02 | Compositions of 25 specimens of kongite
Data03 | Compositions and depth of 25 specimens of boxite
Data04 | Compositions, depths and porosities of 25 specimens of coxite
Data05 | Artic lake sediment samples of different water depth
Data06 | AFM compositions of 23 aphyric Skye lavas
Data07 | Proportions of supervisor's statements assigned to different categories
DATA08 | Household Expenditures
Data09 | Steroid metabolite patterns in adults and children
DATA10 | Activity patterns of a statistician for 20 days
Data11 | White-cell composition of 30 blood samples by two different methods
Data12 | Yatquat fruit evaluation
Data13 | Firework mixtures
Data14 | Color-size compositions of 20 clam colonies from East Bay
Data15 | Color-size compositions of 20 clam colonies from West Bay
Data16 | Serum Protein compositions of blood samples
Data17 | Diagnostic probabilities
DATA18 | Compositions and total pebble counts of 92 glacial tills
Data19 | Honk Kong Pogo-Jumps Championship
Data20 | Proportions of sand, silt and clay in sediments specimens
Data21 | Permeabilities of bayesite
Data22 | Shifts of machine operators
Data23 | Blood samples
Data24 | Measurement of skulls
Data25 | Animal and vegetation measurement
DATA31 | Activity patterns of a statistician for 20 days
dDirichlet | Dirichlet distribution
DiagnosticProb | Diagnostic probabilities
dist | Distances in variouse approaches
dist.default | Distances in variouse approaches
dlnorm.rplus | The multivariate lognormal distribution
dnorm.acomp | Normal distributions on special spaces
dnorm.aplus | Normal distributions on special spaces
dnorm.rmult | Normal distributions on special spaces

## -- E --

ellipses | Draw ellipses
ellipses.acomp | Draw ellipses
ellipses.aplus | Draw ellipses
ellipses.rcomp | Draw ellipses
ellipses.rmult | Draw ellipses
ellipses.rplus | Draw ellipses
endmemberCoordinates | Recast amounts as mixtures of end-members
endmemberCoordinates.acomp | Recast amounts as mixtures of end-members
endmemberCoordinates.aplus | Recast amounts as mixtures of end-members
endmemberCoordinates.default | Recast amounts as mixtures of end-members
endmemberCoordinates.rplus | Recast amounts as mixtures of end-members
endmemberCoordinatesInv | Recast amounts as mixtures of end-members
endmemberCoordinatesInv.acomp | Recast amounts as mixtures of end-members
endmemberCoordinatesInv.aplus | Recast amounts as mixtures of end-members
endmemberCoordinatesInv.rcomp | Recast amounts as mixtures of end-members
endmemberCoordinatesInv.rmult | Recast amounts as mixtures of end-members
endmemberCoordinatesInv.rplus | Recast amounts as mixtures of end-members

## -- F --

Firework | Firework mixtures
fit.lmc | Compositional variogram model fitting
fit.lmc.logratioVariogram | Compositional variogram model fitting
fitDirichlet | Fitting a Dirichlet distribution
fitSameMeanDifferentVarianceModel | Fit Same Mean Different Variance Model

## -- G --

gadic | Treating binary and g-adic numbers
Gauss.test | Classical Gauss Test
geometricmean | The geometric mean
geometricmeanCol | The geometric mean
geometricmeanRow | The geometric mean
getDetectionlimit | Gets the detection limit stored in the data set
getStickyClassOption | Subsetting of compositions
Glacial | Compositions and total pebble counts of 92 glacial tills
groupparts | Group amounts of parts
groupparts.acomp | Group amounts of parts
groupparts.aplus | Group amounts of parts
groupparts.ccomp | Group amounts of parts
groupparts.rcomp | Group amounts of parts
groupparts.rplus | Group amounts of parts
gsi.acompUniformityGOF.test | Compositional Goodness of fit test
gsi.geometricmean | The geometric mean
gsi.geometricmean.Col | The geometric mean
gsi.geometricmean.Row | The geometric mean
gsi.geometricmeanCol | The geometric mean
gsi.geometricmeanRow | The geometric mean
gsi.getV | Automatic common backtransformation for compositions
gsi.orig | Automatic common backtransformation for compositions
gsi.orSum | Treating binary and g-adic numbers
gsi.pStore | Compute distributions of empirical Mahalanobis distances based on simulations

