compositions: Compositional Data Analysis

The package provides functions for the consistent analysis of compositional data (e.g. portions of substances) and positive numbers (e.g. concentrations) in the way proposed by Aitchison and Pawlowsky-Glahn.

AuthorK. Gerald van den Boogaart <boogaart@hzdr.de>, Raimon Tolosana, Matevz Bren
Date of publication2014-06-07 21:11:09
MaintainerK. Gerald van den Boogaart <support@boogaart.de>
LicenseGPL (>= 2)
Version1.40-1
http://www.stat.boogaart.de/compositions

View on CRAN

Man pages

acomp: Aitchison compositions

acomparith: Power transform in the simplex

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

aplusarithm: vectorial arithmetic for data sets with aplus class

apt: Additive planar transform

ArcticLake: Artic lake sediment samples of different water depth

arrows3d: arrows in 3D, based on package rgl

asdataframe: Convert "compositions" classes to data frames

axis3d: Drawing a 3D coordiante system to a plot, based on package...

balancebase: Compute balances for a compositional dataset.

barplot: Bar charts of amounts

Bayesite: Permeabilities of bayesite

binary: Treating binary and g-adic numbers

biplot3d: Three-dimensional biplots, based on package rgl

Blood23: Blood samples

Boxite: Compositions and depth of 25 specimens of boxite

boxplot: Displaying compositions and amounts with box-plots

ccomp: Count compositions

ccompgof: Compositional Goodness of fit test

cdt: 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.

clusterfinder: Heuristics to find subpopulations of outliers

codadendrogram: Dendrogram representation of acomp or rcomp objects

coloredbiplot: A biplot providing somewhat easier access to details of the...

colorsforoutliers: Create a color/char palette or for groups of outliers

CompLinModCo: Compositional Linear Model of Coregionalisation

compmiss: The policy of treatment of missing values in the...

compOKriging: Compositional Ordinary Kriging

compositions: library(compositions)

ConfRadius: Helper to compute confidence ellipsoids

cor: Correlations of amounts and compositions

Coxite: Compositions, depths and porosities of 25 specimens of coxite

cpt: Centered planar transform

DiagnosticProb: Diagnostic probabilities

dist: Distances in variouse approaches

ellipses: Draw ellipses

endmemberCoordinates: Recast amounts as mixtures of end-members

Firework: Firework mixtures

fitdirichlet: Fitting a Dirichlet distribution

fitsamemean: Fit Same Mean Different Variance Model

gausstest: Classical Gauss Test

geometricmean: The geometric mean

getdetectionlimit: Gets the detection limit stored in the data set

Glacial: Compositions and total pebble counts of 92 glacial tills

goftests: Compositional Goodness of fit test

groupparts: Group amounts of parts

gsiadd: Internal functions: Parallel operations of single and...

gsiaddclass: Internal function: give a derived subclass to an object

gsicall: Internal functions of the compositions package

gsiclosespread: Internal functions of the compositions package

gsicoorinfo: Internal functions of the compositions package

gsicsum: Internal function: row and column sums of matrices

gsidiagExtract: Internal functions: Get the diagonal of a matrix

gsidiagGenerate: Internal functions: Generate a diagonal matrix

gsidrop: Internal functions: A conditional drop

gsieps: Internal variable: Negligible differences

gsieq: Internal function: Checking equality of IEEE special numbers

gsiexpandrcomp: Internal function: Scaling rcomp

gsifiltercall: Calling from a function with the own parameters

gsigetbalstruct: An auxiliary functions to compute user-defined ilr and ipt...

gsigetD: Interal function: Get number of samples and number of parts...

gsiinternal: Environment containing the old gsi functions

gsiinvperm: Internal function: Invert a permutation

gsiisSingleRow: Internal function: Can something be considered as a single...

gsimap01: Internal functions: Storing integers as reals

gsimargin: Internal function: Compute a desired compositional margin

gsimerge2signary: Auxiliary functions to compute user-defined ilr and ipt...

