# Compositional Data Analysis

## Documentation for package `compositions' version 0.91-6

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

## -- --

compositions-package | library(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

## -- A --

acomp | Aitchison compositions
acompmargin | Marginal compositions in Aitchison Compositions
Activity10 | Activity patterns of a statistician for 20 days
Activity31 | Activity patterns of a statistician for 20 days
alr | Additive log ratio transform
AnimalVegetation | Animal and vegetation measurement
aplus | Amounts analysed in log-scale
apt | Additive planar transform
ArcticLake | Artic lake sediment samples of different water depth
arrows3D | 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.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 --

barplot.acomp | Bar charts of amounts
barplot.aplus | 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
biplot3D | Three-dimensional biplots, based on package rgl
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 --

cdt | Centered default transform
cdt.inv.acomp | Centered default transform
cdt.inv.aplus | Centered default transform
cdt.inv.default | Centered default transform
cdt.inv.rcomp | Centered default transform
cdt.inv.rmult | Centered default transform
cdt.inv.rplus | Centered default transform
cdt.rcomp | Centered default transform
cdt.rmult | Centered default transform
cdt.rplus | Centered default transform
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.
clrvar2ilr | Convert between clr and ilr, and between cpt and ipt.
CoDaDendrogram | Dendrogram representation of acomp or rcomp objects
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
compositions | library(compositions)
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
convex.rcomp | Arithmetic operations for compositions in a real geometry
cor | Correlations of amounts and compositions
cov | Variances and covariances of amounts and compositions
Coxite | Compositions, depths and porosities of 25 specimens of coxite
cpt | Centered planar transform

## -- D --

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
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
endmemberCoordinates | Recast amounts as mixtures of end-members
endmemberCoordinatesInv | Recast amounts as mixtures of end-members

## -- F --

Firework | Firework mixtures

## -- G --

geometricmean | The geometric mean
getDetectionlimit | Gets the detection limit stored in the data set
Glacial | Compositions and total pebble counts of 92 glacial tills
groupparts | Group amounts of parts
gsi | Internal functions of the compositions package
gsi.add | Internal functions: Parallel operations of single and multiple datasets
gsi.add2pairs | Internal functions of the compositions package
gsi.addclass | Internal function: give a derived subclass to an object
gsi.buildilrBase | Auxiliary functions to compute user-defined ilr and ipt transforms.
gsi.call | Internal functions of the compositions package
gsi.cleanR | Internal function: Recode missings with IEEE number and vice versa
gsi.closespread | Internal functions of the compositions package
gsi.coorInfo | Internal functions of the compositions package
gsi.csum | Internal function: row and column sums of matrices
gsi.diagExtract | Internal functions: Get the diagonal of a matrix
gsi.diagGenerate | Internal functions: Generate a diagonal matrix
gsi.div | Internal functions: Parallel operations of single and multiple datasets
gsi.drop | Internal functions: A conditional drop
gsi.eps | Internal variable: Negligible differences
gsi.eq | Internal function: Checking equality of IEEE special numbers
gsi.expandrcomp | Internal function: Scaling rcomp
gsi.filtercall | Calling from a function with the own parameters
gsi.geometricmean | The geometric mean
gsi.getCoorInfo | Internal functions of the compositions package
gsi.getD | Interal function: Get number of samples and number of parts in a compositional object
gsi.getN | Interal function: Get number of samples and number of parts in a compositional object
gsi.ilrBase | The canonical basis in the clr plane used for ilr and ipt transforms.
gsi.ilrBase2signary | Auxiliary functions to compute user-defined ilr and ipt transforms.
gsi.isSingleRow | Internal function: Can something be considered as a single multivariate data item?
gsi.mapfrom01 | Internal functions: Storing integers as reals
gsi.mapin01 | Internal functions: Storing integers as reals
gsi.mapmax | Internal functions: Storing integers as reals
gsi.mapmin | Internal functions: Storing integers as reals
gsi.margin | Internal function: Compute a desired compositional margin
gsi.merge2signary | Auxiliary functions to compute user-defined ilr and ipt transforms.
gsi.mul | Internal functions: Parallel operations of single and multiple datasets
gsi.optimalilrBase | Auxiliary functions to compute user-defined ilr and ipt transforms.
gsi.OrderIlr | Auxiliary functions to compute user-defined ilr and ipt transforms.
gsi.pairrelativeMatrix | Internal functions of the compositions package
gsi.pairs | Internal functions of the compositions package
gsi.plain | Internal function: Convert to plain vector or matrix
gsi.plotmargin | Internal functions of the compositions package
gsi.plots | Internal functions of the compositions package
gsi.recodeC2M | Internal function: Recode missings with IEEE number and vice versa
gsi.recodeM2C | Internal function: Recode missings with IEEE number and vice versa
gsi.recodeM2Clean | Internal function: Recode missings with IEEE number and vice versa
gsi.reset3D | Internal functions of the compositions package
gsi.rsum | Internal function: row and column sums of matrices
gsi.setCoorInfo | Internal functions of the compositions package
gsi.signary2ilrBase | Auxiliary functions to compute user-defined ilr and ipt transforms.
gsi.simshape | Internal function: Reshape an object to the shape type of another
gsi.spreadToIsoSpace | Internal functions of the compositions package
gsi.sub | Internal functions: Parallel operations of single and multiple datasets
gsi.svdsolve | Internal function: Solves singular and non square equation systems
gsi.textpanel | Internal function: A panel displaying a label only
gsi2.invperm | Internal function: Invert a permutation