## -- H --

has.missings | The policy of treatment of missing values in the "compositions" package
has.missings.default | The policy of treatment of missing values in the "compositions" package
has.missings.rmult | The policy of treatment of missing values in the "compositions" package
HEMF | Household Expenditures
Hongite | Compositions of 25 specimens of hongite
HouseholdExp | Household Expenditures
Hydrochem | Hydrochemical composition data set of Llobregat river basin water (NE Spain)

## -- I --

idt | Isometric default transform
idt.acomp | Isometric default transform
idt.aplus | Isometric default transform
idt.ccomp | Isometric default transform
idt.data.frame | Isometric default transform
idt.default | Isometric default transform
idt.factor | Isometric default transform
idt.rcomp | Isometric default transform
idt.rmult | Isometric default transform
idt.rplus | Isometric default transform
idtInv | Isometric default transform
idtInv.acomp | Isometric default transform
idtInv.aplus | Isometric default transform
idtInv.ccomp | Isometric default transform
idtInv.data.frame | Isometric default transform
idtInv.default | Isometric default transform
idtInv.factor | Isometric default transform
idtInv.rcomp | Isometric default transform
idtInv.rmult | Isometric default transform
idtInv.rplus | Isometric default transform
iit | Isometric identity transform
iitInv | Isometric identity transform
ilr | Isometric log ratio transform
ilr2clr | Convert between clr and ilr, and between cpt and ipt.
ilrBase | The canonical basis in the clr plane used for ilr and ipt transforms.
ilrBaseList | The canonical basis in the clr plane used for ilr and ipt transforms.
ilrInv | Isometric log ratio transform
ilrvar2clr | Convert between clr and ilr, and between cpt and ipt.
ilt | Isometric log transform
iltInv | Isometric log transform
ipt | Isometric planar transform
iptInv | Isometric planar transform
is.acomp | Check for compositional data type
is.aplus | Check for compositional data type
is.BDL | The policy of treatment of missing values in the "compositions" package
is.ccomp | Check for compositional data type
is.clrvar | Convert between clr and ilr, and between cpt and ipt.
is.ilrvar | Convert between clr and ilr, and between cpt and ipt.
is.MAR | The policy of treatment of missing values in the "compositions" package
is.MNAR | The policy of treatment of missing values in the "compositions" package
is.MNV | The policy of treatment of missing values in the "compositions" package
is.NMV | The policy of treatment of missing values in the "compositions" package
is.rcomp | Check for compositional data type
is.rmult | Check for compositional data type
is.rplus | Check for compositional data type
is.SZ | The policy of treatment of missing values in the "compositions" package
is.variation | Variation matrices of amounts and compositions
is.WMNAR | The policy of treatment of missing values in the "compositions" package
is.WZERO | The policy of treatment of missing values in the "compositions" package
IsMahalanobisOutlier | Checking for outliers
isoPortionLines | Isoportion- and Isoproportion-lines
isoPortionLines.acomp | Isoportion- and Isoproportion-lines
isoPortionLines.rcomp | Isoportion- and Isoproportion-lines
isoProportionLines | Isoportion- and Isoproportion-lines
isoProportionLines.acomp | Isoportion- and Isoproportion-lines
isoProportionLines.rcomp | Isoportion- and Isoproportion-lines

## -- J --

jura259 | The jura dataset
juraset | The jura dataset

## -- K --

Kappa | Uncentered log transform
kdeDirichlet | Density estimation on the simplex with Dirichlet kernel
kingTetrahedron | Ploting composition into rotable tetrahedron
Kongite | Compositions of 25 specimens of kongite

## -- L --

lines.acomp | Draws connected lines from point to point.
lines.aplus | Draws connected lines from point to point.
lines.rcomp | Draws connected lines from point to point.
lines.rmult | Draws connected lines from point to point.
lines.rplus | Draws connected lines from point to point.
logratioVariogram | Empirical variograms for compositions
logratioVariogram.acomp | Empirical variograms for compositions

