Compositional Data Analysis


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Documentation for package `compositions' version 0.9-10

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

%*% 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 Aitchisons simplex
*.aplus vectorial arithmetic for datasets with aplus class
*.rcomp Arithmetic operations for composition in real geometry
*.rmult vectorial arithmetic for datasets in a classical vector scale
*.rplus Arithmetik of rplus-scale
+.acomp Perturbation of compositions
+.aplus vectorial arithmetic for datasets with aplus class
+.rcomp Arithmetic operations for composition in real geometry
+.rmult vectorial arithmetic for datasets in a classical vector scale
+.rplus Arithmetik of rplus-scale
-.acomp Perturbation of compositions
-.aplus vectorial arithmetic for datasets with aplus class
-.rcomp Arithmetic operations for composition in real geometry
-.rmult vectorial arithmetic for datasets in a classical vector scale
-.rplus Arithmetik of rplus-scale
/.acomp Power transform in Aitchisons simplex
/.aplus vectorial arithmetic for datasets with aplus class
/.rcomp Arithmetic operations for composition in real geometry
/.rmult vectorial arithmetic for datasets in a classical vector scale
/.rplus Arithmetik of rplus-scale

-- A --

acomp Aitchison compositions
acompmargin Marginal compositions in Aitchison Compositions
alr Additive log ratio transform
aplus Amounts analysed in log-scale
apt Additive planar transform
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

-- B --

barplot.acomp Barcharts of amounts
barplot.aplus Barcharts of amounts
barplot.rcomp Barcharts of amounts
barplot.rplus Barcharts of amounts
boxplot.acomp Displaying compositions and amounts by boxplots
boxplot.aplus Displaying compositions and amounts by boxplots
boxplot.rcomp Displaying compositions and amounts by boxplots
boxplot.rplus Displaying compositions and amounts by boxplots

-- C --

cdt Centered default transform
clo Closure of a composition
clr Centered log ratio transform
clr2ilr Convert between clr and ilr, and between cpt and ipt. Acts in vectors and in bilinear forms.
clrvar2ilr Convert between clr and ilr, and between cpt and ipt. Acts in vectors and in bilinear forms.
convex.rcomp Arithmetic operations for composition in real geometry
cor Correlations of amounts and compositions
cov Variances and covariances of amounts and compositions
cpt Centered planar transform

-- D --

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
endpointCoordinates Amounts in barytic-coordinates
endpointCoordinatesInv Amounts in barytic-coordinates

-- G --

geometricmean The geometric mean
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 an object a derived subclass
gsi.call Internal functions of the compositions package
gsi.closespread Internal functions of the compositions package
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.expandrcomp Internal function: Scaling rcomp
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.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.mul Internal functions: Parallel operations of single and multiple datasets
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.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.textpanel Internal function: A panel displaying a label only
gsi2.invperm Internal function: Invert a permutation

-- H --

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

-- I --

idt Isometric default transform
iit Isometric identity transform
ilr Isometric log ratio transform
ilr2clr Convert between clr and ilr, and between cpt and ipt. Acts in vectors and in bilinear forms.
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. Acts in vectors and in bilinear forms.
ilt Isometric log transform
ipt Isometric planar transform
is.acomp Check for compositional data type
is.aplus Check for compositional data type
is.rcomp Check for compositional data type
is.rmult Check for compositional data type
is.rplus Check for compositional data type

-- K --

Kappa Uncentered log transform

-- 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 --

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
msd Metric summary statistics of real, amount or compositional data
mul.rplus Arithmetik of rplus-scale
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
norm 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 datasets with aplus class
plot.acomp Displaying compositions in ternary diagrams
plot.aplus Displaying amounts in scatterplots
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
power.acomp Power transform in Aitchisons simplex
power.aplus vectorial arithmetic for datasets 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 Principle 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

-- 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
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
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.
SimulatedAmounts Simulated amount datasets
split.acomp Spliting datasets in groups given by factors
split.aplus Spliting datasets in groups given by factors
split.rcomp Spliting datasets in groups given by factors
split.rmult Spliting datasets in groups given by factors
split.rplus Spliting datasets in groups given by factors
straight Draws infinite 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

-- 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 by boxplots
vp.logboxplot Displaying compositions and amounts by boxplots
vp.qqnorm Normal quantile plots for compositions and amounts