gsipairrelativeMatrix: Internal functions of the compositions package

gsipairs: Internal functions of the compositions package

gsiplain: Internal function: Convert to plain vector or matrix

gsiplotmargin: Internal functions of the compositions package

gsiPrinBal: The canonical basis in the clr plane used for ilr and ipt...

gsirecode: Internal function: Recode missings with IEEE number and vice...

gsireset3d: Internal functions of the compositions package

gsisimshape: Internal function: Reshape an object to the shape type of...

gsispreadToIsoSpace: Internal functions of the compositions package

gsisvdsolve: Internal function: Solves singular and non square equation...

gsitextpanel: Internal function: A panel displaying a label only

gsivarwithlosts: Internal function: computes variance of compositional data...

Hongite: Compositions of 25 specimens of hongite

HotellingsTsq: Hotellings T square distribution

HouseholdExp: Household Expenditures

Hydrochem: Hydrochemical composition data set of Llobregat river basin...

idt: Isometric default transform

iit: Isometric identity transform

ilr: Isometric log ratio transform

ilrBase: The canonical basis in the clr plane used for ilr and ipt...

ilt: Isometric log transform

ipt: Isometric planar transform

isAcomp: Check for compositional data type

ismahalanobisoutlier: Checking for outliers

isoportion: Isoportion- and Isoproportion-lines

jura: The jura dataset

kingtetrahedron: Ploting composition into rotable tetrahedron

Kongite: Compositions of 25 specimens of kongite

lines: Draws connected lines from point to point.

logratioVariogram: Empirical variograms for compositions

lrvgram: vgram2lrvgram

mahalanobisdist: Compute Mahalanobis distances based von robust Estimations

matmult: inner product for matrices and vectors

matmultacomp: inner product for datasets with a vector space structure

meanAcomp: Mean amounts and mean compositions

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...

missingsummary: Classify and summarize missing values in a dataset

mix2compositions: Transformations from 'mixtures' to 'compositions' classes

mixRead: Reads a data file in a mixR format

mvar: Metric summary statistics of real, amount or compositional...

names: The names of the parts

norm: Vector space norm

normalize: Normalize vectors to norm 1

oneOrDataset: Treating single compositions as one-row datasets

outlierclassifier: Detect and classify compositional outliers.

outlierplot: Plot various graphics to analyse outliers.

outliers: Analysing outliers in compositions.

pairwisePlot: Creates a paneled plot like pairs for two different datasets.

parametricMat: Unique parametrisations for matrices.

perturbe: Perturbation of compositions

plot: Ternary diagrams

plot3d: plot in 3D based on rgl

plot3dacomp: 3D-plot of compositional data

plot3daplus: 3D-plot of positive data

plot3drmult: plot in 3D based on rgl

plot3drplus: plot in 3D based on rgl

plotlogratioVariogram: Empirical variograms for compositions

plotmissingsummary: Plot a Missing Summary

plotpos: Displaying amounts in scatterplots

PogoJump: Honk Kong Pogo-Jumps Championship

powerofmatrix: power transform of a matrix

princompacomp: Principal component analysis for Aitchison compositions

princompaplus: Principal component analysis for amounts in log geometry

princomprcomp: Principal component analysis for real compositions

princomprmult: Principal component analysis for real data

princomprplus: Principal component analysis for real amounts

print: Printing compositional data.

pwlrPlot: Plots of pairwise logratio against a covariable.

qqnorm: Normal quantile plots for compositions and amounts

R2: R square

raitchison: Aitchison Distribution

ratioLoadings: Loadings of relations of two amounts

rcomp: Compositions as elements of the simplex embedded in the...

rcomparithm: Arithmetic operations for compositions in a real geometry

rcompmargin: Marginal compositions in real geometry

rDirichlet: Dirichlet distribution

readgeoeas: Reads a data file in a geoeas format

replot: Modify parameters of compositional plots.

rlnorm: The multivariate lognormal distribution

rmahalanobis: Compute distributions of empirical Mahalanobis distances...

rmult: Simple treatment of real vectors

rmultarithm: vectorial arithmetic for datasets in a classical vector scale

rmultmatmult: inner product for datasets with vector scale

rnorm: Normal distributions on special spaces

robustness: Handling robustness issues and outliers in compositions.

rplus: Amounts i.e. positive numbers analysed as objects of the real...

rplusarithm: vectorial arithmetic for data sets with rplus class

rpois: Simulate count compositions without overdispersion

runif: The uniform distribution on the simplex

scalar: Parallel scalar products

scale: Normalizing datasets by centering and scaling

Sediments: Proportions of sand, silt and clay in sediments specimens

segments: Draws straight lines from point to point.