## -- M --

MahalanobisDist | Compute Mahalanobis distances based von robust Estimations
MahalanobisDist.acomp | Compute Mahalanobis distances based von robust Estimations
MahalanobisDist.aplus | Compute Mahalanobis distances based von robust Estimations
MahalanobisDist.rcomp | Compute Mahalanobis distances based von robust Estimations
MahalanobisDist.rmult | Compute Mahalanobis distances based von robust Estimations
MahalanobisDist.rplus | Compute Mahalanobis distances based von robust Estimations
MAR | The policy of treatment of missing values in the "compositions" package
MARvalue | The policy of treatment of missing values in the "compositions" package
maxBit | Treating binary and g-adic numbers
maxBit.character | Treating binary and g-adic numbers
maxBit.numeric | Treating binary and g-adic numbers
mcor | Metric summary statistics of real, amount or compositional data
mcor.default | Metric summary statistics of real, amount or compositional data
mcov | Metric summary statistics of real, amount or compositional data
mcov.default | Metric summary statistics of real, amount or compositional data
mean.acomp | Mean amounts and mean compositions
mean.aplus | Mean amounts and mean compositions
mean.ccomp | Mean amounts and mean compositions
mean.col | The arithmetic mean of rows or columns
mean.rcomp | Mean amounts and mean compositions
mean.rmult | Mean amounts and mean compositions
mean.row | The arithmetic mean of rows or columns
mean.rplus | Mean amounts and mean compositions
meanCol | The arithmetic mean of rows or columns
meanRow | The arithmetic mean of rows or columns
Metabolites | Steroid metabolite patterns in adults and children
missingProjector | Returns a projector the the observed space in case of missings.
missingProjector.acomp | Returns a projector the the observed space in case of missings.
missingProjector.aplus | Returns a projector the the observed space in case of missings.
missingProjector.rcomp | Returns a projector the the observed space in case of missings.
missingProjector.rmult | Returns a projector the the observed space in case of missings.
missingProjector.rplus | Returns a projector the the observed space in case of missings.
missings | The policy of treatment of missing values in the "compositions" package
missingsInCompositions | The policy of treatment of missing values in the "compositions" package
missingSummary | Classify and summarize missing values in a dataset
missingType | Classify and summarize missing values in a dataset
mix.2acomp | Transformations from 'mixtures' to 'compositions' classes
mix.2aplus | Transformations from 'mixtures' to 'compositions' classes
mix.2rcomp | Transformations from 'mixtures' to 'compositions' classes
mix.2rmult | Transformations from 'mixtures' to 'compositions' classes
mix.2rplus | Transformations from 'mixtures' to 'compositions' classes
mix.Read | Reads a data file in a mixR format
MNAR | The policy of treatment of missing values in the "compositions" package
MNARvalue | The policy of treatment of missing values in the "compositions" package
msd | Metric summary statistics of real, amount or compositional data
msd.default | Metric summary statistics of real, amount or compositional data
mul.rplus | vectorial arithmetic for data sets with rplus class
mvar | Metric summary statistics of real, amount or compositional data
mvar.default | Metric summary statistics of real, amount or compositional data

## -- N --

names.acomp | The names of the parts
names.aplus | The names of the parts
names.ccomp | The names of the parts
names.rcomp | The names of the parts
names.rmult | The names of the parts
names.rplus | The names of the parts
names<-.acomp | The names of the parts
names<-.aplus | The names of the parts
names<-.ccomp | The names of the parts
names<-.rcomp | The names of the parts
names<-.rmult | The names of the parts
names<-.rplus | The names of the parts
NMV | The policy of treatment of missing values in the "compositions" package
noreplot | Modify parameters of compositional plots.
norm | Vector space norm
norm.acomp | Vector space norm
norm.aplus | Vector space norm
norm.default | Vector space norm
norm.matrix | Vector space norm
norm.rcomp | Vector space norm
norm.rmult | Vector space norm
norm.rplus | Vector space norm
normalize | Normalize vectors to norm 1
normalize.default | Normalize vectors to norm 1

## -- O --

observeWithAdditiveError | Artifical simulation of various kinds of missings/polluted data
observeWithDetectionLimit | Artifical simulation of various kinds of missings/polluted data
observeWithDetectionlimit | Artifical simulation of various kinds of missings/polluted data
oneOrDataset | Treating single compositions as one-row datasets
OutlierClassifier1 | Detect and classify compositional outliers.
OutlierClassifier1.acomp | Detect and classify compositional outliers.
outlierplot | Plot various graphics to analyse outliers.
outlierplot.acomp | Plot various graphics to analyse outliers.
outliersInCompositions | Analysing outliers in compositions.

