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.

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

Files in this package

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

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