Compositional Data Analysis


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Documentation for package ‘compositions’ version 2.0-1

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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
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
as.data.frame.aplus Convert "compositions" classes to data frames
as.data.frame.ccomp Convert "compositions" classes to data frames
as.data.frame.rcomp Convert "compositions" classes to data frames
as.data.frame.rmult Convert "compositions" classes to data frames
as.data.frame.rplus Convert "compositions" classes to data frames
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
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
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

-- 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.acomp Draws straight lines from point to point.
segments.aplus 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