## -- P --

pairs.acomp | Pairs plot method for compositions
pairs.rcomp | Pairs plot method for compositions
pairwisePlot | Creates a paneled plot like pairs for two different datasets.
pairwisePlot.default | Creates a paneled plot like pairs for two different datasets.
parameterPosdefClrMat | Unique parametrisations for matrices.
parameterPosdefMat | Unique parametrisations for matrices.
parameterRank1ClrMat | Unique parametrisations for matrices.
parameterRank1Mat | Unique parametrisations for matrices.
parametricPosdefClrMat | Unique parametrisations for matrices.
parametricPosdefMat | Unique parametrisations for matrices.
parametricRank1ClrMat | Unique parametrisations for matrices.
parametricRank1Mat | Unique parametrisations for matrices.
pchForOutliers1 | Create a color/char palette or for groups of outliers
pEmpiricalMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
perturbe | Perturbation of compositions
perturbe.aplus | vectorial arithmetic for data sets with aplus class
pHotellingsTsq | Hotellings T square distribution
plot.acomp | Ternary diagrams
plot.aplus | Displaying amounts in scatterplots
plot.ccomp | Ternary diagrams
plot.logratioVariogram | Empirical variograms for compositions
plot.missingSummary | Plot a Missing Summary
plot.princomp.acomp | Principal component analysis for Aitchison compositions
plot.princomp.aplus | Principal component analysis for amounts in log geometry
plot.princomp.rcomp | Principal component analysis for real compositions
plot.princomp.rplus | Principal component analysis for real amounts
plot.rcomp | Ternary diagrams
plot.relativeLoadings.princomp.acomp | Loadings of relations of two amounts
plot.relativeLoadings.princomp.aplus | Loadings of relations of two amounts
plot.relativeLoadings.princomp.rcomp | Loadings of relations of two amounts
plot.relativeLoadings.princomp.rplus | Loadings of relations of two amounts
plot.rmult | Displaying amounts in scatterplots
plot.rplus | Displaying amounts in scatterplots
plot3D | plot in 3D based on rgl
plot3D.acomp | 3D-plot of compositional data
plot3D.aplus | 3D-plot of positive data
plot3D.default | plot in 3D based on rgl
plot3D.rcomp | 3D-plot of compositional data
plot3D.rmult | plot in 3D based on rgl
plot3D.rplus | plot in 3D based on rgl
pMaxMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
PogoJump | Honk Kong Pogo-Jumps Championship
PoissonGOF.test | Compositional Goodness of fit test
power.acomp | Power transform in the simplex
power.aplus | vectorial arithmetic for data sets with aplus class
powerofpsdmatrix | power transform of a matrix
pPortionMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
pQuantileMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
predict.princomp.acomp | Principal component analysis for Aitchison compositions
predict.princomp.aplus | Principal component analysis for amounts in log geometry
predict.princomp.rcomp | Principal component analysis for real compositions
predict.princomp.rplus | Principal component analysis for real amounts
princomp.acomp | Principal component analysis for Aitchison compositions
princomp.aplus | Principal component analysis for amounts in log geometry
princomp.rcomp | Principal component analysis for real compositions
princomp.rmult | Principal component analysis for real data
princomp.rplus | Principal component analysis for real amounts
print.acomp | Printing compositional data.
print.aplus | Printing compositional data.
print.princomp.acomp | Principal component analysis for Aitchison compositions
print.princomp.aplus | Principal component analysis for amounts in log geometry
print.princomp.rcomp | Principal component analysis for real compositions
print.princomp.rplus | Principal component analysis for real amounts
print.rcomp | Printing compositional data.
print.relativeLoadings.princomp.acomp | Loadings of relations of two amounts
print.relativeLoadings.princomp.aplus | Loadings of relations of two amounts
print.relativeLoadings.princomp.rcomp | Loadings of relations of two amounts
print.relativeLoadings.princomp.rplus | Loadings of relations of two amounts
print.rmult | Simple treatment of real vectors
print.rplus | Printing compositional data.
pwlr | Pairwise log ratio transform
pwlrInv | Pairwise log ratio transform
pwlrPlot | Plots of pairwise logratio against a covariable.
pwlrplot | Plots of pairwise logratio against a covariable.

