robCompositions: Robust Estimation for Compositional Data

Methods for analysis of compositional data including robust methods, imputation, methods to replace rounded zeros, (robust) outlier detection for compositional data, (robust) principal component analysis for compositional data, (robust) factor analysis for compositional data, (robust) discriminant analysis for compositional data (Fisher rule), robust regression with compositional predictors and (robust) Anderson-Darling normality tests for compositional data as well as popular log-ratio transformations (addLR, cenLR, isomLR, and their inverse transformations). In addition, visualisation and diagnostic tools are implemented as well as high and low-level plot functions for the ternary diagram.

Install the latest version of this package by entering the following in R:
install.packages("robCompositions")
AuthorMatthias Templ, Karel Hron, Peter Filzmoser
Date of publication2017-01-12 00:50:05
MaintainerMatthias Templ <templ@tuwien.ac.at>
LicenseGPL-2
Version2.0.3

View on CRAN

Man pages

addLR: Additive log-ratio transformation

addLRinv: Additive logistic transformaton

aDist: Aitchison distance

adjust: Adjusting for original scale

adtest: Anderson-Darling Normality Tests

adtestWrapper: Wrapper for Anderson-Darling tests

ageCatWorld: Child, middle and eldery population

alcohol: alcohol

alcoholreg: alcoholreg

arcticLake: Arctic lake sediment data

balances: Balance calculation

balZav: New average symmetric coordinates

biomarker: biomarker

biplot.factanal: Biplot method

biplot.pcaCoDa: Biplot method

bootnComp: Bootstrap to find optimal number of components

cancer: Hospital discharges on cancer and distribution of age

cenLR: Centred log-ratio transformation

cenLRinv: Inverse centred log-ratio transformation

clustCoDa: Cluster analysis for compositional data

clustCoDa_qmode: Q-mode cluster analysis for compositional parts

coffee: coffee data set

compareMahal: Compares Mahalanobis distances from two approaches

constSum: Constant sum

corCoDa: Correlations for compositional data

daCoDa: Linear and quadratic discriminant analysis for compositional...

daFisher: Discriminant analysis by Fisher Rule.

economy: Economic indicators

election: Election data

electionATbp: Votes at presidental elections

expenditures: Synthetic household expenditures toy data set

expendituresEU: Mean consumption expenditures data.

gemas: Gemas geochemical data set

gm: gmean

haplogroups: Haplogroups data.

impAll: Replacement of rounded zeros and missing values.

impCoda: Imputation of missing values in compositional data

impKNNa: Imputation of missing values in compositional data using knn...

impRZalr: alr EM-based Imputation for Rounded Zeros

impRZilr: EM-based replacement of rounded zeros in compositional data

imputeBDLs: EM-based replacement of rounded zeros in compositional data

laborForce: Labour force by status in employment

lifeExpGdp: Life expectancy and GDP (2008) for EU-countries

lmCoDaX: Classical and robust regression of non-compositional response...

machineOperators: machine operators

mcad: Metabolomics mcad data set

missPatterns: missing or zero pattern structure.

mortality: Mortality and life expectancy in the EU

nutrients: nutrient contents

nutrients_branded: nutrient contents (branded)

orthbasis: Orthonormal basis

outCoDa: Outlier detection for compositional data

payments: Special payments

pcaCoDa: Robust principal component analysis for compositional data

perturbation: Perturbation and powering

pfa: Factor analysis for compositional data

phd: PhD Students in the EU

pivotCoord: Pivot coordinates and their inverse

plot.imp: Plot method for objects of class imp

plot.pcaCoDa: Plot method

print.imp: Print method for objects of class imp

production: Production

robCompositions-package: Robust Estimation for Compositional Data.

skyeLavas: Aphyric skye lavas data

summary.imp: Summary method for objects of class imp

ternaryDiag: Ternary diagram

ternaryDiagAbline: Adds a line to a ternary diagram.

ternaryDiagEllipse: Adds tolerance ellipses to a ternary diagram.