SerumProtein: Serum Protein compositions of blood samples

ShiftOperators: Shifts of machine operators

simplemissingplot: Ternary diagrams

SimulatedAmounts: Simulated amount datasets

simulatemissing: Artifical simulation of various kinds of missings/polluted...

Skulls: Measurement of skulls

SkyeAFM: AFM compositions of 23 aphyric Skye lavas

split: Splitting datasets in groups given by factors

straight: Draws straight lines.

summaryAcomp: Summarizing a compositional dataset in terms of ratios

summaryAplus: Summaries of amounts

summaryRcomp: Summary of compositions in real geometry

sumprojector: Compute the global projector to the observed subspace.

Supervisor: Proportions of supervisor's statements assigned to different...

ternaryAxis: Axis for ternary diagrams

tests: Compositional Goodness of fit test

totals: Total sum of amounts

tryDebugger: Empirical variograms for compositions

ult: Uncentered log transform

varAcomp: Variances and covariances of amounts and compositions

variation: Variation matrices of amounts and compositions

variograms: Variogram functions

varmlm: Residual variance of a model

vcovAcomp: Variance covariance matrix of parameters in compositional...

vgmFit: Compositional variogram model fitting

WhiteCells: White-cell composition of 30 blood samples by two different...

Yatquat: Yatquat fruit evaluation

zeroreplace: Zero-replacement routine

Files in this package

compositions
compositions/COPYING
compositions/inst
compositions/inst/doc
compositions/inst/doc/index.html
compositions/inst/doc/UsingCompositions.tex.flc
compositions/inst/doc/UsingCompositions.pdf
compositions/tests
compositions/tests/TestSimp.R
compositions/tests/juraset.dat
compositions/tests/quickcheck.R
compositions/tests/LAKE.txt
compositions/tests/TRUE.DAT
compositions/tests/TestSimp.Rout
compositions/tests/missings.R
compositions/tests/RobustTest.R
compositions/tests/missings.Rout
compositions/tests/TestMissing.R
compositions/tests/CheckGeometry.R
compositions/tests/AitchisonTest.R
compositions/tests/acheck.R
compositions/tests/geostat.R
compositions/src
compositions/src/Makevars
compositions/src/compositions.c
compositions/NAMESPACE
compositions/demo
compositions/demo/00Index
compositions/demo/compplots.R
compositions/data
compositions/data/Activity31.rda
compositions/data/PogoJump.rda
compositions/data/SkyeAFM.rda
compositions/data/Skulls.rda
compositions/data/WhiteCells.rda
compositions/data/Coxite.rda
compositions/data/Metabolites.rda
compositions/data/Firework.rda
compositions/data/Activity10.rda
compositions/data/Glacial.rda
compositions/data/Hongite.rda
compositions/data/ClamEast.rda
compositions/data/Kongite.rda
compositions/data/ClamWest.rda
compositions/data/SimulatedAmounts.RData
compositions/data/Blood23.rda
compositions/data/Hydrochem.txt.gz
compositions/data/Bayesite.rda
compositions/data/Boxite.rda
compositions/data/AnimalVegetation.rda
compositions/data/jura259.rda
compositions/data/Yatquat.rda
compositions/data/juraset.rda
compositions/data/HouseholdExp.rda
compositions/data/Supervisor.rda
compositions/data/ArcticLake.rda
compositions/data/ShiftOperators.rda
compositions/data/DiagnosticProb.rda
compositions/data/Sediments.rda
compositions/data/SerumProtein.rda
compositions/R
