Package: robCompositions 2.4.1

robCompositions: Compositional Data Analysis

Methods for analysis of compositional data including robust methods (<doi:10.1007/978-3-319-96422-5>), imputation of missing values (<doi:10.1016/j.csda.2009.11.023>), methods to replace rounded zeros (<doi:10.1080/02664763.2017.1410524>, <doi:10.1016/j.chemolab.2016.04.011>, <doi:10.1016/j.csda.2012.02.012>), count zeros (<doi:10.1177/1471082X14535524>), methods to deal with essential zeros (<doi:10.1080/02664763.2016.1182135>), (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, functional data analysis (<doi:10.1016/j.csda.2015.07.007>) and p-splines (<doi:10.1016/j.csda.2015.07.007>), contingency (<doi:10.1080/03610926.2013.824980>) and compositional tables (<doi:10.1111/sjos.12326>, <doi:10.1111/sjos.12223>, <doi:10.1080/02664763.2013.856871>) 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.

Authors:Matthias Templ [aut, cre], Karel Hron [aut], Peter Filzmoser [aut], Kamila Facevicova [ctb], Petra Kynclova [ctb], Jan Walach [ctb], Veronika Pintar [ctb], Jiajia Chen [ctb], Dominika Miksova [ctb], Bernhard Meindl [ctb], Alessandra Menafoglio [ctb], Alessia Di Blasi [ctb], Federico Pavone [ctb], Nikola Stefelova [ctb], Gianluca Zeni [ctb], Roman Wiederkehr [ctb]

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robCompositions.pdf |robCompositions.html
robCompositions/json (API)
NEWS

# Install 'robCompositions' in R:
install.packages('robCompositions', repos = c('https://matthias-da.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/matthias-da/robcompositions/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

9.21 score 11 stars 2 packages 213 scripts 1.4k downloads 28 mentions 89 exports 118 dependencies

Last updated 1 months agofrom:89bbc37d30. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-win-x86_64NOTENov 17 2024
R-4.5-linux-x86_64NOTENov 17 2024
R-4.4-win-x86_64NOTENov 17 2024
R-4.4-mac-x86_64NOTENov 17 2024
R-4.4-mac-aarch64NOTENov 17 2024
R-4.3-win-x86_64NOTENov 17 2024
R-4.3-mac-x86_64NOTENov 17 2024
R-4.3-mac-aarch64NOTENov 17 2024

Exports:addLRaddLRinvaDistadjustadjustImputedadtestadtestWrapperbalancesbiomarkerbootnCompbpcbpcPcabpcPcaTabbpcRegbpcRegTabbpcTabbpcTabWrappercedcenLRcenLRinvcheckDataclustCoDaclustCoDa_qmodecompareMahalcompositionalSplineconstSumcoordcorCoDacubeCoordcubeCoordWrapperdaCoDadaFisherfcenLRfcenLRinvfcenLRpfcenLRugmgmeangmean_sumilr.2x2impAllimpCodaimpKNNaimpRZalrimpRZilrimputeBDLsimputeUDLsind2x2indTabint2x2intArrayintTabiprodis.equivalentisomLRisomLRinvisomLRinvpisomLRplmCoDaXmissPatternsnorm1orthbasisoutCoDapcaCoDaperturbationpfapivotCoordpivotCoordInvpoweringpTabrdcmrSDevrSDev.testSDevsmoothSplinessmoothSplinesValstatstabCoordtabCoordWrapperternaryDiagternaryDiagAblineternaryDiagEllipseternaryDiagPointstrapzcvariationweightedPivotCoordZBsplineBasiszeroOutzeroPatterns