ternaryDiagPoints: Add points or lines to a given ternary diagram.

trondelagC: Regional geochemical survey of soil C in Norway

trondelagO: Regional geochemical survey of soil O in Norway

variation: Robust and classical variation matrix

zeroOut: Detection of outliers of zero-inflated data

Functions

addLR Man page
addLRinv Man page
aDist Man page
adjust Man page
adjustImputed Man page
adtest Man page
adtestWrapper Man page
ageCatWorld Man page
alcohol Man page
alcoholreg Man page
arcticLake Man page
balances Man page
balZav Man page
biomarker Man page
biplot.factanal Man page
biplot.pcaCoDa Man page
bootnComp Man page
cancer Man page
cenLR Man page
cenLRinv Man page
checkData Man page
clustCoDa Man page
clustCoDa_qmode Man page
coffee Man page
compareMahal Man page
constSum Man page
corCoDa Man page
daCoDa Man page
daFisher Man page
economy Man page
election Man page
electionATbp Man page
expenditures Man page
expendituresEU Man page
gemas Man page
getEstimates Man page
gm Man page
haplogroups Man page
ilrregression Man page
impAll Man page
impCoda Man page
impKNNa Man page
impRZalr Man page
impRZilr Man page
imputeBDLs Man page
iprod Man page
isomLR Man page
isomLRinv Man page
isomLRinvp Man page
isomLRp Man page
laborForce Man page
lifeExpGdp Man page
lmCoDaX Man page
machineOperators Man page
mcad Man page
missPatterns Man page
mortality Man page
nutrients Man page
nutrients_branded Man page
orthbasis Man page
outCoDa Man page
payments Man page
pcaCoDa Man page
perturbation Man page
pfa Man page
phd Man page
pivotCoord Man page
pivotCoordInv Man page
plot.biomarker Man page
plot.clustCoDa Man page
plot.clustCoDa_qmode Man page
plot.estimates Man page
plot.imp Man page
plot.mahal Man page
plot.outCoDa Man page
plot.pcaCoDa Man page
powering Man page
predict.daFisher Man page
print.adtestWrapper Man page
print.biomarker Man page
print.daFisher Man page
print.estimates Man page
print.imp Man page
print.outCoDa Man page
print.pcaCoDa Man page
print.replaced Man page
production Man page
robCompositions Man page
robCompositions-package Man page
robilrregression Man page
skyeLavas Man page
summary.adtestWrapper Man page
summary.biomarker Man page
summary.daFisher Man page
summary.imp Man page
summary.pcaCoDa Man page
ternaryDiag Man page
ternaryDiagAbline Man page
ternaryDiagEllipse Man page
ternaryDiagLines Man page
ternaryDiagPoints Man page
trondelagC Man page
trondelagO Man page
variation Man page
zeroOut Man page
zeroPatterns Man page