## -- Q --

qEmpiricalMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
qHotellingsTsq | Hotellings T square distribution
qMaxMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
qPortionMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
qqnorm.acomp | Normal quantile plots for compositions and amounts
qqnorm.aplus | Normal quantile plots for compositions and amounts
qqnorm.rcomp | Normal quantile plots for compositions and amounts
qqnorm.rplus | Normal quantile plots for compositions and amounts

## -- R --

R2 | R square
R2.default | R square
R2.lm | R square
rAitchison | Aitchison Distribution
rcomp | Compositions as elements of the simplex embedded in the D-dimensional real space
rcomp-class | Class '"rcomp"'
rcompmargin | Marginal compositions in real geometry
rDirichlet | Dirichlet distribution
rDirichlet.acomp | Dirichlet distribution
rDirichlet.rcomp | Dirichlet distribution
read.geoEAS | Reads a data file in a geoeas format
read.geoeas | Reads a data file in a geoeas format
relativeLoadings | Loadings of relations of two amounts
relativeLoadings.princomp.acomp | Loadings of relations of two amounts
relativeLoadings.princomp.aplus | Loadings of relations of two amounts
relativeLoadings.princomp.rcomp | Loadings of relations of two amounts
relativeLoadings.princomp.rplus | Loadings of relations of two amounts
rEmpiricalMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
replot | Modify parameters of compositional plots.
replotable | Modify parameters of compositional plots.
rlnorm.rplus | The multivariate lognormal distribution
rMaxMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
rmult | Simple treatment of real vectors
rmult-class | Class '"rmult"'
rmultinom.ccomp | Simulate count compositions without overdispersion
rnorm.acomp | Normal distributions on special spaces
rnorm.aplus | Normal distributions on special spaces
rnorm.ccomp | Normal distributions on special spaces
rnorm.rcomp | Normal distributions on special spaces
rnorm.rmult | Normal distributions on special spaces
rnorm.rplus | Normal distributions on special spaces
robust | Handling robustness issues and outliers in compositions.
robustnessInCompositions | Handling robustness issues and outliers in compositions.
rplus | Amounts i.e. positive numbers analysed as objects of the real vector space
rplus-class | Class '"rplus"'
rpois.ccomp | Simulate count compositions without overdispersion
rPortionMahalanobis | Compute distributions of empirical Mahalanobis distances based on simulations
Rsquare | R square
runif.acomp | The uniform distribution on the simplex
runif.rcomp | The uniform distribution on the simplex