Dependencies:abindashbackportsbitopsbootbroomcarcarDataclasscliclustercolorspacecowplotcpp11crayoncvToolsdata.tableDEoptimRDerivdeSolvediptestdoBydplyre1071fansifarverfdafdsflexmixFNNforcatsFormulafpcgenericsGGallyggfortifyggplot2ggstatsgluegridExtragtablehdrcdehmsisobandkernlabKernSmoothkslabelinglaekenlatticelifecyclelme4lmtestlocfitmagrittrMASSMatrixMatrixModelsmclustmgcvmicrobenchmarkminqamodelrmodeltoolsmulticoolmunsellmvtnormNADAnlmenloptrnnetnumDerivpatchworkpbkrtestpcaPPperrypillarpkgconfigplsplyrprabcluspracmaprettyunitsprogressproxypurrrquantregR6rainbowrangerRColorBrewerRcppRcppArmadilloRcppEigenRCurlreshape2rlangrobustbaserobustHDrrcovscalesspSparseMstringistringrsurvivaltibbletidyrtidyselecttruncnormutf8vcdvctrsVIMviridisLitewithrzCompositionszoo

Imputation Methods in robCompositions

Rendered fromimputation.Rnwusingknitr::knitron Nov 17 2024.

Last update: 2019-05-14
Started: 2013-11-20

Overview of the robCompostions package

Rendered fromrobCompositions-overview.Rnwusingutils::Sweaveon Nov 17 2024.