Files

inst
inst/CITATION
inst/doc
inst/doc/gm.cpp
inst/doc/imputation.Rnw
inst/doc/robCompositions-overview.pdf
inst/doc/robCompositions-overview.Rnw
inst/doc/imputation.pdf
inst/doc/imputation.R
tests
tests/importFood.R tests/imp_test.R tests/rz.R
src
src/robCompositions.c
NAMESPACE
NEWS
data
data/mcad.rda
data/production.rda
data/economy.rda
data/alcohol.rda
data/gemas.rda
data/machineOperators.rda
data/payments.rda
data/coffee.rda
data/electionATbp.rda
data/haplogroups.rda
data/trondelagO.rda
data/trondelagC.rda
data/phd.rda
data/expendituresEU.rda
data/alcoholreg.rda
data/expenditures.rda
data/cancer.rda
data/nutrients_branded.rda
data/skyeLavas.rda
data/election.rda
data/laborForce.rda
data/mortality.rda
data/ageCatWorld.rda
data/nutrients.rda
data/arcticLake.rda
data/lifeExpGdp.rda
R
R/dataSets.R R/robilrregression.R R/gm.R R/compareMahal.R R/utils.R R/impRZalr.R R/ternaryDiagEllipse.R R/zeroOut.R R/adjust.R R/addLRinv.R R/factanal.fit.principal1.R R/alphablend.R R/balZav.R R/biplot.factanal.R R/impKNNa.R R/balances.R R/biomarker.R R/outCoDa.R R/daFisher.R R/impCoda.R R/ternaryDiagAbline.R R/impAll.R R/plot.imp.R R/ternaryDiagLines.R R/constSum.R R/aDist.R R/clustCoDa.R R/pcaCoDa.R R/ilrregression.R R/adtestWrapper.R R/summary.imp.R R/cenLR.R R/cenLRinv.R R/missPatterns.R R/isomLR.R R/biplot.pcaCoDa.R R/center.R R/corCoDa.R R/imputeBDLs.R R/addLR.R R/robCompositions-package.R R/perturbation.R R/ternaryDiag.R R/daCoDa.R R/print.imp.R R/variation.R R/impPCA.R R/impRZilr.R R/ternaryDiagPoints.R R/adtest.R R/clustCoDa_qmode.R R/lmCoDaX.R R/zzz.R R/pfa.R R/orthbasis.R R/gm_backup.R R/plot.pcaCoDa.R
vignettes
vignettes/imputation-concordance.tex
vignettes/ilr.pdf
vignettes/imputation-plot4.pdf
vignettes/refPCS.bib
vignettes/logo.pdf
vignettes/pcaOrig.pdf
vignettes/imputation.Rnw
vignettes/plainnat.bst
vignettes/boxplot.pdf
vignettes/imputation-plot1.pdf
vignettes/refPCSn.bib
vignettes/robCompositions-overview.Rnw
vignettes/ternary.pdf
vignettes/natbib.sty
vignettes/ref.bib
vignettes/plot-acomp.pdf
vignettes/pca1.pdf
vignettes/framed.sty
vignettes/CoDaWork.sty
vignettes/subfigure.sty
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/print.imp.Rd man/impAll.Rd man/outCoDa.Rd man/lmCoDaX.Rd man/impRZalr.Rd man/trondelagO.Rd man/constSum.Rd man/nutrients.Rd man/pcaCoDa.Rd man/robCompositions-package.Rd man/clustCoDa.Rd man/skyeLavas.Rd man/phd.Rd man/compareMahal.Rd man/addLRinv.Rd man/daCoDa.Rd man/biplot.pcaCoDa.Rd man/plot.pcaCoDa.Rd man/laborForce.Rd man/expendituresEU.Rd man/nutrients_branded.Rd man/electionATbp.Rd man/cancer.Rd man/adtestWrapper.Rd man/perturbation.Rd man/cenLR.Rd man/addLR.Rd man/expenditures.Rd man/mcad.Rd man/adtest.Rd man/machineOperators.Rd man/gemas.Rd man/impRZilr.Rd man/adjust.Rd man/ternaryDiagEllipse.Rd man/balances.Rd man/aDist.Rd man/ternaryDiag.Rd man/missPatterns.Rd man/daFisher.Rd man/orthbasis.Rd man/cenLRinv.Rd man/trondelagC.Rd man/payments.Rd man/zeroOut.Rd man/plot.imp.Rd man/haplogroups.Rd man/economy.Rd man/variation.Rd man/clustCoDa_qmode.Rd man/corCoDa.Rd man/mortality.Rd man/impCoda.Rd man/pivotCoord.Rd man/gm.Rd man/alcoholreg.Rd man/pfa.Rd man/summary.imp.Rd man/coffee.Rd man/arcticLake.Rd man/ternaryDiagAbline.Rd man/production.Rd man/biplot.factanal.Rd man/election.Rd man/imputeBDLs.Rd man/biomarker.Rd man/balZav.Rd man/bootnComp.Rd man/lifeExpGdp.Rd man/impKNNa.Rd man/ternaryDiagPoints.Rd man/alcohol.Rd man/ageCatWorld.Rd

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

Please suggest features or report bugs with the GitHub issue tracker.

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