## -- H --

has.missings | 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.inv.acomp | Isometric default transform
idt.inv.aplus | Isometric default transform
idt.inv.default | Isometric default transform
idt.inv.rcomp | Isometric default transform
idt.inv.rmult | Isometric default transform
idt.inv.rplus | Isometric default transform
idt.rcomp | Isometric default transform
idt.rmult | Isometric default transform
idt.rplus | Isometric default transform
iit | 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.
ilrvar2clr | Convert between clr and ilr, and between cpt and ipt.
ilt | Isometric log transform
ipt | 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.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.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
isoPortionLines | Isoportion- and Isoproportion-lines
isoProportionLines | Isoportion- and Isoproportion-lines

## -- 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.

## -- M --

MAR | The policy of treatment of missing values in the "compositions" package
MARvalue | The policy of treatment of missing values in the "compositions" package
mcor | Metric summary statistics of real, amount or compositional data
mcov | Metric summary statistics of real, amount or compositional data
mean.acomp | Mean amounts and mean compositions
mean.aplus | 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
Metabolites | Steroid metabolite patterns in adults and children
missingProjector | Returns a projector the the observed space in case of missings.
missings | 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
mul.rplus | vectorial arithmetic for data sets with rplus class
mvar | 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.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
norm.acomp | Vector space norm
norm.aplus | Vector space norm
norm.default | Vector space norm
norm.rcomp | Vector space norm
norm.rmult | Vector space norm
norm.rplus | Vector space norm
normalize | Normalize vectors to norm 1

## -- O --

oneOrDataset | Treating single compositions as one-row datasets

## -- P --

perturbe | Perturbation of compositions
perturbe.aplus | vectorial arithmetic for data sets with aplus class
plot.acomp | Displaying compositions in ternary diagrams
plot.aplus | Displaying amounts in scatterplots
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 | Displaying compositions in 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
PogoJump | Honk Kong Pogo-Jumps Championship
power.acomp | Power transform in the simplex
power.aplus | vectorial arithmetic for data sets with aplus class
powerofpsdmatrix | power transform of a matrix
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.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.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

## -- Q --

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 --

rcomp | Compositions as elements of the simplex embedded in the D-dimensional real space
rcompmargin | Marginal compositions in real geometry
rDirichlet | 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
rlnorm.rplus | The multivariate lognormal distribution
rmult | Simple treatment of real vectors
rnorm.acomp | Normal distributions on special spaces
rnorm.aplus | 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
rplus | Amounts i.e. positive numbers analysed as objects of the real vector space
runif.acomp | The uniform distribution on the simplex
runif.rcomp | The uniform distribution on the simplex

## -- S --

sa.dirichlet | Simulated amount datasets
sa.dirichlet5 | Simulated amount datasets
sa.groups | Simulated amount datasets
sa.groups5 | Simulated amount datasets
sa.lognormals | Simulated amount datasets
sa.lognormals5 | Simulated amount datasets
sa.tnormals | Simulated amount datasets
sa.tnormals5 | Simulated amount datasets
sa.uniform | Simulated amount datasets
sa.uniform5 | Simulated amount datasets
scalar | Parallel scalar products
scale.acomp | Normalizing datasets by centering and scaling
scale.aplus | 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
ShiftOperators | Shifts of machine operators
SimulatedAmounts | Simulated amount datasets
simulateMissings | Artifical simulation of various kinds of missings
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.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.
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.
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 --

totals | Total sum of amounts

## -- U --

ucipt.inv | Isometric planar transform
ult | Uncentered log transform

## -- V --

var | Variances and covariances of amounts and compositions
variation | Variation matrices of amounts and compositions
vp.boxplot | Displaying compositions and amounts with box-plots
vp.logboxplot | Displaying compositions and amounts with box-plots
vp.qqnorm | Normal quantile plots for compositions and amounts

## -- W --

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

## -- Y --

Yatquat | Yatquat fruit evaluation

## -- Z --

zeroreplace | Zero-replacement routine