## -- S --

sa.dirichlet | Simulated amount datasets
sa.dirichlet.dil | Simulated amount datasets
sa.dirichlet.mix | Simulated amount datasets
sa.dirichlet5 | Simulated amount datasets
sa.dirichlet5.dil | Simulated amount datasets
sa.dirichlet5.mix | Simulated amount datasets
sa.groups | Simulated amount datasets
sa.groups.area | Simulated amount datasets
sa.groups.dil | Simulated amount datasets
sa.groups.mix | Simulated amount datasets
sa.groups5 | Simulated amount datasets
sa.groups5.area | Simulated amount datasets
sa.groups5.dil | Simulated amount datasets
sa.groups5.mix | Simulated amount datasets
sa.lognormals | Simulated amount datasets
sa.lognormals.dil | Simulated amount datasets
sa.lognormals.mix | Simulated amount datasets
sa.lognormals5 | Simulated amount datasets
sa.lognormals5.dil | Simulated amount datasets
sa.lognormals5.mix | Simulated amount datasets
sa.missings | Simulated amount datasets
sa.missings5 | Simulated amount datasets
sa.outliers1 | Simulated amount datasets
sa.outliers2 | Simulated amount datasets
sa.outliers3 | Simulated amount datasets
sa.outliers4 | Simulated amount datasets
sa.outliers5 | Simulated amount datasets
sa.outliers6 | Simulated amount datasets
sa.tnormals | Simulated amount datasets
sa.tnormals.dil | Simulated amount datasets
sa.tnormals.mix | Simulated amount datasets
sa.tnormals5 | Simulated amount datasets
sa.tnormals5.dil | Simulated amount datasets
sa.tnormals5.mix | Simulated amount datasets
sa.uniform | Simulated amount datasets
sa.uniform.dil | Simulated amount datasets
sa.uniform.mix | Simulated amount datasets
sa.uniform5 | Simulated amount datasets
sa.uniform5.dil | Simulated amount datasets
sa.uniform5.mix | Simulated amount datasets
scalar | Parallel scalar products
scalar.default | Parallel scalar products
scale | Normalizing datasets by centering and scaling
scale.acomp | Normalizing datasets by centering and scaling
scale.aplus | Normalizing datasets by centering and scaling
scale.default | Normalizing datasets by centering and scaling
scale.rcomp | Normalizing datasets by centering and scaling
scale.rmult | Normalizing datasets by centering and scaling
scale.rplus | Normalizing datasets by centering and scaling
Sediments | Proportions of sand, silt and clay in sediments specimens
segments | Draws straight lines from point to point.
segments.acomp | Draws straight lines from point to point.
segments.aplus | Draws straight lines from point to point.
segments.default | Draws straight lines from point to point.
segments.rcomp | Draws straight lines from point to point.
segments.rmult | Draws straight lines from point to point.
segments.rplus | Draws straight lines from point to point.
SerumProtein | Serum Protein compositions of blood samples
setStickyClassOption | Subsetting of compositions
ShiftOperators | Shifts of machine operators
simpleMissingSubplot | Ternary diagrams
SimulatedAmounts | Simulated amount datasets
simulateMissings | Artifical simulation of various kinds of missings/polluted data
Skulls | Measurement of skulls
SkyeAFM | AFM compositions of 23 aphyric Skye lavas
split.acomp | Splitting datasets in groups given by factors
split.aplus | Splitting datasets in groups given by factors
split.ccomp | Splitting datasets in groups given by factors
split.rcomp | Splitting datasets in groups given by factors
split.rmult | Splitting datasets in groups given by factors
split.rplus | Splitting datasets in groups given by factors
straight | Draws straight lines.
straight.acomp | Draws straight lines.
straight.aplus | Draws straight lines.
straight.rcomp | Draws straight lines.
straight.rmult | Draws straight lines.
straight.rplus | Draws straight lines.
summary.acomp | Summarizing a compositional dataset in terms of ratios
summary.aplus | Summaries of amounts
summary.rcomp | Summary of compositions in real geometry
summary.rmult | Summaries of amounts
summary.rplus | Summaries of amounts
sumMissingProjector | Compute the global projector to the observed subspace.
sumMissingProjector.acomp | Compute the global projector to the observed subspace.
sumMissingProjector.aplus | Compute the global projector to the observed subspace.
sumMissingProjector.rcomp | Compute the global projector to the observed subspace.
sumMissingProjector.rmult | Compute the global projector to the observed subspace.
sumMissingProjector.rplus | Compute the global projector to the observed subspace.
Supervisor | Proportions of supervisor's statements assigned to different categories
SZ | The policy of treatment of missing values in the "compositions" package
SZvalue | The policy of treatment of missing values in the "compositions" package

## -- T --

ternaryAxis | Axis for ternary diagrams
totals | Total sum of amounts
totals.acomp | Total sum of amounts
totals.aplus | Total sum of amounts
totals.ccomp | Total sum of amounts
totals.rcomp | Total sum of amounts
totals.rplus | Total sum of amounts
tryDebugger | Empirical variograms for compositions

## -- U --

uciptInv | Isometric planar transform
ult | Uncentered log transform
ultInv | Uncentered log transform
unbinary | Treating binary and g-adic numbers