Last update: 2013-11-20
Started: 2013-11-20

Readme and manuals

Help Manual

Help pageTopics
Robust Estimation for Compositional Data.robCompositions-package robCompositions
Additive logratio coordinatesaddLR
Inverse additive logratio mappingaddLRinv
Aitchison distanceaDist iprod
Adjusting for original scaleadjust
Anderson-Darling Normality Testsadtest
Wrapper for Anderson-Darling testsadtestWrapper print.adtestWrapper summary.adtestWrapper
child, middle and eldery populationageCatWorld
alcohol consumptions by country and type of alcoholalcohol
regional alcohol per capita (15+) consumption by WHO regionalcoholreg
arctic lake sediment dataarcticLake
Balance calculationbalances
biomarkerbiomarker plot.biomarker print.biomarker summary.biomarker
Biplot methodbiplot.factanal
Biplot methodbiplot.pcaCoDa
Bootstrap to find optimal number of componentsbootnComp
Backwards pivot coordinates and their inversebpc
Principal component analysis based on backwards pivot coordinatesbpcPca
Principal component analysis of compositional tables based on backwards pivot coordinatesbpcPcaTab
Classical and robust regression based on backwards pivot coordinatesbpcReg
Classical and robust regression based on backwards pivot coordinatesbpcRegTab
Backwards pivot coordinates and their inversebpcTab
Backwards pivot coordinates and their inversebpcTabWrapper
hospital discharges on cancer and distribution of agecancer
malignant neoplasms cancercancerMN
Compositional error deviationced
Centred logratio coefficientscenLR
Inverse centred logratio mappingcenLRinv
C-horizon of the Kola data with rounded zeroschorizonDL
Cluster analysis for compositional dataclustCoDa plot.clustCoDa
Q-mode cluster analysis for compositional partsclustCoDa_qmode plot.clustCoDa_qmode
coffee data setcoffee
Compares Mahalanobis distances from two approachescompareMahal getEstimates plot.estimates plot.mahal print.estimates
Compositional splinecompositionalSpline
Constant sumconstSum
Coordinate representation of compositional tablescoord print.coord
Correlations for compositional datacorCoDa
Coordinate representation of a compositional cube and of a sample of compositional cubescubeCoord cubeCoordWrapper
Linear and quadratic discriminant analysis for compositional data.daCoDa
Discriminant analysis by Fisher Rule.daFisher predict.daFisher print.daFisher summary.daFisher
economic indicatorseconomy
education level of father (F) and mother (M)educFM
efsa nutrition consumptionefsa
election dataelection
Austrian presidential election dataelectionATbp
employment in different countries by gender and status.employment
Employment in different countries by gender and status.employment_df
Employment in different countries by Sex, Age, Contract, Valueemployment2
synthetic household expenditures toy data setexpenditures
mean consumption expenditures data.expendituresEU
fcenLR transformation (functional)fcenLR
Inverse of fcenLR transformations (functional)fcenLRinv
fcenLRp transformation (functional)fcenLRp
fcenLRu transformation (functional)fcenLRu
country food balancesfoodbalance
GDP satisfactionGDPsatis
GEMAS geochemical data setgemas
gjovikgjovik
gmeangm
Geometric meangmean gmean_sum
government spendinggovexp
haplogroups data.haplogroups
honey compositionshoney
ilr coordinates in 2x2 compositional tablesilr.2x2
Replacement of rounded zeros and missing values.impAll
Imputation of missing values in compositional dataimpCoda
Imputation of missing values in compositional data using knn methodsimpKNNa
alr EM-based imputation of rounded zerosimpRZalr
EM-based replacement of rounded zeros in compositional dataimpRZilr
EM-based replacement of rounded zeros in compositional dataadjustImputed checkData imputeBDLs print.replaced
Imputation of values above an upper detection limit in compositional dataimputeUDLs
Independence 2x2 compositional tableind2x2
Independence tableindTab
value added, output and input for different ISIC codes and countries.instw
Interaction 2x2 tableint2x2
Interaction arrayintArray
Interaction tableintTab
equivalence classis.equivalent
ISIC codes by nameisic32
labour force by status in employmentlaborForce
European land coverlandcover
life expectancy and GDP (2008) for EU-countrieslifeExpGdp
Classical and robust regression of non-compositional (real) response on compositional and non-compositional predictorsilrregression lmCoDaX robilrregression
machine operatorsmachineOperators
Distribution of manufacturing outputmanu_abs
metabolomics mcad data setmcad
missing or zero pattern structure.missPatterns zeroPatterns
mortality and life expectancy in the EUmortality
mortality tablemortality_tab
Normalize a vector to length 1norm1
nutrient contentsnutrients
nutrient contents (branded)nutrients_branded
Orthonormal basisorthbasis
Outlier detection for compositional dataoutCoDa plot.outCoDa print.outCoDa
special paymentspayments
Robust principal component analysis for compositional datapcaCoDa print.pcaCoDa summary.pcaCoDa
Perturbation and poweringperturbation powering
Factor analysis for compositional datapfa
PhD students in the EUphd
PhD students in the EU (totals)phd_totals
Pivot coordinates and their inverseisomLR isomLRinv isomLRinvp isomLRp pivotCoord pivotCoordInv
Plot method for objects of class impplot.imp
Plot methodplot.pcaCoDa
plot smoothSplplot.smoothSpl
24-hour precipitationprecipitation
Print method for objects of class impprint.imp
production splitted by nationality on enterprise levelproduction
Propability tablepTab
codes for UNIDO tablesrcodes
relative difference between covariance matricesrdcm
Relative simplicial deviancerSDev
Relative simplicial deviance testsrSDev.test
saffron compositionssaffron
Simplicial devianceSDev
aphyric skye lavas dataskyeLavas
Estimate density from histogramsmoothSplines
Estimate density from histogram - for different 'alpha'smoothSplinesVal
social expendituressocExp
Classical estimates for tablesstats
Summary method for objects of class impsummary.imp
Coordinate representation of compositional tables and a sample of compositional tablestabCoord tabCoordWrapper
teaching stuffteachingStuff
Ternary diagramternaryDiag
Adds a line to a ternary diagram.ternaryDiagAbline
Adds tolerance ellipses to a ternary diagram.ternaryDiagEllipse
Add points or lines to a given ternary diagram.ternaryDiagLines ternaryDiagPoints
Trapezoidal formula for numerical integrationtrapzc
regional geochemical survey of soil C in NorwaytrondelagC
regional geochemical survey of soil O in NorwaytrondelagO
unemployed of young peopleunemployed
Robust and classical variation matrixvariation
Weighted pivot coordinatesweightedPivotCoord
ZB-spline basisZBsplineBasis
Detection of outliers of zero-inflated datazeroOut