compositions/R/codadendrogram.R compositions/R/and.R compositions/R/ctests.R compositions/R/Geostat.R compositions/R/3d.R compositions/R/binary.R compositions/R/mix2comp.R compositions/R/PrincipalBalances.R compositions/R/compreg.R compositions/R/FunctionOutliers.R compositions/R/robust.R compositions/R/OldStuff.R compositions/R/zzz.R compositions/R/zerotreatment.R compositions/R/compositions.R
compositions/vignettes
compositions/vignettes/UsingCompositions.tex
compositions/MD5
compositions/DESCRIPTION
compositions/ChangeLog
compositions/man
compositions/man/Glacial.Rd compositions/man/isAcomp.Rd compositions/man/ArcticLake.Rd compositions/man/gsiaddclass.Rd compositions/man/arrows3d.Rd compositions/man/ismahalanobisoutlier.Rd compositions/man/rlnorm.Rd compositions/man/mixRead.Rd compositions/man/gsigetD.Rd compositions/man/plot3daplus.Rd compositions/man/ipt.Rd compositions/man/plot3d.Rd compositions/man/gsigetbalstruct.Rd compositions/man/ilt.Rd compositions/man/scale.Rd compositions/man/princomprmult.Rd compositions/man/axis3d.Rd compositions/man/matmultacomp.Rd compositions/man/gsivarwithlosts.Rd compositions/man/norm.Rd compositions/man/groupparts.Rd compositions/man/simplemissingplot.Rd compositions/man/clr2ilr.Rd compositions/man/rmultarithm.Rd compositions/man/Sediments.Rd compositions/man/names.Rd compositions/man/simulatemissing.Rd compositions/man/gsisvdsolve.Rd compositions/man/rnorm.Rd compositions/man/summaryAplus.Rd compositions/man/rplusarithm.Rd compositions/man/sumprojector.Rd compositions/man/balancebase.Rd compositions/man/idt.Rd compositions/man/rmult.Rd compositions/man/gsimargin.Rd compositions/man/acompmargin.Rd compositions/man/HotellingsTsq.Rd compositions/man/gsiexpandrcomp.Rd compositions/man/asdataframe.Rd compositions/man/acomparith.Rd compositions/man/ClamWest.Rd compositions/man/codadendrogram.Rd compositions/man/SimulatedAmounts.Rd compositions/man/rcompmargin.Rd compositions/man/Activity31.Rd compositions/man/apt.Rd compositions/man/barplot.Rd compositions/man/alr.Rd compositions/man/princomprplus.Rd compositions/man/PogoJump.Rd compositions/man/SkyeAFM.Rd compositions/man/gsiPrinBal.Rd compositions/man/readgeoeas.Rd compositions/man/gausstest.Rd compositions/man/Yatquat.Rd compositions/man/Blood23.Rd compositions/man/fitdirichlet.Rd compositions/man/clusterfinder.Rd compositions/man/outlierclassifier.Rd compositions/man/cor.Rd compositions/man/gsimerge2signary.Rd compositions/man/Firework.Rd compositions/man/pwlrPlot.Rd compositions/man/clr.Rd compositions/man/gsimap01.Rd compositions/man/lrvgram.Rd compositions/man/summaryAcomp.Rd compositions/man/raitchison.Rd compositions/man/tests.Rd compositions/man/compositions.Rd compositions/man/vcovAcomp.Rd compositions/man/plotlogratioVariogram.Rd compositions/man/colorsforoutliers.Rd compositions/man/meanrow.Rd compositions/man/replot.Rd compositions/man/compOKriging.Rd compositions/man/ilr.Rd compositions/man/gsiinvperm.Rd compositions/man/gsieps.Rd compositions/man/split.Rd compositions/man/ult.Rd compositions/man/Metabolites.Rd compositions/man/outlierplot.Rd compositions/man/gsidrop.Rd compositions/man/cpt.Rd compositions/man/R2.Rd compositions/man/iit.Rd compositions/man/gsiplotmargin.Rd compositions/man/powerofmatrix.Rd compositions/man/gsicall.Rd compositions/man/gsipairrelativeMatrix.Rd compositions/man/Skulls.Rd