R: Compositional Data Analysis

# Compositional Data Analysis

## Documentation for package ‘robCompositions’ version 2.6.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I L M N O P R S T U V W Z

robCompositions-package | Robust Estimation for Compositional Data.

## -- A --

addLR | Additive logratio coordinates
addLRinv | Inverse additive logratio mapping
aDist | Aitchison distance
adjust | Adjusting for original scale
adjustImputed | EM-based replacement of rounded zeros in compositional data
adtest | Anderson-Darling Normality Tests
adtestWrapper | Wrapper for Anderson-Darling tests
ageCatWorld | child, middle and eldery population
alcohol | alcohol consumptions by country and type of alcohol
alcoholreg | regional alcohol per capita (15+) consumption by WHO region
arcticLake | arctic lake sediment data

## -- B --

balances | Balance calculation
biomarker | biomarker
biplot.factanal | Biplot method
biplot.pcaCoDa | Biplot method
bootnComp | Bootstrap to find optimal number of components
bpc | Backwards pivot coordinates and their inverse
bpcPca | Principal component analysis based on backwards pivot coordinates
bpcPcaTab | Principal component analysis of compositional tables based on backwards pivot coordinates
bpcReg | Classical and robust regression based on backwards pivot coordinates
bpcRegTab | Classical and robust regression based on backwards pivot coordinates
bpcTab | Backwards pivot coordinates and their inverse
bpcTabWrapper | Backwards pivot coordinates and their inverse

## -- C --

cancer | hospital discharges on cancer and distribution of age
cancerMN | malignant neoplasms cancer
ced | Compositional error deviation
cellNetCoDa | Cellwise-robust network estimation for compositional data
cellPcaCoDa | Cellwise-robust PCA for compositional data
cenLR | Centred logratio coefficients
cenLRinv | Inverse centred logratio mapping
checkData | EM-based replacement of rounded zeros in compositional data
chorizonDL | C-horizon of the Kola data with rounded zeros
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
compositionalSpline | Compositional spline
constSum | Constant sum
contaminate_simplex | Generate cellwise-contaminated compositional data
coord | Coordinate representation of compositional tables
corCoDa | Correlations for compositional data
cubeCoord | Coordinate representation of a compositional cube and of a sample of compositional cubes
cubeCoordWrapper | Coordinate representation of a compositional cube and of a sample of compositional cubes

## -- D --

daCoDa | Linear and quadratic discriminant analysis for compositional data.
daFisher | Discriminant analysis by Fisher Rule.

## -- E --

economy | economic indicators
educFM | education level of father (F) and mother (M)
efsa | efsa nutrition consumption
election | election data
electionATbp | Austrian presidential election data
employment | employment in different countries by gender and status.
employment2 | Employment in different countries by Sex, Age, Contract, Value
employment_df | Employment in different countries by gender and status.
expenditures | synthetic household expenditures toy data set
expendituresEU | mean consumption expenditures data.

## -- F --

fBPUpChi_PLS | Title
fcenLR | fcenLR transformation (functional)
fcenLRinv | Inverse of fcenLR transformations (functional)
fcenLRp | fcenLRp transformation (functional)
fcenLRu | fcenLRu transformation (functional)
foodbalance | country food balances

## -- G --

GDPsatis | GDP satisfaction
gemas | GEMAS geochemical data set
getEstimates | Compares Mahalanobis distances from two approaches
gjovik | gjovik
gm | gmean
gmean | Geometric mean
gmean_sum | Geometric mean
govexp | government spending

## -- H --

haplogroups | haplogroups data
honey | honey compositions

## -- I --

ilr.2x2 | ilr coordinates in 2x2 compositional tables
ilrregression | Classical and robust regression of non-compositional (real) response on compositional and non-compositional predictors
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 methods
impRZalr | alr EM-based imputation of rounded zeros
impRZilr | EM-based replacement of rounded zeros in compositional data
imputeBDL | EM-based replacement of rounded zeros in compositional data
imputeBDLs | EM-based replacement of rounded zeros in compositional data
imputeUDLs | Imputation of values above an upper detection limit in compositional data
ind2x2 | Independence 2x2 compositional table
indTab | Independence table
instw | value added, output and input for different ISIC codes and countries.
int2x2 | Interaction 2x2 table
intArray | Interaction array
intTab | Interaction table
iprod | Aitchison distance
is.equivalent | equivalence class
isic32 | ISIC codes by name
isomLR | Pivot coordinates and their inverse
isomLRinv | Pivot coordinates and their inverse
isomLRinvp | Pivot coordinates and their inverse
isomLRp | Pivot coordinates and their inverse

