compositions: Compositional Data Analysis

Share:

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.

Author
K. Gerald van den Boogaart <boogaart@hzdr.de>, Raimon Tolosana, Matevz Bren
Date of publication
2014-06-07 21:11:09
Maintainer
K. Gerald van den Boogaart <support@boogaart.de>
License
GPL (>= 2)
Version
1.40-1
URLs

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