compositions/man/geometricmean.Rd compositions/man/mix2compositions.Rd compositions/man/Coxite.Rd compositions/man/pairwisePlot.Rd compositions/man/goftests.Rd compositions/man/lines.Rd compositions/man/jura.Rd compositions/man/robustness.Rd compositions/man/gsipairs.Rd compositions/man/matmult.Rd compositions/man/straight.Rd compositions/man/Kongite.Rd compositions/man/rcomp.Rd compositions/man/qqnorm.Rd compositions/man/fitsamemean.Rd compositions/man/ClamEast.Rd compositions/man/gsisimshape.Rd compositions/man/AnimalVegetation.Rd compositions/man/plot3drplus.Rd compositions/man/rmahalanobis.Rd compositions/man/totals.Rd compositions/man/missingProjector.Rd compositions/man/Hydrochem.Rd compositions/man/rmultmatmult.Rd compositions/man/boxplot.Rd compositions/man/gsifiltercall.Rd compositions/man/gsirecode.Rd compositions/man/summaryRcomp.Rd compositions/man/gsicoorinfo.Rd compositions/man/cdt.Rd compositions/man/mvar.Rd compositions/man/oneOrDataset.Rd compositions/man/gsieq.Rd compositions/man/CompLinModCo.Rd compositions/man/ratioLoadings.Rd compositions/man/ccomp.Rd compositions/man/variation.Rd compositions/man/HouseholdExp.Rd compositions/man/compmiss.Rd compositions/man/scalar.Rd compositions/man/WhiteCells.Rd compositions/man/gsitextpanel.Rd compositions/man/missingsummary.Rd compositions/man/clo.Rd compositions/man/logratioVariogram.Rd compositions/man/tryDebugger.Rd compositions/man/plotpos.Rd compositions/man/gsiisSingleRow.Rd compositions/man/princompacomp.Rd compositions/man/gsiinternal.Rd compositions/man/meanAcomp.Rd compositions/man/rDirichlet.Rd compositions/man/ccompgof.Rd compositions/man/gsidiagExtract.Rd compositions/man/gsiadd.Rd compositions/man/ConfRadius.Rd compositions/man/normalize.Rd compositions/man/acomp.Rd compositions/man/varAcomp.Rd compositions/man/princompaplus.Rd compositions/man/gsidiagGenerate.Rd compositions/man/gsiplain.Rd compositions/man/DiagnosticProb.Rd compositions/man/getdetectionlimit.Rd compositions/man/isoportion.Rd compositions/man/plot3drmult.Rd compositions/man/Hongite.Rd compositions/man/kingtetrahedron.Rd compositions/man/SerumProtein.Rd compositions/man/plot3dacomp.Rd compositions/man/ShiftOperators.Rd compositions/man/Supervisor.Rd compositions/man/Activity10.Rd compositions/man/endmemberCoordinates.Rd compositions/man/coloredbiplot.Rd compositions/man/Bayesite.Rd compositions/man/gsiclosespread.Rd compositions/man/ellipses.Rd compositions/man/print.Rd compositions/man/gsispreadToIsoSpace.Rd compositions/man/aplus.Rd compositions/man/vgmFit.Rd compositions/man/variograms.Rd compositions/man/runif.Rd compositions/man/plotmissingsummary.Rd compositions/man/plot.Rd compositions/man/gsireset3d.Rd compositions/man/biplot3d.Rd compositions/man/rpois.Rd compositions/man/Boxite.Rd compositions/man/rplus.Rd compositions/man/segments.Rd compositions/man/dist.Rd compositions/man/zeroreplace.Rd compositions/man/varmlm.Rd compositions/man/aplusarithm.Rd compositions/man/binary.Rd compositions/man/gsicsum.Rd compositions/man/ilrBase.Rd compositions/man/parametricMat.Rd compositions/man/mahalanobisdist.Rd compositions/man/princomprcomp.Rd compositions/man/outliers.Rd compositions/man/perturbe.Rd compositions/man/ternaryAxis.Rd compositions/man/rcomparithm.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.