## -- L --

laborForce | labour force by status in employment
landcover | European land cover
lifeExpGdp | life expectancy and GDP (2008) for EU-countries
lmCoDaX | Classical and robust regression of non-compositional (real) response on compositional and non-compositional predictors

## -- M --

machineOperators | machine operators
manu_abs | Distribution of manufacturing output
mcad | metabolomics mcad data set
missPatterns | missing or zero pattern structure.
mortality | mortality and life expectancy in the EU
mortality_tab | mortality table

## -- N --

norm1 | Normalize a vector to length 1
nutrients | nutrient contents
nutrients_branded | nutrient contents (branded)

## -- O --

orthbasis | Orthonormal basis
outCoDa | Outlier detection for compositional data

## -- P --

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
phd_totals | PhD students in the EU (totals)
pivotCoord | Pivot coordinates and their inverse
pivotCoordInv | Pivot coordinates and their inverse
plot.biomarker | biomarker
plot.cellNetCoDa | Plot method for cellwise-robust compositional networks
plot.cellPcaCoDa | Plot method for cellwise-robust compositional PCA
plot.clustCoDa | Cluster analysis for compositional data
plot.clustCoDa_qmode | Q-mode cluster analysis for compositional parts
plot.estimates | Compares Mahalanobis distances from two approaches
plot.imp | Plot method for objects of class imp
plot.mahal | Compares Mahalanobis distances from two approaches
plot.outCoDa | Outlier detection for compositional data
plot.pcaCoDa | Plot method
plot.smoothSpl | plot smoothSpl
pls_pb | Function calculating a set of (D-1) principal balances based on PLS.
powering | Perturbation and powering
precipitation | 24-hour precipitation
predict.daFisher | Discriminant analysis by Fisher Rule.
print.adtestWrapper | Wrapper for Anderson-Darling tests
print.biomarker | biomarker
print.cellNetCoDa | Print method for cellwise-robust compositional networks
print.cellPcaCoDa | Print method for cellwise-robust compositional PCA
print.coord | Coordinate representation of compositional tables
print.daFisher | Discriminant analysis by Fisher Rule.
print.estimates | Compares Mahalanobis distances from two approaches
print.imp | Print method for objects of class imp
print.outCoDa | Outlier detection for compositional data
print.pcaCoDa | Robust principal component analysis for compositional data
print.replaced | EM-based replacement of rounded zeros in compositional data
production | production splitted by nationality on enterprise level
pTab | Propability table

## -- R --

rcodes | codes for UNIDO tables
rdcm | relative difference between covariance matrices
robCompositions | Robust Estimation for Compositional Data.
robilrregression | Classical and robust regression of non-compositional (real) response on compositional and non-compositional predictors
rSDev | Relative simplicial deviance
rSDev.test | Relative simplicial deviance tests

## -- S --

saffron | saffron compositions
SDev | Simplicial deviance
skyeLavas | aphyric skye lavas data
smoothSplines | Estimate density from histogram
smoothSplinesVal | Estimate density from histogram - for different 'alpha'
socExp | social expenditures
spca_logrs | Function making a matrix of D(D-1) logratios and calculating sparse PCA.
stats | Classical estimates for tables
summary.adtestWrapper | Wrapper for Anderson-Darling tests
summary.biomarker | biomarker
summary.cellNetCoDa | Summary method for cellwise-robust compositional networks
summary.cellPcaCoDa | Summary method for cellwise-robust compositional PCA
summary.daFisher | Discriminant analysis by Fisher Rule.
summary.imp | Summary method for objects of class imp
summary.pcaCoDa | Robust principal component analysis for compositional data

## -- T --

tabCoord | Coordinate representation of compositional tables and a sample of compositional tables
tabCoordWrapper | Coordinate representation of compositional tables and a sample of compositional tables
teachingStuff | teaching stuff
ternaryDiag | Ternary diagram
ternaryDiagAbline | Adds a line to a ternary diagram.
ternaryDiagEllipse | Adds tolerance ellipses to a ternary diagram.
ternaryDiagLines | Add points or lines to a given ternary diagram.
ternaryDiagPoints | Add points or lines to a given ternary diagram.
trapzc | Trapezoidal formula for numerical integration
trondelagC | regional geochemical survey of soil C in Norway
trondelagO | regional geochemical survey of soil O in Norway

## -- U --

unemployed | unemployed of young people

## -- V --

variation | Robust and classical variation matrix

## -- W --

weightedPivotCoord | Weighted pivot coordinates

## -- Z --

ZBsplineBasis | ZB-spline basis
zeroOut | Detection of outliers of zero-inflated data
zeroPatterns | missing or zero pattern structure.