## -- V --

var | Variances and covariances of amounts and compositions
var.acomp | Variances and covariances of amounts and compositions
var.aplus | Variances and covariances of amounts and compositions
var.default | Variances and covariances of amounts and compositions
var.lm | Residual variance of a model
var.mlm | Residual variance of a model
var.rcomp | Variances and covariances of amounts and compositions
var.rmult | Variances and covariances of amounts and compositions
var.rplus | Variances and covariances of amounts and compositions
variation | Variation matrices of amounts and compositions
variation.acomp | Variation matrices of amounts and compositions
variation.aplus | Variation matrices of amounts and compositions
variation.default | Variation matrices of amounts and compositions
variation.rcomp | Variation matrices of amounts and compositions
variation.rmult | Variation matrices of amounts and compositions
variation.rplus | Variation matrices of amounts and compositions
variation2clrvar | Convert between clr and ilr, and between cpt and ipt.
vcovAcomp | Variance covariance matrix of parameters in compositional regression
vgmFit | Compositional variogram model fitting
vgmFit2lrv | Compositional variogram model fitting
vgmGetParameters | Compositional variogram model fitting
vgmGof | Compositional variogram model fitting
vgmSetParameters | Compositional variogram model fitting
vgram.cardsin | Variogram functions
vgram.exp | Variogram functions
vgram.gauss | Variogram functions
vgram.lin | Variogram functions
vgram.nugget | Variogram functions
vgram.pow | Variogram functions
vgram.sph | Variogram functions
vgram2lrvgram | vgram2lrvgram
vp.boxplot | Displaying compositions and amounts with box-plots
vp.diffdensityplot | Pairs plot method for compositions
vp.kde2dplot | Pairs plot method for compositions
vp.logboxplot | Displaying compositions and amounts with box-plots
vp.lrboxplot | Pairs plot method for compositions
vp.lrdensityplot | Pairs plot method for compositions
vp.qqnorm | Normal quantile plots for compositions and amounts

## -- W --

whichBits | Treating binary and g-adic numbers
WhiteCells | White-cell composition of 30 blood samples by two different methods

## -- Y --

Yatquat | Yatquat fruit evaluation

## -- Z --

zeroreplace | Zero-replacement routine

## -- misc --

$.acomp | Subsetting of compositions
$.aplus | Subsetting of compositions
$.ccomp | Subsetting of compositions
$.rcomp | Subsetting of compositions
$.rmult | Subsetting of compositions
$.rplus | Subsetting of compositions
%*% | inner product for matrices and vectors
%*%.acomp | inner product for datasets with a vector space structure
%*%.aplus | inner product for datasets with a vector space structure
%*%.default | inner product for matrices and vectors
%*%.rmult | inner product for datasets with vector scale
*.acomp | Power transform in the simplex
*.aplus | vectorial arithmetic for data sets with aplus class
*.rcomp | Arithmetic operations for compositions in a real geometry
*.rmult | vectorial arithmetic for datasets in a classical vector scale
*.rplus | vectorial arithmetic for data sets with rplus class
+.acomp | Perturbation of compositions
+.aplus | vectorial arithmetic for data sets with aplus class
+.rcomp | Arithmetic operations for compositions in a real geometry
+.rmult | vectorial arithmetic for datasets in a classical vector scale
+.rplus | vectorial arithmetic for data sets with rplus class
-.acomp | Perturbation of compositions
-.aplus | vectorial arithmetic for data sets with aplus class
-.rcomp | Arithmetic operations for compositions in a real geometry
-.rmult | vectorial arithmetic for datasets in a classical vector scale
-.rplus | vectorial arithmetic for data sets with rplus class
/.acomp | Power transform in the simplex
/.aplus | vectorial arithmetic for data sets with aplus class
/.rcomp | Arithmetic operations for compositions in a real geometry
/.rmult | vectorial arithmetic for datasets in a classical vector scale
/.rplus | vectorial arithmetic for data sets with rplus class
[.acomp | Subsetting of compositions
[.aplus | Subsetting of compositions
[.ccomp | Subsetting of compositions
[.rcomp | Subsetting of compositions
[.rmult | Subsetting of compositions
[.rplus | Subsetting of compositions